From 9f3d5604885171b94455062ca8329c8d871a5e96 Mon Sep 17 00:00:00 2001 From: Orion Banks <49208907+Bankso@users.noreply.github.com> Date: Fri, 30 Aug 2024 15:45:27 -0700 Subject: [PATCH] Attempt to use static files --- files/JSON/HTAN_tangled_tree.json | 810 +--------- files/JSON/deprecated/HTAN_tangled_tree.json | 809 ++++++++++ files/JSON/mc2_rfc_test_8.30.24.json | 1 - files/Merged/HTAN_attribute_table.csv | 1346 ++--------------- .../deprecated/HTAN_attribute_table.csv | 1194 +++++++++++++++ files/Merged/mc2_rfc_test_8.30.24.csv | 152 -- files/config.yml | 2 +- js/PrepareRender.js | 18 +- 8 files changed, 2166 insertions(+), 2166 deletions(-) create mode 100644 files/JSON/deprecated/HTAN_tangled_tree.json delete mode 100644 files/JSON/mc2_rfc_test_8.30.24.json create mode 100644 files/Merged/deprecated/HTAN_attribute_table.csv delete mode 100644 files/Merged/mc2_rfc_test_8.30.24.csv diff --git a/files/JSON/HTAN_tangled_tree.json b/files/JSON/HTAN_tangled_tree.json index c5cde32..bf3d41c 100644 --- a/files/JSON/HTAN_tangled_tree.json +++ b/files/JSON/HTAN_tangled_tree.json @@ -1,809 +1 @@ -[ - [ - { - "id": "Demographics", - "parents": [], - "direct_children": [ - "Patient" - ], - "children": [ - "SarcomaTier3", - "ScATAC-seqLevel2", - "ColorectalCancerTier3", - "Biospecimen", - "HTANRPPAAntibodyTable", - "ImagingLevel1", - "NeuroblastomaandGliomaTier3", - "ScATAC-seqLevel3", - "OvarianCancerTier3", - "SRRSClinicalDataTier2", - "ScATAC-seqLevel1", - "BulkWESLevel1", - "SRRSImagingLevel2", - "BulkWESLevel3", - "ProstateCancerTier3", - "Patient", - "OtherAssay", - "BulkWESLevel2", - "ScRNA-seqLevel4", - "BulkRNA-seqLevel3", - "ScRNA-seqLevel3", - "RPPALevel2", - "LungCancerTier3", - "MelanomaTier3", - "ScATAC-seqLevel4", - "PancreaticCancerTier3", - "AcuteLymphoblasticLeukemiaTier3", - "ImagingLevel3Segmentation", - "BreastCancerTier3", - "ScRNA-seqLevel1", - "BulkRNA-seqLevel2", - "ImagingLevel3Image", - "ClinicalDataTier2", - "SRRSBiospecimen", - "ScRNA-seqLevel2", - "BulkRNA-seqLevel1", - "ImagingLevel2" - ] - }, - { - "id": "FamilyHistory", - "parents": [], - "direct_children": [ - "Patient" - ], - "children": [ - "SarcomaTier3", - "ScATAC-seqLevel2", - "ColorectalCancerTier3", - "Biospecimen", - "HTANRPPAAntibodyTable", - "ImagingLevel1", - "NeuroblastomaandGliomaTier3", - "ScATAC-seqLevel3", - "OvarianCancerTier3", - "SRRSClinicalDataTier2", - "ScATAC-seqLevel1", - "BulkWESLevel1", - "SRRSImagingLevel2", - "BulkWESLevel3", - "ProstateCancerTier3", - "Patient", - "OtherAssay", - "BulkWESLevel2", - "ScRNA-seqLevel4", - "BulkRNA-seqLevel3", - "ScRNA-seqLevel3", - "RPPALevel2", - "LungCancerTier3", - "MelanomaTier3", - "ScATAC-seqLevel4", - "PancreaticCancerTier3", - "AcuteLymphoblasticLeukemiaTier3", - "ImagingLevel3Segmentation", - "BreastCancerTier3", - "ScRNA-seqLevel1", - "BulkRNA-seqLevel2", - "ImagingLevel3Image", - "ClinicalDataTier2", - "SRRSBiospecimen", - "ScRNA-seqLevel2", - "BulkRNA-seqLevel1", - "ImagingLevel2" - ] - }, - { - "id": "Exposure", - "parents": [], - "direct_children": [ - "Patient" - ], - "children": [ - "SarcomaTier3", - "ScATAC-seqLevel2", - "ColorectalCancerTier3", - "Biospecimen", - "HTANRPPAAntibodyTable", - "ImagingLevel1", - "NeuroblastomaandGliomaTier3", - "ScATAC-seqLevel3", - "OvarianCancerTier3", - "SRRSClinicalDataTier2", - "ScATAC-seqLevel1", - "BulkWESLevel1", - "SRRSImagingLevel2", - "BulkWESLevel3", - "ProstateCancerTier3", - "Patient", - "OtherAssay", - "BulkWESLevel2", - "ScRNA-seqLevel4", - "BulkRNA-seqLevel3", - "ScRNA-seqLevel3", - "RPPALevel2", - "LungCancerTier3", - "MelanomaTier3", - "ScATAC-seqLevel4", - "PancreaticCancerTier3", - "AcuteLymphoblasticLeukemiaTier3", - "ImagingLevel3Segmentation", - "BreastCancerTier3", - "ScRNA-seqLevel1", - "BulkRNA-seqLevel2", - "ImagingLevel3Image", - "ClinicalDataTier2", - "SRRSBiospecimen", - "ScRNA-seqLevel2", - "BulkRNA-seqLevel1", - "ImagingLevel2" - ] - }, - { - "id": "FollowUp", - "parents": [], - "direct_children": [ - "Patient" - ], - "children": [ - "SarcomaTier3", - "ScATAC-seqLevel2", - "ColorectalCancerTier3", - "Biospecimen", - "HTANRPPAAntibodyTable", - "ImagingLevel1", - "NeuroblastomaandGliomaTier3", - "ScATAC-seqLevel3", - "OvarianCancerTier3", - "SRRSClinicalDataTier2", - "ScATAC-seqLevel1", - "BulkWESLevel1", - "SRRSImagingLevel2", - "BulkWESLevel3", - "ProstateCancerTier3", - "Patient", - "OtherAssay", - "BulkWESLevel2", - "ScRNA-seqLevel4", - "BulkRNA-seqLevel3", - "ScRNA-seqLevel3", - "RPPALevel2", - "LungCancerTier3", - "MelanomaTier3", - "ScATAC-seqLevel4", - "PancreaticCancerTier3", - "AcuteLymphoblasticLeukemiaTier3", - "ImagingLevel3Segmentation", - "BreastCancerTier3", - "ScRNA-seqLevel1", - "BulkRNA-seqLevel2", - "ImagingLevel3Image", - "ClinicalDataTier2", - "SRRSBiospecimen", - "ScRNA-seqLevel2", - "BulkRNA-seqLevel1", - "ImagingLevel2" - ] - }, - { - "id": "Diagnosis", - "parents": [], - "direct_children": [ - "Patient" - ], - "children": [ - "SarcomaTier3", - "ScATAC-seqLevel2", - "ColorectalCancerTier3", - "Biospecimen", - "HTANRPPAAntibodyTable", - "ImagingLevel1", - "NeuroblastomaandGliomaTier3", - "ScATAC-seqLevel3", - "OvarianCancerTier3", - "SRRSClinicalDataTier2", - "ScATAC-seqLevel1", - "BulkWESLevel1", - "SRRSImagingLevel2", - "BulkWESLevel3", - "ProstateCancerTier3", - "Patient", - "OtherAssay", - "BulkWESLevel2", - "ScRNA-seqLevel4", - "BulkRNA-seqLevel3", - "ScRNA-seqLevel3", - "RPPALevel2", - "LungCancerTier3", - "MelanomaTier3", - "ScATAC-seqLevel4", - "PancreaticCancerTier3", - "AcuteLymphoblasticLeukemiaTier3", - "ImagingLevel3Segmentation", - "BreastCancerTier3", - "ScRNA-seqLevel1", - "BulkRNA-seqLevel2", - "ImagingLevel3Image", - "ClinicalDataTier2", - "SRRSBiospecimen", - "ScRNA-seqLevel2", - "BulkRNA-seqLevel1", - "ImagingLevel2" - ] - }, - { - "id": "Therapy", - "parents": [], - "direct_children": [ - "Patient" - ], - "children": [ - "SarcomaTier3", - "ScATAC-seqLevel2", - "ColorectalCancerTier3", - "Biospecimen", - "HTANRPPAAntibodyTable", - "ImagingLevel1", - "NeuroblastomaandGliomaTier3", - "ScATAC-seqLevel3", - "OvarianCancerTier3", - "SRRSClinicalDataTier2", - "ScATAC-seqLevel1", - "BulkWESLevel1", - "SRRSImagingLevel2", - "BulkWESLevel3", - "ProstateCancerTier3", - "Patient", - "OtherAssay", - "BulkWESLevel2", - "ScRNA-seqLevel4", - "BulkRNA-seqLevel3", - "ScRNA-seqLevel3", - "RPPALevel2", - "LungCancerTier3", - "MelanomaTier3", - "ScATAC-seqLevel4", - "PancreaticCancerTier3", - "AcuteLymphoblasticLeukemiaTier3", - "ImagingLevel3Segmentation", - "BreastCancerTier3", - "ScRNA-seqLevel1", - "BulkRNA-seqLevel2", - "ImagingLevel3Image", - "ClinicalDataTier2", - "SRRSBiospecimen", - "ScRNA-seqLevel2", - "BulkRNA-seqLevel1", - "ImagingLevel2" - ] - }, - { - "id": "MolecularTest", - "parents": [], - "direct_children": [ - "Patient" - ], - "children": [ - "SarcomaTier3", - "ScATAC-seqLevel2", - "ColorectalCancerTier3", - "Biospecimen", - "HTANRPPAAntibodyTable", - "ImagingLevel1", - "NeuroblastomaandGliomaTier3", - "ScATAC-seqLevel3", - "OvarianCancerTier3", - "SRRSClinicalDataTier2", - "ScATAC-seqLevel1", - "BulkWESLevel1", - "SRRSImagingLevel2", - "BulkWESLevel3", - "ProstateCancerTier3", - "Patient", - "OtherAssay", - "BulkWESLevel2", - "ScRNA-seqLevel4", - "BulkRNA-seqLevel3", - "ScRNA-seqLevel3", - "RPPALevel2", - "LungCancerTier3", - "MelanomaTier3", - "ScATAC-seqLevel4", - "PancreaticCancerTier3", - "AcuteLymphoblasticLeukemiaTier3", - "ImagingLevel3Segmentation", - "BreastCancerTier3", - "ScRNA-seqLevel1", - "BulkRNA-seqLevel2", - "ImagingLevel3Image", - "ClinicalDataTier2", - "SRRSBiospecimen", - "ScRNA-seqLevel2", - "BulkRNA-seqLevel1", - "ImagingLevel2" - ] - } - ], - [ - { - "id": "Patient", - "parents": [ - "Demographics", - "FamilyHistory", - "Exposure", - "FollowUp", - "Diagnosis", - "Therapy", - "MolecularTest" - ], - "direct_children": [ - "Biospecimen", - "ClinicalDataTier2", - "SRRSClinicalDataTier2", - "LungCancerTier3", - "ColorectalCancerTier3", - "BreastCancerTier3", - "NeuroblastomaandGliomaTier3", - "AcuteLymphoblasticLeukemiaTier3", - "OvarianCancerTier3", - "ProstateCancerTier3", - "SarcomaTier3", - "PancreaticCancerTier3", - "MelanomaTier3", - "SRRSBiospecimen" - ], - "children": [ - "SarcomaTier3", - "ScATAC-seqLevel2", - "ColorectalCancerTier3", - "Biospecimen", - "HTANRPPAAntibodyTable", - "ImagingLevel1", - "NeuroblastomaandGliomaTier3", - "ScATAC-seqLevel3", - "OvarianCancerTier3", - "SRRSClinicalDataTier2", - "ScATAC-seqLevel1", - "BulkWESLevel1", - "SRRSImagingLevel2", - "BulkWESLevel3", - "ProstateCancerTier3", - "OtherAssay", - "BulkWESLevel2", - "ScRNA-seqLevel4", - "BulkRNA-seqLevel3", - "ScRNA-seqLevel3", - "RPPALevel2", - "LungCancerTier3", - "MelanomaTier3", - "ScATAC-seqLevel4", - "PancreaticCancerTier3", - "AcuteLymphoblasticLeukemiaTier3", - "ImagingLevel3Segmentation", - "BreastCancerTier3", - "ScRNA-seqLevel1", - "BulkRNA-seqLevel2", - "ImagingLevel3Image", - "ClinicalDataTier2", - "SRRSBiospecimen", - "ScRNA-seqLevel2", - "BulkRNA-seqLevel1", - "ImagingLevel2" - ] - } - ], - [ - { - "id": "Biospecimen", - "parents": [ - "Patient" - ], - "direct_children": [ - "OtherAssay", - "ScRNA-seqLevel1", - "BulkRNA-seqLevel1", - "BulkWESLevel1", - "ScATAC-seqLevel1", - "ImagingLevel1", - "SRRSImagingLevel2", - "RPPALevel2" - ], - "children": [ - "ScATAC-seqLevel2", - "BulkRNA-seqLevel3", - "ScRNA-seqLevel3", - "RPPALevel2", - "HTANRPPAAntibodyTable", - "ScATAC-seqLevel4", - "ImagingLevel3Segmentation", - "ImagingLevel1", - "ScATAC-seqLevel3", - "ScRNA-seqLevel1", - "BulkRNA-seqLevel2", - "ImagingLevel3Image", - "ScATAC-seqLevel1", - "BulkWESLevel1", - "SRRSImagingLevel2", - "BulkWESLevel3", - "ScRNA-seqLevel2", - "BulkRNA-seqLevel1", - "ScRNA-seqLevel4", - "BulkWESLevel2", - "OtherAssay", - "ImagingLevel2" - ] - }, - { - "id": "ClinicalDataTier2", - "parents": [ - "Patient" - ], - "direct_children": [], - "children": [] - }, - { - "id": "SRRSClinicalDataTier2", - "parents": [ - "Patient" - ], - "direct_children": [], - "children": [] - }, - { - "id": "LungCancerTier3", - "parents": [ - "Patient" - ], - "direct_children": [], - "children": [] - }, - { - "id": "ColorectalCancerTier3", - "parents": [ - "Patient" - ], - "direct_children": [], - "children": [] - }, - { - "id": "BreastCancerTier3", - "parents": [ - "Patient" - ], - "direct_children": [], - "children": [] - }, - { - "id": "NeuroblastomaandGliomaTier3", - "parents": [ - "Patient" - ], - "direct_children": [], - "children": [] - }, - { - "id": "AcuteLymphoblasticLeukemiaTier3", - "parents": [ - "Patient" - ], - "direct_children": [], - "children": [] - }, - { - "id": "OvarianCancerTier3", - "parents": [ - "Patient" - ], - "direct_children": [], - "children": [] - }, - { - "id": "ProstateCancerTier3", - "parents": [ - "Patient" - ], - "direct_children": [], - "children": [] - }, - { - "id": "SarcomaTier3", - "parents": [ - "Patient" - ], - "direct_children": [], - "children": [] - }, - { - "id": "PancreaticCancerTier3", - "parents": [ - "Patient" - ], - "direct_children": [], - "children": [] - }, - { - "id": "MelanomaTier3", - "parents": [ - "Patient" - ], - "direct_children": [], - "children": [] - }, - { - "id": "SRRSBiospecimen", - "parents": [ - "Patient" - ], - "direct_children": [], - "children": [] - } - ], - [ - { - "id": "ScRNA-seqLevel1", - "parents": [ - "Biospecimen" - ], - "direct_children": [ - "ScRNA-seqLevel2" - ], - "children": [ - "ScRNA-seqLevel3", - "ScRNA-seqLevel4", - "ScRNA-seqLevel2" - ] - }, - { - "id": "ScATAC-seqLevel1", - "parents": [ - "Biospecimen" - ], - "direct_children": [ - "ScATAC-seqLevel2" - ], - "children": [ - "ScATAC-seqLevel4", - "ScATAC-seqLevel2", - "ScATAC-seqLevel3" - ] - }, - { - "id": "BulkRNA-seqLevel1", - "parents": [ - "Biospecimen" - ], - "direct_children": [ - "BulkRNA-seqLevel2" - ], - "children": [ - "BulkRNA-seqLevel2", - "BulkRNA-seqLevel3" - ] - }, - { - "id": "BulkWESLevel1", - "parents": [ - "Biospecimen" - ], - "direct_children": [ - "BulkWESLevel2" - ], - "children": [ - "BulkWESLevel2", - "BulkWESLevel3" - ] - }, - { - "id": "ImagingLevel1", - "parents": [ - "Biospecimen" - ], - "direct_children": [ - "ImagingLevel2" - ], - "children": [ - "ImagingLevel3Image", - "ImagingLevel3Segmentation", - "ImagingLevel2" - ] - }, - { - "id": "RPPALevel2", - "parents": [ - "Biospecimen" - ], - "direct_children": [ - "HTANRPPAAntibodyTable" - ], - "children": [ - "HTANRPPAAntibodyTable" - ] - }, - { - "id": "OtherAssay", - "parents": [ - "Biospecimen" - ], - "direct_children": [], - "children": [] - }, - { - "id": "SRRSImagingLevel2", - "parents": [ - "Biospecimen" - ], - "direct_children": [], - "children": [] - } - ], - [ - { - "id": "ScRNA-seqLevel2", - "parents": [ - "ScRNA-seqLevel1" - ], - "direct_children": [ - "ScRNA-seqLevel3" - ], - "children": [ - "ScRNA-seqLevel3", - "ScRNA-seqLevel4" - ] - }, - { - "id": "ScATAC-seqLevel2", - "parents": [ - "ScATAC-seqLevel1" - ], - "direct_children": [ - "ScATAC-seqLevel3" - ], - "children": [ - "ScATAC-seqLevel4", - "ScATAC-seqLevel3" - ] - }, - { - "id": "BulkRNA-seqLevel2", - "parents": [ - "BulkRNA-seqLevel1" - ], - "direct_children": [ - "BulkRNA-seqLevel3" - ], - "children": [ - "BulkRNA-seqLevel3" - ] - }, - { - "id": "BulkWESLevel2", - "parents": [ - "BulkWESLevel1" - ], - "direct_children": [ - "BulkWESLevel3" - ], - "children": [ - "BulkWESLevel3" - ] - }, - { - "id": "ImagingLevel2", - "parents": [ - "ImagingLevel1" - ], - "direct_children": [ - "ImagingLevel3Segmentation", - "ImagingLevel3Image" - ], - "children": [ - "ImagingLevel3Image", - "ImagingLevel3Segmentation" - ] - }, - { - "id": "HTANRPPAAntibodyTable", - "parents": [ - "RPPALevel2" - ], - "direct_children": [], - "children": [] - }, - { - "id": "ImagingLevel3Channels", - "parents": [], - "direct_children": [ - "ImagingLevel3Image", - "ImagingLevel4" - ], - "children": [ - "ImagingLevel4", - "ImagingLevel3Image" - ] - } - ], - [ - { - "id": "ScRNA-seqLevel3", - "parents": [ - "ScRNA-seqLevel2" - ], - "direct_children": [ - "ScRNA-seqLevel4" - ], - "children": [ - "ScRNA-seqLevel4" - ] - }, - { - "id": "ScATAC-seqLevel3", - "parents": [ - "ScATAC-seqLevel2" - ], - "direct_children": [ - "ScATAC-seqLevel4" - ], - "children": [ - "ScATAC-seqLevel4" - ] - }, - { - "id": "BulkRNA-seqLevel3", - "parents": [ - "BulkRNA-seqLevel2" - ], - "direct_children": [], - "children": [] - }, - { - "id": "BulkWESLevel3", - "parents": [ - "BulkWESLevel2" - ], - "direct_children": [], - "children": [] - }, - { - "id": "ImagingLevel3Segmentation", - "parents": [ - "ImagingLevel2" - ], - "direct_children": [], - "children": [] - }, - { - "id": "ImagingLevel3Image", - "parents": [ - "ImagingLevel3Channels", - "ImagingLevel2" - ], - "direct_children": [], - "children": [] - }, - { - "id": "ImagingLevel4", - "parents": [ - "ImagingLevel3Channels" - ], - "direct_children": [], - "children": [] - } - ], - [ - { - "id": "ScRNA-seqLevel4", - "parents": [ - "ScRNA-seqLevel3" - ], - "direct_children": [], - "children": [] - }, - { - "id": "ScATAC-seqLevel4", - "parents": [ - "ScATAC-seqLevel3" - ], - "direct_children": [], - "children": [] - } - ] -] \ No newline at end of file +[[{"id": "GrantView", "parents": [], "direct_children": ["Study"], "children": ["FileView", "10xVisiumSpatialTranscriptomics-RNA-seqLevel4", "Study", "Biospecimen", "10xVisiumSpatialTranscriptomics-RNA-seqLevel1", "10xVisiumSpatialTranscriptomics-RNA-seqLevel2", "10xVisiumSpatialTranscriptomics-AuxiliaryFiles", "10xVisiumSpatialTranscriptomics-RNA-seqLevel3"]}], [{"id": "Study", "parents": ["GrantView"], "direct_children": ["Biospecimen"], "children": ["FileView", "10xVisiumSpatialTranscriptomics-RNA-seqLevel4", "Biospecimen", "10xVisiumSpatialTranscriptomics-RNA-seqLevel1", "10xVisiumSpatialTranscriptomics-RNA-seqLevel2", "10xVisiumSpatialTranscriptomics-AuxiliaryFiles", "10xVisiumSpatialTranscriptomics-RNA-seqLevel3"]}], [{"id": "Biospecimen", "parents": ["Study"], "direct_children": ["FileView"], "children": ["FileView", "10xVisiumSpatialTranscriptomics-RNA-seqLevel4", "10xVisiumSpatialTranscriptomics-RNA-seqLevel1", "10xVisiumSpatialTranscriptomics-RNA-seqLevel2", "10xVisiumSpatialTranscriptomics-AuxiliaryFiles", "10xVisiumSpatialTranscriptomics-RNA-seqLevel3"]}], [{"id": "FileView", "parents": ["Biospecimen"], "direct_children": ["10xVisiumSpatialTranscriptomics-AuxiliaryFiles", "10xVisiumSpatialTranscriptomics-RNA-seqLevel1"], "children": ["10xVisiumSpatialTranscriptomics-RNA-seqLevel4", "10xVisiumSpatialTranscriptomics-RNA-seqLevel1", "10xVisiumSpatialTranscriptomics-RNA-seqLevel2", "10xVisiumSpatialTranscriptomics-AuxiliaryFiles", "10xVisiumSpatialTranscriptomics-RNA-seqLevel3"]}], [{"id": "10xVisiumSpatialTranscriptomics-RNA-seqLevel1", "parents": ["FileView"], "direct_children": ["10xVisiumSpatialTranscriptomics-RNA-seqLevel2"], "children": ["10xVisiumSpatialTranscriptomics-RNA-seqLevel3", "10xVisiumSpatialTranscriptomics-RNA-seqLevel2", "10xVisiumSpatialTranscriptomics-RNA-seqLevel4"]}, {"id": "10xVisiumSpatialTranscriptomics-AuxiliaryFiles", "parents": ["FileView"], "direct_children": [], "children": []}], [{"id": "10xVisiumSpatialTranscriptomics-RNA-seqLevel2", "parents": ["10xVisiumSpatialTranscriptomics-RNA-seqLevel1"], "direct_children": ["10xVisiumSpatialTranscriptomics-RNA-seqLevel3"], "children": ["10xVisiumSpatialTranscriptomics-RNA-seqLevel3", "10xVisiumSpatialTranscriptomics-RNA-seqLevel4"]}], [{"id": "10xVisiumSpatialTranscriptomics-RNA-seqLevel3", "parents": ["10xVisiumSpatialTranscriptomics-RNA-seqLevel2"], "direct_children": ["10xVisiumSpatialTranscriptomics-RNA-seqLevel4"], "children": ["10xVisiumSpatialTranscriptomics-RNA-seqLevel4"]}], [{"id": "10xVisiumSpatialTranscriptomics-RNA-seqLevel4", "parents": ["10xVisiumSpatialTranscriptomics-RNA-seqLevel3"], "direct_children": [], "children": []}]] \ No newline at end of file diff --git a/files/JSON/deprecated/HTAN_tangled_tree.json b/files/JSON/deprecated/HTAN_tangled_tree.json new file mode 100644 index 0000000..c5cde32 --- /dev/null +++ b/files/JSON/deprecated/HTAN_tangled_tree.json @@ -0,0 +1,809 @@ +[ + [ + { + "id": "Demographics", + "parents": [], + "direct_children": [ + "Patient" + ], + "children": [ + "SarcomaTier3", + "ScATAC-seqLevel2", + "ColorectalCancerTier3", + "Biospecimen", + "HTANRPPAAntibodyTable", + "ImagingLevel1", + "NeuroblastomaandGliomaTier3", + "ScATAC-seqLevel3", + "OvarianCancerTier3", + "SRRSClinicalDataTier2", + "ScATAC-seqLevel1", + "BulkWESLevel1", + "SRRSImagingLevel2", + "BulkWESLevel3", + "ProstateCancerTier3", + "Patient", + "OtherAssay", + "BulkWESLevel2", + "ScRNA-seqLevel4", + "BulkRNA-seqLevel3", + "ScRNA-seqLevel3", + "RPPALevel2", + "LungCancerTier3", + "MelanomaTier3", + "ScATAC-seqLevel4", + "PancreaticCancerTier3", + "AcuteLymphoblasticLeukemiaTier3", + "ImagingLevel3Segmentation", + "BreastCancerTier3", + "ScRNA-seqLevel1", + "BulkRNA-seqLevel2", + "ImagingLevel3Image", + "ClinicalDataTier2", + "SRRSBiospecimen", + "ScRNA-seqLevel2", + "BulkRNA-seqLevel1", + "ImagingLevel2" + ] + }, + { + "id": "FamilyHistory", + "parents": [], + "direct_children": [ + "Patient" + ], + "children": [ + "SarcomaTier3", + "ScATAC-seqLevel2", + "ColorectalCancerTier3", + "Biospecimen", + "HTANRPPAAntibodyTable", + "ImagingLevel1", + "NeuroblastomaandGliomaTier3", + "ScATAC-seqLevel3", + "OvarianCancerTier3", + "SRRSClinicalDataTier2", + "ScATAC-seqLevel1", + "BulkWESLevel1", + "SRRSImagingLevel2", + "BulkWESLevel3", + "ProstateCancerTier3", + "Patient", + "OtherAssay", + "BulkWESLevel2", + "ScRNA-seqLevel4", + "BulkRNA-seqLevel3", + "ScRNA-seqLevel3", + "RPPALevel2", + "LungCancerTier3", + "MelanomaTier3", + "ScATAC-seqLevel4", + "PancreaticCancerTier3", + "AcuteLymphoblasticLeukemiaTier3", + "ImagingLevel3Segmentation", + "BreastCancerTier3", + "ScRNA-seqLevel1", + "BulkRNA-seqLevel2", + "ImagingLevel3Image", + "ClinicalDataTier2", + "SRRSBiospecimen", + "ScRNA-seqLevel2", + "BulkRNA-seqLevel1", + "ImagingLevel2" + ] + }, + { + "id": "Exposure", + "parents": [], + "direct_children": [ + "Patient" + ], + "children": [ + "SarcomaTier3", + "ScATAC-seqLevel2", + "ColorectalCancerTier3", + "Biospecimen", + "HTANRPPAAntibodyTable", + "ImagingLevel1", + "NeuroblastomaandGliomaTier3", + "ScATAC-seqLevel3", + "OvarianCancerTier3", + "SRRSClinicalDataTier2", + "ScATAC-seqLevel1", + "BulkWESLevel1", + "SRRSImagingLevel2", + "BulkWESLevel3", + "ProstateCancerTier3", + "Patient", + "OtherAssay", + "BulkWESLevel2", + "ScRNA-seqLevel4", + "BulkRNA-seqLevel3", + "ScRNA-seqLevel3", + "RPPALevel2", + "LungCancerTier3", + "MelanomaTier3", + "ScATAC-seqLevel4", + "PancreaticCancerTier3", + "AcuteLymphoblasticLeukemiaTier3", + "ImagingLevel3Segmentation", + "BreastCancerTier3", + "ScRNA-seqLevel1", + "BulkRNA-seqLevel2", + "ImagingLevel3Image", + "ClinicalDataTier2", + "SRRSBiospecimen", + "ScRNA-seqLevel2", + "BulkRNA-seqLevel1", + "ImagingLevel2" + ] + }, + { + "id": "FollowUp", + "parents": [], + "direct_children": [ + "Patient" + ], + "children": [ + "SarcomaTier3", + "ScATAC-seqLevel2", + "ColorectalCancerTier3", + "Biospecimen", + "HTANRPPAAntibodyTable", + "ImagingLevel1", + "NeuroblastomaandGliomaTier3", + "ScATAC-seqLevel3", + "OvarianCancerTier3", + "SRRSClinicalDataTier2", + "ScATAC-seqLevel1", + "BulkWESLevel1", + "SRRSImagingLevel2", + "BulkWESLevel3", + "ProstateCancerTier3", + "Patient", + "OtherAssay", + "BulkWESLevel2", + "ScRNA-seqLevel4", + "BulkRNA-seqLevel3", + "ScRNA-seqLevel3", + "RPPALevel2", + "LungCancerTier3", + "MelanomaTier3", + "ScATAC-seqLevel4", + "PancreaticCancerTier3", + "AcuteLymphoblasticLeukemiaTier3", + "ImagingLevel3Segmentation", + "BreastCancerTier3", + "ScRNA-seqLevel1", + "BulkRNA-seqLevel2", + "ImagingLevel3Image", + "ClinicalDataTier2", + "SRRSBiospecimen", + "ScRNA-seqLevel2", + "BulkRNA-seqLevel1", + "ImagingLevel2" + ] + }, + { + "id": "Diagnosis", + "parents": [], + "direct_children": [ + "Patient" + ], + "children": [ + "SarcomaTier3", + "ScATAC-seqLevel2", + "ColorectalCancerTier3", + "Biospecimen", + "HTANRPPAAntibodyTable", + "ImagingLevel1", + "NeuroblastomaandGliomaTier3", + "ScATAC-seqLevel3", + "OvarianCancerTier3", + "SRRSClinicalDataTier2", + "ScATAC-seqLevel1", + "BulkWESLevel1", + "SRRSImagingLevel2", + "BulkWESLevel3", + "ProstateCancerTier3", + "Patient", + "OtherAssay", + "BulkWESLevel2", + "ScRNA-seqLevel4", + "BulkRNA-seqLevel3", + "ScRNA-seqLevel3", + "RPPALevel2", + "LungCancerTier3", + "MelanomaTier3", + "ScATAC-seqLevel4", + "PancreaticCancerTier3", + "AcuteLymphoblasticLeukemiaTier3", + "ImagingLevel3Segmentation", + "BreastCancerTier3", + "ScRNA-seqLevel1", + "BulkRNA-seqLevel2", + "ImagingLevel3Image", + "ClinicalDataTier2", + "SRRSBiospecimen", + "ScRNA-seqLevel2", + "BulkRNA-seqLevel1", + "ImagingLevel2" + ] + }, + { + "id": "Therapy", + "parents": [], + "direct_children": [ + "Patient" + ], + "children": [ + "SarcomaTier3", + "ScATAC-seqLevel2", + "ColorectalCancerTier3", + "Biospecimen", + "HTANRPPAAntibodyTable", + "ImagingLevel1", + "NeuroblastomaandGliomaTier3", + "ScATAC-seqLevel3", + "OvarianCancerTier3", + "SRRSClinicalDataTier2", + "ScATAC-seqLevel1", + "BulkWESLevel1", + "SRRSImagingLevel2", + "BulkWESLevel3", + "ProstateCancerTier3", + "Patient", + "OtherAssay", + "BulkWESLevel2", + "ScRNA-seqLevel4", + "BulkRNA-seqLevel3", + "ScRNA-seqLevel3", + "RPPALevel2", + "LungCancerTier3", + "MelanomaTier3", + "ScATAC-seqLevel4", + "PancreaticCancerTier3", + "AcuteLymphoblasticLeukemiaTier3", + "ImagingLevel3Segmentation", + "BreastCancerTier3", + "ScRNA-seqLevel1", + "BulkRNA-seqLevel2", + "ImagingLevel3Image", + "ClinicalDataTier2", + "SRRSBiospecimen", + "ScRNA-seqLevel2", + "BulkRNA-seqLevel1", + "ImagingLevel2" + ] + }, + { + "id": "MolecularTest", + "parents": [], + "direct_children": [ + "Patient" + ], + "children": [ + "SarcomaTier3", + "ScATAC-seqLevel2", + "ColorectalCancerTier3", + "Biospecimen", + "HTANRPPAAntibodyTable", + "ImagingLevel1", + "NeuroblastomaandGliomaTier3", + "ScATAC-seqLevel3", + "OvarianCancerTier3", + "SRRSClinicalDataTier2", + "ScATAC-seqLevel1", + "BulkWESLevel1", + "SRRSImagingLevel2", + "BulkWESLevel3", + "ProstateCancerTier3", + "Patient", + "OtherAssay", + "BulkWESLevel2", + "ScRNA-seqLevel4", + "BulkRNA-seqLevel3", + "ScRNA-seqLevel3", + "RPPALevel2", + "LungCancerTier3", + "MelanomaTier3", + "ScATAC-seqLevel4", + "PancreaticCancerTier3", + "AcuteLymphoblasticLeukemiaTier3", + "ImagingLevel3Segmentation", + "BreastCancerTier3", + "ScRNA-seqLevel1", + "BulkRNA-seqLevel2", + "ImagingLevel3Image", + "ClinicalDataTier2", + "SRRSBiospecimen", + "ScRNA-seqLevel2", + "BulkRNA-seqLevel1", + "ImagingLevel2" + ] + } + ], + [ + { + "id": "Patient", + "parents": [ + "Demographics", + "FamilyHistory", + "Exposure", + "FollowUp", + "Diagnosis", + "Therapy", + "MolecularTest" + ], + "direct_children": [ + "Biospecimen", + "ClinicalDataTier2", + "SRRSClinicalDataTier2", + "LungCancerTier3", + "ColorectalCancerTier3", + "BreastCancerTier3", + "NeuroblastomaandGliomaTier3", + "AcuteLymphoblasticLeukemiaTier3", + "OvarianCancerTier3", + "ProstateCancerTier3", + "SarcomaTier3", + "PancreaticCancerTier3", + "MelanomaTier3", + "SRRSBiospecimen" + ], + "children": [ + "SarcomaTier3", + "ScATAC-seqLevel2", + "ColorectalCancerTier3", + "Biospecimen", + "HTANRPPAAntibodyTable", + "ImagingLevel1", + "NeuroblastomaandGliomaTier3", + "ScATAC-seqLevel3", + "OvarianCancerTier3", + "SRRSClinicalDataTier2", + "ScATAC-seqLevel1", + "BulkWESLevel1", + "SRRSImagingLevel2", + "BulkWESLevel3", + "ProstateCancerTier3", + "OtherAssay", + "BulkWESLevel2", + "ScRNA-seqLevel4", + "BulkRNA-seqLevel3", + "ScRNA-seqLevel3", + "RPPALevel2", + "LungCancerTier3", + "MelanomaTier3", + "ScATAC-seqLevel4", + "PancreaticCancerTier3", + "AcuteLymphoblasticLeukemiaTier3", + "ImagingLevel3Segmentation", + "BreastCancerTier3", + "ScRNA-seqLevel1", + "BulkRNA-seqLevel2", + "ImagingLevel3Image", + "ClinicalDataTier2", + "SRRSBiospecimen", + "ScRNA-seqLevel2", + "BulkRNA-seqLevel1", + "ImagingLevel2" + ] + } + ], + [ + { + "id": "Biospecimen", + "parents": [ + "Patient" + ], + "direct_children": [ + "OtherAssay", + "ScRNA-seqLevel1", + "BulkRNA-seqLevel1", + "BulkWESLevel1", + "ScATAC-seqLevel1", + "ImagingLevel1", + "SRRSImagingLevel2", + "RPPALevel2" + ], + "children": [ + "ScATAC-seqLevel2", + "BulkRNA-seqLevel3", + "ScRNA-seqLevel3", + "RPPALevel2", + "HTANRPPAAntibodyTable", + "ScATAC-seqLevel4", + "ImagingLevel3Segmentation", + "ImagingLevel1", + "ScATAC-seqLevel3", + "ScRNA-seqLevel1", + "BulkRNA-seqLevel2", + "ImagingLevel3Image", + "ScATAC-seqLevel1", + "BulkWESLevel1", + "SRRSImagingLevel2", + "BulkWESLevel3", + "ScRNA-seqLevel2", + "BulkRNA-seqLevel1", + "ScRNA-seqLevel4", + "BulkWESLevel2", + "OtherAssay", + "ImagingLevel2" + ] + }, + { + "id": "ClinicalDataTier2", + "parents": [ + "Patient" + ], + "direct_children": [], + "children": [] + }, + { + "id": "SRRSClinicalDataTier2", + "parents": [ + "Patient" + ], + "direct_children": [], + "children": [] + }, + { + "id": "LungCancerTier3", + "parents": [ + "Patient" + ], + "direct_children": [], + "children": [] + }, + { + "id": "ColorectalCancerTier3", + "parents": [ + "Patient" + ], + "direct_children": [], + "children": [] + }, + { + "id": "BreastCancerTier3", + "parents": [ + "Patient" + ], + "direct_children": [], + "children": [] + }, + { + "id": "NeuroblastomaandGliomaTier3", + "parents": [ + "Patient" + ], + "direct_children": [], + "children": [] + }, + { + "id": "AcuteLymphoblasticLeukemiaTier3", + "parents": [ + "Patient" + ], + "direct_children": [], + "children": [] + }, + { + "id": "OvarianCancerTier3", + "parents": [ + "Patient" + ], + "direct_children": [], + "children": [] + }, + { + "id": "ProstateCancerTier3", + "parents": [ + "Patient" + ], + "direct_children": [], + "children": [] + }, + { + "id": "SarcomaTier3", + "parents": [ + "Patient" + ], + "direct_children": [], + "children": [] + }, + { + "id": "PancreaticCancerTier3", + "parents": [ + "Patient" + ], + "direct_children": [], + "children": [] + }, + { + "id": "MelanomaTier3", + "parents": [ + "Patient" + ], + "direct_children": [], + "children": [] + }, + { + "id": "SRRSBiospecimen", + "parents": [ + "Patient" + ], + "direct_children": [], + "children": [] + } + ], + [ + { + "id": "ScRNA-seqLevel1", + "parents": [ + "Biospecimen" + ], + "direct_children": [ + "ScRNA-seqLevel2" + ], + "children": [ + "ScRNA-seqLevel3", + "ScRNA-seqLevel4", + "ScRNA-seqLevel2" + ] + }, + { + "id": "ScATAC-seqLevel1", + "parents": [ + "Biospecimen" + ], + "direct_children": [ + "ScATAC-seqLevel2" + ], + "children": [ + "ScATAC-seqLevel4", + "ScATAC-seqLevel2", + "ScATAC-seqLevel3" + ] + }, + { + "id": "BulkRNA-seqLevel1", + "parents": [ + "Biospecimen" + ], + "direct_children": [ + "BulkRNA-seqLevel2" + ], + "children": [ + "BulkRNA-seqLevel2", + "BulkRNA-seqLevel3" + ] + }, + { + "id": "BulkWESLevel1", + "parents": [ + "Biospecimen" + ], + "direct_children": [ + "BulkWESLevel2" + ], + "children": [ + "BulkWESLevel2", + "BulkWESLevel3" + ] + }, + { + "id": "ImagingLevel1", + "parents": [ + "Biospecimen" + ], + "direct_children": [ + "ImagingLevel2" + ], + "children": [ + "ImagingLevel3Image", + "ImagingLevel3Segmentation", + "ImagingLevel2" + ] + }, + { + "id": "RPPALevel2", + "parents": [ + "Biospecimen" + ], + "direct_children": [ + "HTANRPPAAntibodyTable" + ], + "children": [ + "HTANRPPAAntibodyTable" + ] + }, + { + "id": "OtherAssay", + "parents": [ + "Biospecimen" + ], + "direct_children": [], + "children": [] + }, + { + "id": "SRRSImagingLevel2", + "parents": [ + "Biospecimen" + ], + "direct_children": [], + "children": [] + } + ], + [ + { + "id": "ScRNA-seqLevel2", + "parents": [ + "ScRNA-seqLevel1" + ], + "direct_children": [ + "ScRNA-seqLevel3" + ], + "children": [ + "ScRNA-seqLevel3", + "ScRNA-seqLevel4" + ] + }, + { + "id": "ScATAC-seqLevel2", + "parents": [ + "ScATAC-seqLevel1" + ], + "direct_children": [ + "ScATAC-seqLevel3" + ], + "children": [ + "ScATAC-seqLevel4", + "ScATAC-seqLevel3" + ] + }, + { + "id": "BulkRNA-seqLevel2", + "parents": [ + "BulkRNA-seqLevel1" + ], + "direct_children": [ + "BulkRNA-seqLevel3" + ], + "children": [ + "BulkRNA-seqLevel3" + ] + }, + { + "id": "BulkWESLevel2", + "parents": [ + "BulkWESLevel1" + ], + "direct_children": [ + "BulkWESLevel3" + ], + "children": [ + "BulkWESLevel3" + ] + }, + { + "id": "ImagingLevel2", + "parents": [ + "ImagingLevel1" + ], + "direct_children": [ + "ImagingLevel3Segmentation", + "ImagingLevel3Image" + ], + "children": [ + "ImagingLevel3Image", + "ImagingLevel3Segmentation" + ] + }, + { + "id": "HTANRPPAAntibodyTable", + "parents": [ + "RPPALevel2" + ], + "direct_children": [], + "children": [] + }, + { + "id": "ImagingLevel3Channels", + "parents": [], + "direct_children": [ + "ImagingLevel3Image", + "ImagingLevel4" + ], + "children": [ + "ImagingLevel4", + "ImagingLevel3Image" + ] + } + ], + [ + { + "id": "ScRNA-seqLevel3", + "parents": [ + "ScRNA-seqLevel2" + ], + "direct_children": [ + "ScRNA-seqLevel4" + ], + "children": [ + "ScRNA-seqLevel4" + ] + }, + { + "id": "ScATAC-seqLevel3", + "parents": [ + "ScATAC-seqLevel2" + ], + "direct_children": [ + "ScATAC-seqLevel4" + ], + "children": [ + "ScATAC-seqLevel4" + ] + }, + { + "id": "BulkRNA-seqLevel3", + "parents": [ + "BulkRNA-seqLevel2" + ], + "direct_children": [], + "children": [] + }, + { + "id": "BulkWESLevel3", + "parents": [ + "BulkWESLevel2" + ], + "direct_children": [], + "children": [] + }, + { + "id": "ImagingLevel3Segmentation", + "parents": [ + "ImagingLevel2" + ], + "direct_children": [], + "children": [] + }, + { + "id": "ImagingLevel3Image", + "parents": [ + "ImagingLevel3Channels", + "ImagingLevel2" + ], + "direct_children": [], + "children": [] + }, + { + "id": "ImagingLevel4", + "parents": [ + "ImagingLevel3Channels" + ], + "direct_children": [], + "children": [] + } + ], + [ + { + "id": "ScRNA-seqLevel4", + "parents": [ + "ScRNA-seqLevel3" + ], + "direct_children": [], + "children": [] + }, + { + "id": "ScATAC-seqLevel4", + "parents": [ + "ScATAC-seqLevel3" + ], + "direct_children": [], + "children": [] + } + ] +] \ No newline at end of file diff --git a/files/JSON/mc2_rfc_test_8.30.24.json b/files/JSON/mc2_rfc_test_8.30.24.json deleted file mode 100644 index bf3d41c..0000000 --- a/files/JSON/mc2_rfc_test_8.30.24.json +++ /dev/null @@ -1 +0,0 @@ -[[{"id": "GrantView", "parents": [], "direct_children": ["Study"], "children": ["FileView", "10xVisiumSpatialTranscriptomics-RNA-seqLevel4", "Study", "Biospecimen", "10xVisiumSpatialTranscriptomics-RNA-seqLevel1", "10xVisiumSpatialTranscriptomics-RNA-seqLevel2", "10xVisiumSpatialTranscriptomics-AuxiliaryFiles", "10xVisiumSpatialTranscriptomics-RNA-seqLevel3"]}], [{"id": "Study", "parents": ["GrantView"], "direct_children": ["Biospecimen"], "children": ["FileView", "10xVisiumSpatialTranscriptomics-RNA-seqLevel4", "Biospecimen", "10xVisiumSpatialTranscriptomics-RNA-seqLevel1", "10xVisiumSpatialTranscriptomics-RNA-seqLevel2", "10xVisiumSpatialTranscriptomics-AuxiliaryFiles", "10xVisiumSpatialTranscriptomics-RNA-seqLevel3"]}], [{"id": "Biospecimen", "parents": ["Study"], "direct_children": ["FileView"], "children": ["FileView", "10xVisiumSpatialTranscriptomics-RNA-seqLevel4", "10xVisiumSpatialTranscriptomics-RNA-seqLevel1", "10xVisiumSpatialTranscriptomics-RNA-seqLevel2", "10xVisiumSpatialTranscriptomics-AuxiliaryFiles", "10xVisiumSpatialTranscriptomics-RNA-seqLevel3"]}], [{"id": "FileView", "parents": ["Biospecimen"], "direct_children": ["10xVisiumSpatialTranscriptomics-AuxiliaryFiles", "10xVisiumSpatialTranscriptomics-RNA-seqLevel1"], "children": ["10xVisiumSpatialTranscriptomics-RNA-seqLevel4", "10xVisiumSpatialTranscriptomics-RNA-seqLevel1", "10xVisiumSpatialTranscriptomics-RNA-seqLevel2", "10xVisiumSpatialTranscriptomics-AuxiliaryFiles", "10xVisiumSpatialTranscriptomics-RNA-seqLevel3"]}], [{"id": "10xVisiumSpatialTranscriptomics-RNA-seqLevel1", "parents": ["FileView"], "direct_children": ["10xVisiumSpatialTranscriptomics-RNA-seqLevel2"], "children": ["10xVisiumSpatialTranscriptomics-RNA-seqLevel3", "10xVisiumSpatialTranscriptomics-RNA-seqLevel2", "10xVisiumSpatialTranscriptomics-RNA-seqLevel4"]}, {"id": "10xVisiumSpatialTranscriptomics-AuxiliaryFiles", "parents": ["FileView"], "direct_children": [], "children": []}], [{"id": "10xVisiumSpatialTranscriptomics-RNA-seqLevel2", "parents": ["10xVisiumSpatialTranscriptomics-RNA-seqLevel1"], "direct_children": ["10xVisiumSpatialTranscriptomics-RNA-seqLevel3"], "children": ["10xVisiumSpatialTranscriptomics-RNA-seqLevel3", "10xVisiumSpatialTranscriptomics-RNA-seqLevel4"]}], [{"id": "10xVisiumSpatialTranscriptomics-RNA-seqLevel3", "parents": ["10xVisiumSpatialTranscriptomics-RNA-seqLevel2"], "direct_children": ["10xVisiumSpatialTranscriptomics-RNA-seqLevel4"], "children": ["10xVisiumSpatialTranscriptomics-RNA-seqLevel4"]}], [{"id": "10xVisiumSpatialTranscriptomics-RNA-seqLevel4", "parents": ["10xVisiumSpatialTranscriptomics-RNA-seqLevel3"], "direct_children": [], "children": []}]] \ No newline at end of file diff --git a/files/Merged/HTAN_attribute_table.csv b/files/Merged/HTAN_attribute_table.csv index f96ed55..e166d1e 100644 --- a/files/Merged/HTAN_attribute_table.csv +++ b/files/Merged/HTAN_attribute_table.csv @@ -1,1194 +1,152 @@ -,Attribute,Label,Description,Required,Cond_Req,Valid Values,Conditional Requirements,Component -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,Patient -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Patient -Days to Birth,Days to Birth,DaystoBirth,Number of days between the date used for index and the date from a person's date of birth represented as a calculated negative number of days.,False,,,,Demographics -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,Demographics -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Demographics -Weeks Gestation at Birth,Weeks Gestation at Birth,WeeksGestationatBirth,Numeric value used to describe the number of weeks starting from the approximate date of the biological mother's last menstrual period and ending with the birth of the patient.,False,,,,Demographics -Vital Status,Vital Status,VitalStatus,The survival state of the person registered on the protocol.,True,,"['Alive', 'Unknown', 'Dead', 'Not Reported']",,Demographics -Age Is Obfuscated,Age Is Obfuscated,AgeIsObfuscated,The age of the patient has been modified for compliance reasons. The actual age differs from what is reported. Other date intervals for this patient may also be modified.,False,,"['False', 'True', '']",,Demographics -Race,Race,Race,"An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation withina a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution.",True,,"['white', 'Not Reported', 'american indian or alaska native', 'asian', 'Other', 'Unknown', 'native hawaiian or other pacific islander', 'not allowed to collect', 'black or african american']",,Demographics -Occupation Duration Years,Occupation Duration Years,OccupationDurationYears,The number of years a patient worked in a specific occupation.,False,,,,Demographics -Year Of Birth,Year Of Birth,YearOfBirth,Numeric value to represent the calendar year in which an individual was born.,False,,,,Demographics -Gender,Gender,Gender,"Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.]",True,,"['Not Reported', 'unspecified', 'Unknown', 'female', 'male']",,Demographics -Premature At Birth,Premature At Birth,PrematureAtBirth,The yes/no/unknown indicator used to describe whether the patient was premature (less than 37 weeks gestation) at birth.,False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,Demographics -Ethnicity,Ethnicity,Ethnicity,"An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.",True,,"['Not Reported', 'Unknown', 'hispanic or latino', 'not hispanic or latino', 'not allowed to collect']",,Demographics -Country of Residence,Country of Residence,CountryofResidence,Country of Residence at enrollment,False,,"['Belize', 'Monaco', 'Bahrain', 'Iraq', 'South Africa', 'Vietnam', 'Niue', 'Poland', 'Albania', 'Burundi', 'Spain', 'Bhutan', 'Saudi Arabia', 'Madagascar', 'Gambia', 'Switzerland', 'Laos', 'Saint Lucia', 'Myanmar', 'Mayotte', 'Guadeloupe', 'South Korea', 'Tokelau', 'Syria', 'Pakistan', 'Isle of Man', 'Yemen', 'Svalbard & Jan Mayen Islands', 'Jersey', 'Bosnia and Herzegovina', 'Eritrea', 'Guinea', 'Philippines', 'Guinea-Bissau', 'Azerbaijan', 'Somalia', 'Sudan', 'Cambodia', 'Cuba', 'Rwanda', 'Tonga', 'Saint Kitts and Nevis', 'Finland', 'Paraguay', 'Malawi', 'Falkland Islands (Malvinas)', 'Federated States of Micronesia', 'Niger', 'Colombia', 'Democratic Republic of the Congo', 'North Macedonia', 'Haiti', 'Timor-Leste', 'Austria', 'Chad', 'Iceland', 'Dominica', 'Malta', 'Denmark', 'Kosovo', 'Martinique', 'Bangladesh', 'San Marino', 'South Sudan', 'Georgia', 'Nigeria', 'Gibraltar', 'Nauru', 'Tajikistan', 'Montserrat', 'Sweden', 'Antigua and Barbuda', 'Indonesia', 'Sri Lanka', 'Greece', 'Gabon', 'Japan', 'Mauritania', 'Nicaragua', 'China', 'Cape Verde', 'Grenada', 'French Polynesia', 'Moldova', 'Cayman Islands', 'Dominican Republic', 'Liechtenstein', 'Senegal', 'Holy See', 'Mali', 'Vanuatu', 'India', 'Bermuda', 'Netherlands', 'Ireland', 'Zambia', 'North Korea', 'Macau', 'Romania', 'Solomon Islands', 'Suriname', 'Nepal', 'Croatia', 'Reunion', 'Ghana', 'Saint Helena Ascension and Tristan da Cunha', 'Israel', 'Faroe Islands', 'Greenland', 'State of Palestine', 'Wallis and Futuna', 'Ecuador', 'French Guiana', 'Angola', 'Aruba', 'Guyana', 'Kuwait', 'Taiwan', 'Singapore', 'Togo', 'Andorra', 'Lebanon', 'Northern Mariana Islands', 'Armenia', 'Iran', 'New Zealand', 'Bolivia', 'Cameroon', 'Norway', 'Panama', 'Papua New Guinea', 'Qatar', 'Tanzania', 'Portugal', 'Slovakia', 'Equatorial Guinea', 'Estonia', 'Mongolia', 'Chile', 'Burkina Faso', 'Ethiopia', 'Hungary', 'Djibouti', 'Kenya', 'Kiribati', 'Botswana', 'Australia', 'Guam', 'Congo', 'Belarus', 'Uruguay', 'Czech Republic (Czechia)', 'Lesotho', 'United Kingdom', 'Lithuania', 'Russia', 'Thailand', 'Oman', 'Benin', 'Tunisia', 'Uganda', 'Namibia', 'Honduras', 'Algeria', 'Turkey', 'Morocco', 'Barbados', 'Sierra Leone', 'Venezuela', 'Saint Pierre and Miquelon', 'Kyrgyzstan', 'Trinidad and Tobago', 'Serbia', 'Peru', 'Comoros', 'Canada', 'Hong Kong', 'Liberia', 'Malaysia', 'Puerto Rico', 'Brazil', 'Virgin Islands British', 'Zimbabwe', 'Latvia', 'Eswatini', ""Cote d'Ivoire"", 'United Arab Emirates', 'Bahamas', 'Curacao', 'Slovenia', 'Central African Republic', 'Guatemala', 'Jordan', 'Egypt', 'Germany', 'Mozambique', 'Fiji', 'Turkmenistan', 'Mexico', 'Brunei', 'France', 'Kazakhstan', 'Argentina', 'Uzbekistan', 'Samoa', 'Bulgaria', 'Virgin Islands U.S.', 'Maldives', 'Cyprus', 'Costa Rica', 'Italy', 'Libya', 'Jamaica', 'Tuvalu', 'United States', 'Saint Vincent and the Grenadines', 'Palau', 'Western Sahara', 'Guernsey', 'Mauritius', 'El Salvador', 'Afghanistan', 'Belgium', 'Luxembourg', 'Ukraine', 'Marshall Islands', 'Montenegro', 'Cook Islands', 'Seychelles', 'Sao Tome and Principe', 'New Caledonia', 'Anguilla', '']",,Demographics -Year of Death,Year of Death,YearofDeath,Numeric value to represent the year of the death of an individual.,False,True,," If Vital Status is ""Dead"" then ""Year of Death"" is required",Demographics -Cause of Death Source,Cause of Death Source,CauseofDeathSource,The text term used to describe the source used to determine the patient's cause of death.,False,True,"['Medical Record', 'Not Reported', 'Unknown', 'Death Certificate', 'Autopsy', 'Social Security Death Index', '']"," If Vital Status is ""Dead"" then ""Cause of Death Source"" is required",Demographics -Cause of Death,Cause of Death,CauseofDeath,The cause of death,False,True,"['Cancer Related', 'Not Reported', 'Renal Disorder NOS', 'Not Applicable', 'Spinal Muscular Atrophy', 'End-stage Renal Disease', 'Not Cancer Related', 'Unknown', 'Infection', 'Surgical Complications', 'Cardiovascular Disorder NOS', 'Toxicity', '']"," If Vital Status is ""Dead"" then ""Cause of Death"" is required",Demographics -Days to Death,Days to Death,DaystoDeath,Number of days between the date used for index and the date from a person's date of death represented as a calculated number of days.,False,True,," If Vital Status is ""Dead"" then ""Days to Death"" is required",Demographics -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,FamilyHistory -Relative with Cancer History,Relative with Cancer History,RelativewithCancerHistory,The yes/no/unknown indicator used to describe whether any of the patient's relatives have a history of cancer.,False,,"['None', 'Yes - Cancer History Relative', 'Not Reported', 'Unknown', '']",,FamilyHistory -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,FamilyHistory -Relationship Gender,Relationship Gender,RelationshipGender,The text term used to describe the gender of the patient's relative with a history of cancer.,False,True,"['Not Reported', 'unspecified', 'Unknown', 'female', 'male', '']"," If Relative with Cancer History is ""Yes - Cancer History Relative"" then ""Relationship Gender"" is required",FamilyHistory -Relationship Type,Relationship Type,RelationshipType,The subgroup that describes the state of connectedness between members of the unit of society organized around kinship ties.,False,True,"['Unrelated', 'Adoptive Father', 'Stepdaughter', 'Foster Father', 'Cousin', 'Identical Twin Sibling', 'Domestic Partner', 'Natural Father', 'Identical Twin Brother', 'Parent', 'Paternal Aunt', 'Paternal Half Sister', 'Maternal Great Aunt', 'Fraternal Twin Brother', 'Adopted Son', 'Identical Twin Sister', 'Not Reported', 'Child', 'Maternal Great Grandparent', 'Step Sibling', 'Maternal Aunt', 'Paternal Grandfather', 'Maternal First Cousin', 'Stepson', 'Son-in-law', 'Fraternal Twin Sibling', 'Other', 'Wife', 'Foster Sister', 'Nephew', 'Paternal Grandmother', 'Adoptive Mother', 'Maternal Uncle', 'Natural Sibling', 'Grandson', 'Grandfather', 'Half Sibling', 'Spouse', 'Paternal First Cousin', 'Stepbrother', 'Natural Grandparent', 'Paternal First Cousin Once Removed', 'Unknown', 'Paternal Grandparent', 'Sibling', 'Stepfather', 'Grandmother', 'Maternal Half Sibling', 'Paternal Half Brother', 'Grand Nephew', 'Half Brother', 'Stepsister', 'Stepmother', 'Full Brother', 'Refused', 'Foster Brother', 'Fraternal Twin Sister', 'Natural Grandchild', 'Grandchild', 'Male Cousin', 'Uncle', 'Niece', 'Foster Son', 'First Cousin', 'Brother-in-law', 'Natural Parent', 'Husband', 'Paternal Uncle', 'First Cousin Once Removed', 'Granddaughter', 'Mother', 'Natural Child', 'Sister', 'Adoptive Sister', 'Paternal Great Grandparent', 'Niece Second Degree Relative', 'Son', 'Maternal Grandfather', 'Daughter-in-law', 'Half Sister', 'Natural Daughter', 'Paternal Great Uncle', 'Maternal Grandparent', 'Natural Son', 'Aunt', 'Maternal First Cousin Once Removed', 'Maternal Half Sister', 'Grandparent', 'Step Child', 'Natural Grandmother', 'Full Sister', 'Legal Guardian', 'Adopted Daughter', 'Natural Sister', 'Twin Sibling', 'Paternal Half Sibling', 'Sister-in-law', 'Natural Brother', 'Ward', 'Paternal Great Aunt', 'Father-in-law', 'Adoptive Brother', 'Female Cousin', 'Father', 'Natural Mother', 'Natural Grandfather', 'Grand Niece', 'Great Grandchild', 'Daughter', 'Maternal Grandmother', 'Brother', 'Foster Daughter', 'Maternal Great Uncle', 'Foster Mother', 'Maternal Half Brother', 'Mother-in-law', '']"," If Relative with Cancer History is ""Yes - Cancer History Relative"" then ""Relationship Type"" is required",FamilyHistory -Relationship Age at Diagnosis,Relationship Age at Diagnosis,RelationshipAgeatDiagnosis,The age (in years) when the patient's relative was first diagnosed.,False,True,," If Relative with Cancer History is ""Yes - Cancer History Relative"" then ""Relationship Age at Diagnosis"" is required",FamilyHistory -Relatives with Cancer History Count,Relatives with Cancer History Count,RelativeswithCancerHistoryCount,The number of relatives the patient has with a known history of cancer.,False,True,," If Relative with Cancer History is ""Yes - Cancer History Relative"" then ""Relatives with Cancer History Count"" is required",FamilyHistory -Relationship Primary Diagnosis,Relationship Primary Diagnosis,RelationshipPrimaryDiagnosis,The text term used to describe the malignant diagnosis of the patient's relative with a history of cancer.,False,True,"['Sarcoma', 'Lymphoma', 'Bladder Cancer', 'Tonsillar Cancer', 'Chondrosarcoma', 'Kaposi Sarcoma', 'Esophageal Cancer', 'Gynecologic Cancer', 'Uterine Cancer', 'Leukemia', 'Wilms Tumor', 'Lung Cancer', 'Liver Cancer', 'Osteosarcoma', 'Throat Cancer', 'Mesothelioma', 'Bone Cancer', 'Ewing Sarcoma', 'Melanoma', 'Head and Neck Cancer', 'Unknown', 'Blood Cancer', 'Kidney Cancer', 'Brain Cancer', 'Adrenal Gland Cancer', 'Glioblastoma', 'Skin Cancer', 'Not Reported', 'Cervical Cancer', 'Basal Cell Cancer', 'Tongue Cancer', 'Hematologic Cancer', 'Multiple Myeloma', 'Ovarian Cancer', 'Laryngeal Cancer', 'Breast Cancer', 'Rectal Cancer', 'Spleen Cancer', 'Rhabdomyosarcoma', 'Prostate Cancer', 'Pancreas Cancer', 'Bile Duct Cancer', 'Gallbladder Cancer', 'Testicular Cancer', 'CNS Cancer', 'Neuroblastoma', 'Thyroid Cancer', 'Lymph Node Cancer', 'Colorectal Cancer', 'Cancer', 'Gastric Cancer', '']"," If Relative with Cancer History is ""Yes - Cancer History Relative"" then ""Relationship Primary Diagnosis"" is required",FamilyHistory -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,Exposure -Coal Dust Exposure,Coal Dust Exposure,CoalDustExposure,The yes/no/unknown indicator used to describe whether a patient was exposed to fine powder derived by the crushing of coal.,False,,"['No', 'Unknown', 'Yes', '']",,Exposure -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Exposure -Radon Exposure,Radon Exposure,RadonExposure,The yes/no/unknown indicator used to describe whether the patient was exposed to radon.,False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,Exposure -Respirable Crystalline Silica Exposure,Respirable Crystalline Silica Exposure,RespirableCrystallineSilicaExposure,"The yes/no/unknown indicator used to describe whether a patient was exposured to respirable crystalline silica, a widespread, naturally occurring, crystalline metal oxide that consists of different forms including quartz, cristobalite, tridymite, tripoli, ganister, chert and novaculite.",False,,"['No', 'Unknown', 'Yes', '']",,Exposure -Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,Exposure -Alcohol Exposure,Alcohol Exposure,AlcoholExposure,Indicate if individual has alcohol exposure,True,,"['Not Reported', 'No - Alcohol Exposure', 'Yes - Alcohol Exposure']",,Exposure -Environmental Tobacco Smoke Exposure,Environmental Tobacco Smoke Exposure,EnvironmentalTobaccoSmokeExposure,"The yes/no/unknown indicator used to describe whether a patient was exposed to smoke that is emitted from burning tobacco, including cigarettes, pipes, and cigars. This includes tobacco smoke exhaled by smokers.",False,,"['No', 'Unknown', 'Yes', '']",,Exposure -Smoking Exposure,Smoking Exposure,SmokingExposure,Indicate if individual has smoking exposure,True,,"['No - Smoking Exposure', 'Not Reported', 'Yes - Smoking Exposure']",,Exposure -Asbestos Exposure,Asbestos Exposure,AsbestosExposure,The yes/no/unknown indicator used to describe whether the patient was exposed to asbestos.,False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,Exposure -Alcohol Drinks Per Day,Alcohol Drinks Per Day,AlcoholDrinksPerDay,Numeric value used to describe the average number of alcoholic beverages a person consumes per day.,False,True,," If Alcohol Exposure is ""Yes - Alcohol Exposure"" then ""Alcohol Drinks Per Day"" is required",Exposure -Alcohol Days Per Week,Alcohol Days Per Week,AlcoholDaysPerWeek,Numeric value used to describe the average number of days each week that a person consumes an alcoholic beverage.,False,True,," If Alcohol Exposure is ""Yes - Alcohol Exposure"" then ""Alcohol Days Per Week"" is required",Exposure -Alcohol Intensity,Alcohol Intensity,AlcoholIntensity,Category to describe the patient's current level of alcohol use as self-reported by the patient.,False,True,"['Non-Drinker', 'Not Reported', 'Unknown', 'Lifelong Non-Drinker', 'Occasional Drinker', 'Drinker', 'Heavy Drinker', '']"," If Alcohol Exposure is ""Yes - Alcohol Exposure"" then ""Alcohol Intensity"" is required",Exposure -Alcohol Type,Alcohol Type,AlcoholType,Type of alcohol use,False,True,"['Beer', 'Wine', 'Not Reported', 'Other', 'Unknown', 'Liquor', '']"," If Alcohol Exposure is ""Yes - Alcohol Exposure"" then ""Alcohol Type"" is required",Exposure -Alcohol History,Alcohol History,AlcoholHistory,A response to a question that asks whether the participant has consumed at least 12 drinks of any kind of alcoholic beverage in their lifetime.,False,True,"['No', 'Unknown', 'Not Reported', 'Yes', '']"," If Alcohol Exposure is ""Yes - Alcohol Exposure"" then ""Alcohol History"" is required",Exposure -Tobacco Smoking Quit Year,Tobacco Smoking Quit Year,TobaccoSmokingQuitYear,The year in which the participant quit smoking.,False,True,," If Smoking Exposure is ""Yes - Smoking Exposure"" then ""Tobacco Smoking Quit Year"" is required",Exposure -Smoking Frequency,Smoking Frequency,SmokingFrequency,The text term used to generally decribe how often the patient smokes.,False,True,"['Unknown', 'Some days', 'Every day', '']"," If Smoking Exposure is ""Yes - Smoking Exposure"" then ""Smoking Frequency"" is required",Exposure -Tobacco Smoking Status,Tobacco Smoking Status,TobaccoSmokingStatus,Category describing current smoking status and smoking history as self-reported by a patient,False,True,"['Smoking history not documented', 'Not Reported', 'Current Reformed Smoker for > 15 yrs', 'Unknown', 'Current Reformed Smoker for < or = 15 yrs', 'Lifelong Non-Smoker', 'Current Smoker', 'Duration Not Specified', 'Current Reformed Smoker', '']"," If Smoking Exposure is ""Yes - Smoking Exposure"" then ""Tobacco Smoking Status"" is required",Exposure -Tobacco Use per Day,Tobacco Use per Day,TobaccoUseperDay,Numeric value that represents the number of times the patient uses tobacco each day.,False,True,," If Smoking Exposure is ""Yes - Smoking Exposure"" then ""Tobacco Use per Day"" is required",Exposure -Type of Smoke Exposure,Type of Smoke Exposure,TypeofSmokeExposure,The text term used to describe the patient's specific type of smoke exposure.,False,True,"['Workrelated smoke artificial smoke machines', 'Workrelated smoke fire fighting', 'No Smoke Exposure', 'Workrelated smoke foundry', 'Volcanic smoke', 'Factory smokestack smoke', 'Field burning smoke', 'Hashish smoke', 'Grilling smoke', 'Accidental building fire smoke', 'Indoor wood burning stove or fireplace smoke', 'Oil burning smoke Kerosene', 'Workrelated smoke generators', 'Workrelated smoke paint baking', 'Accidental fire smoke NOS', 'Indoor coal burning stove or fireplace smoke', 'Tobacco smoke cigarettes', 'Workrelated smoke military', 'Tobacco smoke cigar', 'Unknown', 'Fire smoke NOS', 'Smokehouse smoke', 'Wood burning smoke factory', 'Accidental vehicle fire smoke', 'Aircraft smoke', 'Waste burning smoke', 'Wood burning smoke NOS', 'Machine smoke', 'Oil burning smoke NOS', 'Workrelated smoke plumbing', 'Coal smoke NOS', 'Tobacco smoke pipe', 'Furnace or boiler smoke', 'Accidental forest fire smoke', 'Marijuana smoke', 'Workrelated smoke plastics factory', 'Smoke exposure NOS', 'Gas burning smoke propane', 'Cooking related smoke NOS', 'Electrical fire smoke', 'Burning tree smoke', 'Indoor stove or fireplace smoke NOS', 'Electronic cigarette smoke NOS', 'Environmental tobacco smoke', 'Accidental grass fire smoke', 'Workrelated smoke soldering/welding', 'Recreational fire smoke', 'Workrelated smoke NOS', 'Grease fire smoke', '']"," If Smoking Exposure is ""Yes - Smoking Exposure"" then ""Type of Smoke Exposure"" is required",Exposure -Time between Waking and First Smoke,Time between Waking and First Smoke,TimebetweenWakingandFirstSmoke,TBD,False,True,," If Smoking Exposure is ""Yes - Smoking Exposure"" then ""Time between Waking and First Smoke"" is required",Exposure -Tobacco Smoking Onset Year,Tobacco Smoking Onset Year,TobaccoSmokingOnsetYear,The year in which the participant began smoking.,False,True,," If Smoking Exposure is ""Yes - Smoking Exposure"" then ""Tobacco Smoking Onset Year"" is required",Exposure -Cigarettes per Day,Cigarettes per Day,CigarettesperDay,The average number of cigarettes smoked per day.,False,True,," If Smoking Exposure is ""Yes - Smoking Exposure"" then ""Cigarettes per Day"" is required",Exposure -Years Smoked,Years Smoked,YearsSmoked,Numeric value (or unknown) to represent the number of years a person has been smoking.,False,True,," If Smoking Exposure is ""Yes - Smoking Exposure"" then ""Years Smoked"" is required",Exposure -Smokeless Tobacco Quit Age,Smokeless Tobacco Quit Age,SmokelessTobaccoQuitAge,Smokeless tobacco quit age,False,True,," If Smoking Exposure is ""Yes - Smoking Exposure"" then ""Smokeless Tobacco Quit Age"" is required",Exposure -Smoke Exposure Duration,Smoke Exposure Duration,SmokeExposureDuration,Text term used to describe the length of time the patient was exposed to an environmental factor.,False,True,"['Unknown', 'Not Reported', 'Six Weeks or More', '']"," If Smoking Exposure is ""Yes - Smoking Exposure"" then ""Smoke Exposure Duration"" is required",Exposure -Secondhand Smoke as Child,Secondhand Smoke as Child,SecondhandSmokeasChild,The text term used to indicate whether the patient was exposed to secondhand smoke as a child.,False,True,"['No', 'Unknown', 'Not Reported', 'Yes', '']"," If Smoking Exposure is ""Yes - Smoking Exposure"" then ""Secondhand Smoke as Child"" is required",Exposure -Type of Tobacco Used,Type of Tobacco Used,TypeofTobaccoUsed,The text term used to describe the specific type of tobacco used by the patient.,False,True,"['Cigar', 'Marijuana', 'Other', 'Cigarettes', 'Pipe', 'Smokeless Tobacco', 'Electronic Cigarette', '']"," If Smoking Exposure is ""Yes - Smoking Exposure"" then ""Type of Tobacco Used"" is required",Exposure -Pack Years Smoked,Pack Years Smoked,PackYearsSmoked,Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes smoked per day x number of years smoked divided by 20.,False,True,," If Smoking Exposure is ""Yes - Smoking Exposure"" then ""Pack Years Smoked"" is required",Exposure -Marijuana Use Per Week,Marijuana Use Per Week,MarijuanaUsePerWeek,Numeric value that represents the number of times the patient uses marijuana each day.,False,True,," If Type is ""Marijuana smoke"" then ""Marijuana Use Per Week"" is required",Exposure -Karnofsky Performance Status,Karnofsky Performance Status,KarnofskyPerformanceStatus,Text term used to describe the classification used of the functional capabilities of a person.,False,,"['100', '40', '30', '70', '90', '50', '60', '10', '20', '80', '0', '']",,FollowUp -Barretts Esophagus Goblet Cells Present,Barretts Esophagus Goblet Cells Present,BarrettsEsophagusGobletCellsPresent,TBD,False,,,,FollowUp -Imaging Result,Imaging Result,ImagingResult,The text term used to describe the result of the imaging or scan performed on the patient.,False,,"['Not Reported', 'Not Performed', 'Positive', 'Unknown', 'Indeterminate', 'Negative', '']",,FollowUp -Pregnancy Outcome,Pregnancy Outcome,PregnancyOutcome,The text term used to describe the type of pregnancy the patient had,False,,"['Induced Abortion', 'Ectopic Pregnancy', 'Not Reported', 'Miscarriage', 'Unknown', 'Live Birth', 'Stillbirth', '']",,FollowUp -Days to Follow Up,Days to Follow Up,DaystoFollowUp,Number of days between the date used for index and the date of the patient's last follow-up appointment or contact.,True,,,,FollowUp -Hysterectomy Type,Hysterectomy Type,HysterectomyType,The text term used to describe the type of hysterectomy the patient had.,False,,"['Not Reported', 'Radical Hysterectomy', 'Unknown', 'Simple Hysterectomy', 'Hysterectomy NOS', 'Not performed', '']",,FollowUp -Immunosuppressive Treatment Type,Immunosuppressive Treatment Type,ImmunosuppressiveTreatmentType,The text term used to describe the type of immunosuppresive treatment the patient received.,False,,"['Anti-TNFTherapy', 'None', 'Methotrexate', 'Not Reported', 'Azathioprine', 'Other', 'Unknown', 'Cyclophosphamide', '']",,FollowUp -CDC HIV Risk Factors,CDC HIV Risk Factors,CDCHIVRiskFactors,"The text term used to describe a risk factor for human immunodeficiency virus, as described by the Center for Disease Control.",False,,"['None', 'Homosexual Contact', 'Not Reported', 'Hemophiliac', 'Intravenous Drug User', 'Unknown', 'Transfusion Recipient', 'Heterosexual Contact', '']",,FollowUp -Adverse Event,Adverse Event,AdverseEvent,Text that represents the Common Terminology Criteria for Adverse Events low level term name for an adverse event.,False,,"['Intraoperative Ear Injury', 'Depression', 'Hiccups', 'Tumor Lysis Syndrome', 'Paroxysmal Atrial Tachycardia', 'Stridor', 'Hypoxia', 'Intestinal Stoma Obstruction', 'Pancreatic Anastomotic Leak', 'Urostomy Stenosis', 'Colonic Stenosis', 'Soft Tissue Necrosis Upper Limb', 'Pneumothorax', 'Encephalomyelitis Infection', 'Ischemia Cerebrovascular', 'Bladder Perforation', 'Intraoperative Arterial Injury', 'Disseminated Intravascular Coagulation', 'Venous Injury', 'Tooth Development Disorder', 'Back Pain', 'Hip Fracture', 'Injury', 'Intestinal Stoma Site Bleeding', 'Nipple Deformity', 'Cytokine Release Syndrome', 'Pulmonary Hypertension', 'Ovulation Pain', 'Fibrosis Deep Connective Tissue', 'Peritoneal Necrosis', 'Hemolytic Uremic Syndrome', 'Alkalosis', 'Proctitis', 'Urinary Tract Infection', 'Psychiatric Disorders Other', 'Infective Myositis', 'Prolapse of Intestinal Stoma', 'Facial Pain', 'Esophageal Perforation', 'Laryngeal Stenosis', 'Joint Infection', 'Pulmonary Fistula', 'Infusion Site Extravasation', 'Ileal Ulcer', 'Perineal Pain', 'Gastric Stenosis', 'Muscle Weakness Left-Sided', 'Platelet Count Decreased', 'Duodenal Ulcer', 'Malignant and Unspecified (Incl Cysts and Polyps) Other', 'Infections and Infestations Other', 'Peritoneal Infection', 'Mitral Valve Disease', 'Intraoperative Cardiac Injury', 'Upper Gastrointestinal Hemorrhage', 'Lymph Gland Infection', 'Breast Pain', 'Precocious Puberty', 'Bone Infection', 'Rectal Perforation', 'Biliary Tract Infection', 'Hirsutism', 'Testicular Disorder', 'Gastroparesis', 'Anorexia', 'Atrial Fibrillation', 'Extraocular Muscle Paresis', 'Erythroderma', 'Tumor Pain', 'Pericardial Effusion', 'Supraventricular Tachycardia', 'Congenital', 'Pharyngeal Stenosis', 'Bladder Spasm', 'Osteonecrosis of Jaw', 'Transient Ischemic Attacks', 'Anal Fistula', 'Palmar-Plantar Erythrodysesthesia Syndrome', 'Spermatic Cord Hemorrhage', 'Splenic Infection', 'Nausea', 'Kidney Infection', 'Unintended Pregnancy', 'Dysarthria', 'Rectal Anastomotic Leak', 'Mediastinal Infection', 'Skin Hyperpigmentation', 'Intraoperative Ocular Injury', 'Lung Infection', 'Vaginal Discharge', 'Rectal Fistula', 'Hemorrhoidal Hemorrhage', 'Thromboembolic Event', 'Large Intestinal Anastomotic Leak', 'Pleuritic Pain', 'Pulmonary Valve Disease', 'Dehydration', 'Diarrhea', 'Laryngeal Obstruction', 'Salivary Gland Infection', 'Uterine Fistula', 'Intraoperative Hepatobiliary Injury', 'Uterine Hemorrhage', 'Scrotal Infection', 'General Disorders and Administration Site Conditions Other', 'Seizure', 'Trismus', 'Hyperthyroidism', 'Radiation Recall Reaction (Dermatologic)', 'Neck Pain', 'Endocarditis Infective', 'Pharyngeal Fistula', 'Oral Dysesthesia', 'Urinary Frequency', 'Facial Muscle Weakness', 'Perforation Bile Duct', 'Scrotal Pain', 'Myocarditis', 'Rectal Stenosis', 'Endocrine Disorders Other', 'Eye Pain', 'Pharyngitis', 'Genital Edema', 'Spleen Disorder', 'Puerperium and Perinatal Conditions Other', 'Sneezing', 'External Ear Inflammation', 'Ileal Perforation', 'Edema Limbs', 'Death NOS', 'Renal and Urinary Disorders Other', 'Proteinuria', 'Unequal Limb Length', 'Alkaline Phosphatase Increased', 'Testicular Hemorrhage', 'Tracheal Mucositis', 'Dizziness', 'Pleural Effusion', 'Laryngeal Inflammation', 'Electrocardiogram QT Corrected Interval Prolonged', 'Azoospermia', 'Dysphagia', 'Ejection Fraction Decreased', 'Atrial Flutter', 'Telangiectasia', 'Prostate Infection', 'Vasculitis', 'Bronchial Fistula', 'Aortic Valve Disease', 'Papulopustular Rash', 'Oral Hemorrhage', 'Allergic Reaction', 'Bronchopulmonary Hemorrhage', 'Wheezing', 'Neck Edema', 'Right Ventricular Dysfunction', 'Stoma Site Infection', 'Neuralgia', 'Bile Duct Stenosis', 'Esophageal Obstruction', 'Cholesterol High', 'Gastric Hemorrhage', 'Vomiting', 'Joint Range of Motion Decreased Lumbar Spine', 'Gallbladder Infection', 'Chills', 'Eye Infection', 'Typhlitis', 'Meningismus', 'Laryngeal Fistula', 'Intraoperative Skin Injury', 'Dry Eye', 'Intraoperative Breast Injury', 'Arteritis Infective', 'Uterine Perforation', 'Feminization Acquired', 'Lymphocyte Count Increased', 'Alcohol Intolerance', 'Esophageal Necrosis', 'CD4 Lymphocytes Decreased', 'Esophagitis', 'Hypercalcemia', 'Nystagmus', 'Activated Partial Thromboplastin Time Prolonged', 'Lipohypertrophy', 'Vaginismus', 'Prolapse of Urostomy', 'Vitreous Hemorrhage', 'Vulval Infection', 'Erectile Dysfunction', 'Fibrinogen Decreased', 'Oculomotor Nerve Disorder', 'Irritability', 'Rectal Ulcer', 'Gastric Ulcer', 'Stenosis of Gastrointestinal Stoma', 'Otitis Externa', 'Febrile Neutropenia', 'Recurrent Laryngeal Nerve Palsy', 'Generalized Muscle Weakness', 'Skin Hypopigmentation', 'Glucose Intolerance', 'Pleural Infection', 'Growth Suppression', 'Lordosis', 'Creatinine Increased', 'Tracheal Stenosis', 'Hematuria', 'Lethargy', 'Hepatitis Viral', 'Hemorrhoids', 'Superficial Thrombophlebitis', 'Penile Pain', 'Tracheal Hemorrhage', 'Ventricular Arrhythmia', 'Hypertriglyceridemia', 'Cerebrospinal Fluid Leakage', 'Olfactory Nerve Disorder', 'Enterocolitis', 'Lactation Disorder', 'Mucosal Infection', 'Serum Amylase Increased', 'Growth Accelerated', 'Injection Site Reaction', 'Flatulence', 'Pancreatic Fistula', 'Optic Nerve Disorder', 'Rectal Mucositis', 'Phantom Pain', 'Urethral Infection', 'Skin Induration', 'Gallbladder Pain', 'Non-Cardiac Chest Pain', 'Movements Involuntary', 'Joint Range of Motion Decreased Cervical Spine', 'Enterovesical Fistula', 'Hepatobiliary Disorders Other', 'Purpura', 'Paresthesia', 'Cough', 'Wound Complication', 'Penile Infection', 'Palpitations', 'Libido Increased', 'Menorrhagia', 'IVth Nerve Disorder', 'Delirium', 'Uterine Pain', 'Obstruction Gastric', 'Floaters', 'Small Intestine Ulcer', 'Wrist Fracture', 'Gum Infection', 'Injury to Carotid Artery', 'Injury to Jugular Vein', 'Duodenal Perforation', 'Pruritus', 'Intraoperative Gastrointestinal Injury', 'Gait Disturbance', 'Bruising', 'Pancreatic Enzymes Decreased', 'Conjunctivitis', 'Injury to Inferior Vena Cava', 'Ventricular Tachycardia', 'Pain in Extremity', 'Mobitz (Type) II Atrioventricular Block', 'Salivary Duct Inflammation', 'Corneal Infection', 'Small Intestinal Mucositis', 'Rectal Necrosis', 'Suicide Attempt', 'Hyperparathyroidism', 'Psychosis', 'Sore Throat', 'Dysmenorrhea', 'Vaginal Perforation', 'Infusion Related Reaction', 'Gastrointestinal Disorders Other', 'Pulmonary Fibrosis', 'Blood Antidiuretic Hormone Abnormal', 'Lip Pain', 'Toxic Epidermal Necrolysis', 'Pneumonitis', 'Fecal Incontinence', 'Urostomy Obstruction', 'Premature Menopause', 'Agitation', 'Fatigue', 'Keratitis', 'Gastrointestinal Stoma Necrosis', 'Abdominal Soft Tissue Necrosis', 'Intraoperative Endocrine Injury', 'Leukocytosis', 'Gynecomastia', 'Ileal Fistula', 'Otitis Media', 'Poisoning and Procedural Complications Other', 'Small Intestinal Anastomotic Leak', 'Leukemia Secondary to Oncology Chemotherapy', 'Immune System Disorders Other', 'Vertigo', 'Neck Soft Tissue Necrosis', 'Acute Kidney Injury', 'Gallbladder Fistula', 'Jejunal Perforation', 'Breast Atrophy', 'Gallbladder Obstruction', 'Hypothermia', 'Intestinal Stoma Leak', 'Spermatic Cord Obstruction', 'Vaginal Infection', 'Vas Deferens Anastomotic Leak', 'Anxiety', 'Radiculitis', 'Vital Capacity Abnormal', 'Cecal Hemorrhage', 'Gastrointestinal Fistula', 'Pregnancy', 'Mediastinal Hemorrhage', 'Bladder Anastomotic Leak', 'Intraoperative Neurological Injury', 'Rectal Hemorrhage', 'Pelvic Infection', 'Confusion', 'Hearing Impaired', 'Hypoalbuminemia', 'Leukoencephalopathy', 'Carbon Monoxide Diffusing Capacity Decreased', 'Pharyngolaryngeal Pain', 'Chest Pain Cardiac', 'Osteoporosis', 'Accessory Nerve Disorder', 'Laryngitis', 'Gastric Anastomotic Leak', 'Gastritis', 'Hypotension', 'Ovarian Hemorrhage', 'Flu Like Symptoms', 'Autoimmune Disorder', 'Small Intestine Infection', 'Sinusitis', 'Tricuspid Valve Disease', 'Restlessness', 'Fallopian Tube Stenosis', 'Hypermagnesemia', 'Hypocalcemia', 'Respiratory Failure', 'Ovarian Rupture', 'Pelvic Pain', 'Weight Loss', 'Esophageal Hemorrhage', 'Peripheral Motor Neuropathy', 'Arthritis', 'Euphoria', 'Lymphocyte Count Decreased', 'Laryngospasm', 'Small Intestinal Perforation', 'Urticaria', 'Dyspepsia', 'GGT Increased', 'Ankle Fracture', 'Gallbladder Necrosis', 'Anorgasmia', 'Hyponatremia', 'Hyperhidrosis', 'Pericarditis', 'Dyspareunia', 'Laryngeal Edema', 'Ear Pain', 'Fat Atrophy', 'Heart Failure', 'Cardiac Disorders Other', 'Jejunal Obstruction', 'Abdominal Infection', 'Myelodysplastic Syndrome', 'Renal Calculi', 'Urinary Urgency', 'Joint Range of Motion Decreased', 'Gingival Pain', 'Hemolysis', 'Cervicitis Infection', 'Personality Change', 'Allergic Rhinitis', 'Hematosalpinx', 'Oral Cavity Fistula', 'Flank Pain', 'Pyramidal Tract Syndrome', 'Cataract', 'Hypoparathyroidism', 'Delayed Puberty', 'Appendicitis Perforated', 'Lymphedema', 'Pleural Hemorrhage', 'Trigeminal Nerve Disorder', 'Encephalopathy', 'Hypohidrosis', 'Vaginal Dryness', 'Hemoglobinuria', 'Apnea', 'Multi-Organ Failure', 'Presyncope', 'Intraoperative Renal Injury', 'Duodenal Obstruction', 'Ataxia', 'Thrombotic Thrombocytopenic Purpura', 'Nasal Congestion', 'Sinus Pain', 'Erythema Multiforme', 'Sudden Death NOS', 'Myalgia', 'Cystitis Noninfective', 'Toothache', 'Brachial Plexopathy', 'Urostomy Leak', 'Treatment Related Secondary Malignancy', 'Gastric Perforation', 'Flushing', 'Papilledema', 'Pancreatic Hemorrhage', 'Esophageal Ulcer', 'Hypertrichosis', 'Retinal Tear', 'Vaginal Inflammation', 'Cardiac Troponin T Increased', 'Pericardial Tamponade', 'Aphonia', 'Uterine Anastomotic Leak', 'Joint Effusion', 'Reproductive System and Breast Disorders Other', 'Lower Gastrointestinal Hemorrhage', 'Tracheostomy Site Bleeding', 'Cardiac Arrest', 'Localized Edema', 'Nervous System Disorders Other', 'Fracture', 'Neutrophil Count Decreased', 'Prostatic Obstruction', 'Device Related Infection', 'Oral Pain', 'Tracheitis', 'Libido Decreased', 'Colonic Obstruction', 'Forced Expiratory Volume Decreased', 'Acidosis', 'Bone Marrow Hypocellular', 'Breast Infection', 'Encephalitis Infection', 'Hepatic Infection', 'Urinary Retention', 'Bronchial Infection', 'Urine Output Decreased', 'Amnesia', 'Flashing Lights', 'Vaginal Hemorrhage', 'Vestibular Disorder', 'Arterial Injury', 'Hypophosphatemia', 'Dermatitis Radiation', 'Productive Cough', 'Dysphasia', 'Kyphosis', 'White Blood Cell Decreased', 'INR Increased', 'Wound Dehiscence', 'Sleep Apnea', 'Fetal Growth Retardation', 'Pharyngeal Anastomotic Leak', 'Cushingoid', 'Nail Ridging', 'Scoliosis', 'Akathisia', 'Malabsorption', 'Phlebitis', 'Concentration Impairment', 'Pancreas Infection', 'Vaginal Stricture', 'Glossopharyngeal Nerve Disorder', 'Intra-Abdominal Hemorrhage', 'Hot Flashes', 'Cognitive Disturbance', 'Stomal Ulcer', 'Dry Mouth', 'Esophageal Varices Hemorrhage', 'Renal Colic', 'Esophageal Stenosis', 'Pulmonary Edema', 'Bone Pain', 'Vasovagal Reaction', 'Duodenal Fistula', 'Dyspnea', 'Intraoperative Urinary Injury', 'Metabolism and Nutrition Disorders Other', 'Hypernatremia', 'Gastrointestinal Anastomotic Leak', 'Ileal Obstruction', 'Abducens Nerve Disorder', 'Night Blindness', 'Fallopian Tube Obstruction', 'Watering Eyes', 'Peripheral Nerve Infection', 'Photosensitivity', 'Rhinitis Infective', 'Hepatic Pain', 'Respiratory', 'Acute Coronary Syndrome', 'Constipation', 'Hypoglycemia', 'Muscle Weakness Lower Limb', 'Bronchial Stricture', 'Chylothorax', 'Vascular Access Complication', 'Syncope', 'Memory Impairment', 'Tracheal Obstruction', 'Hyperuricemia', 'Esophageal Anastomotic Leak', 'Periorbital Infection', 'Neoplasms Benign', 'Rash Pustular', 'Social Circumstances Other', 'Phlebitis Infective', 'Uveitis', 'Virilization', 'Enterocolitis Infectious', 'Postnasal Drip', 'Gastrointestinal Pain', 'Conduction Disorder', 'Mania', 'Malaise', 'Burn', 'Kidney Anastomotic Leak', 'Retinal Detachment', 'Visceral Arterial Ischemia', 'Blood Corticotrophin Decreased', 'Hemoglobin Increased', 'Colonic Perforation', 'Pancreatic Necrosis', 'Hypersomnia', 'Adult Respiratory Distress Syndrome', 'Duodenal Stenosis', 'Lymph Leakage', 'Stomach Pain', 'Aspartate Aminotransferase Increased', 'Aspiration', 'Depressed Level of Consciousness', 'Surgical and Medical Procedures Other', 'Soft Tissue Necrosis Lower Limb', 'Epistaxis', 'Vaginal Fistula', 'Intraoperative Musculoskeletal Injury', 'Pancreatitis', 'Sepsis', 'Fetal Death', 'Pancreatic Duct Stenosis', 'Female Genital Tract Fistula', 'Retinopathy', 'Jejunal Hemorrhage', 'Skin Ulceration', 'Atelectasis', 'Facial Nerve Disorder', 'Premature Delivery', 'Eye Disorders Other', 'Somnolence', 'Edema Trunk', 'Small Intestinal Obstruction', 'Injury to Superior Vena Cava', 'Voice Alteration', 'Peripheral Ischemia', 'Rash Acneiform', 'Scalp Pain', 'Periodontal Disease', 'Intraoperative Head and Neck Injury', 'Skin and Subcutaneous Tissue Disorders Other', 'Blood Bilirubin Increased', 'Hematoma', 'Esophageal Fistula', 'Vaginal Anastomotic Leak', 'CPK Increased', 'Colitis', 'Retinoic Acid Syndrome', 'Abdominal Distension', 'Buttock Pain', 'Dental Caries', 'Muscle Weakness Upper Limb', 'Head Soft Tissue Necrosis', 'Cardiac Troponin I Increased', 'Pharyngeal Necrosis', 'Skin Infection', 'Sick Sinus Syndrome', 'Adrenal Insufficiency', 'Delusions', 'Hypokalemia', 'Ileus', 'Uterine Infection', 'Growth Hormone Abnormal', 'Hypoglossal Nerve Disorder', 'Investigations Other', 'Blood Gonadotrophin Abnormal', 'Edema Cerebral', 'Pharyngeal Mucositis', 'Stevens-Johnson Syndrome', 'Ear and Labyrinth Disorders Other', 'Atrioventricular Block First Degree', 'Nail Infection', 'Prostatic Hemorrhage', 'Cheilitis', 'Colonic Ulcer', 'Menopause', 'Periorbital Edema', 'Ejaculation Disorder', 'Rectal Pain', 'Acoustic Nerve Disorder NOS', 'Familial and Genetic Disorders Other', 'Anal Hemorrhage', 'Haptoglobin Decreased', 'Intraoperative Hemorrhage', 'Intraoperative Splenic Injury', 'Iron Overload', 'Pelvic Soft Tissue Necrosis', 'Urine Discoloration', 'Obesity', 'Duodenal Infection', 'Ileal Stenosis', 'Chest Wall Pain', 'Lipase Increased', 'Laryngopharyngeal Dysesthesia', 'Ovarian Infection', 'Urinary Incontinence', 'Blood Prolactin Abnormal', 'Hoarseness', 'Capillary Leak Syndrome', 'Portal Hypertension', 'Hydrocephalus', 'Fallopian Tube Perforation', 'Intraoperative Venous Injury', 'External Ear Pain', 'Prostatic Pain', 'Spasticity', 'Hepatic Necrosis', 'Bronchopleural Fistula', 'Bronchial Obstruction', 'Esophageal Infection', 'Soft Tissue Infection', 'Anal Stenosis', 'Anaphylaxis', 'Urethral Anastomotic Leak', 'Mucositis Oral', 'Peripheral Sensory Neuropathy', 'Nail Loss', 'Spermatic Cord Anastomotic Leak', 'Hypothyroidism', 'Anal Necrosis', 'Postoperative Hemorrhage', 'Renal Hemorrhage', 'Sinus Bradycardia', 'Uterine Obstruction', 'Serum Sickness', 'Superficial Soft Tissue Fibrosis', 'Glaucoma', 'Intraoperative Reproductive Tract Injury', 'Myocardial Infarction', 'Laryngeal Mucositis', 'Blurred Vision', 'Thoracic and Mediastinal Disorders Other', 'Urinary Tract Pain', 'Bloating', 'Musculoskeletal and Connective Tissue Disorders Other', 'Paronychia', 'Left Ventricular Systolic Dysfunction', 'Aortic Injury', 'Salivary Gland Fistula', 'Tooth Discoloration', 'Exostosis', 'Dry Skin', 'Hyperkalemia', 'Tremor', 'Myositis', 'Muscle Weakness Right-Sided', 'Irregular Menstruation', 'Ileal Hemorrhage', 'Anal Ulcer', 'Testicular Pain', 'Abdominal Pain', 'Gallbladder Perforation', 'Urostomy Site Bleeding', 'Colonic Hemorrhage', 'Insomnia', 'Dysgeusia', 'Mobitz Type I', 'Body Odor', 'Avascular Necrosis', 'Colonic Fistula', 'Pain', 'Constrictive Pericarditis', 'Lymph Node Pain', 'Biliary Fistula', 'Anorectal Infection', 'Asystole', 'Lip Infection', 'Vaginal Obstruction', 'Skin Atrophy', 'Delayed Orgasm', 'Gastric Fistula', 'Central Nervous System Necrosis', 'Arthralgia', 'Oligospermia', 'Arachnoiditis', 'Duodenal Hemorrhage', 'Musculoskeletal Deformity', 'Scleral Disorder', 'Fall', 'Rash Maculo-Papular', 'Death Neonatal', 'Headache', 'Reversible Posterior Leukoencephalopathy Syndrome', 'Middle Ear Inflammation', 'Appendicitis', 'Hallucinations', 'Hyperglycemia', 'Ascites', 'Rectal Obstruction', 'Vascular Disorders Other', 'Chronic Kidney Disease', 'Anal Pain', 'Pharyngeal Hemorrhage', 'Cholecystitis', 'Endophthalmitis', 'Esophageal Pain', 'Wound Infection', 'Anal Mucositis', 'Biliary Anastomotic Leak', 'Bladder Infection', 'Nail Discoloration', 'Extrapyramidal Disorder', 'Atrioventricular Block Complete', 'Intraoperative Respiratory Injury', 'Portal Vein Thrombosis', 'Retinal Vascular Disorder', 'Suicidal Ideation', 'Sinus Tachycardia', 'Intracranial Hemorrhage', 'Restrictive Cardiomyopathy', 'Upper Respiratory Infection', 'Anemia', 'Myelitis', 'Pelvic Floor Muscle Weakness', 'Ventricular Fibrillation', 'Lymphocele', 'Wolff-Parkinson-White Syndrome', 'Cecal Infection', 'Hepatic Failure', 'Jejunal Fistula', 'Laryngeal Hemorrhage', 'Sinus Disorder', 'Jejunal Ulcer', 'Postoperative Thoracic Procedure Complication', 'Conjunctivitis Infective', 'Fever', 'Meningitis', 'Tooth Infection', 'Weight Gain', 'Urinary Fistula', 'Cranial Nerve Infection', 'Jejunal Stenosis', 'Superior Vena Cava Syndrome', 'Retroperitoneal Hemorrhage', 'Hypomagnesemia', 'Ureteric Anastomotic Leak', 'Muscle Weakness Trunk', 'Vaginal Pain', 'Stroke', 'Fallopian Tube Anastomotic Leak', 'Photophobia', 'Bronchospasm', 'Alopecia', 'Tinnitus', 'Gastroesophageal Reflux Disease', 'Hypertension', 'Seroma', 'Small Intestinal Stenosis', 'Gastric Necrosis', 'Spinal Fracture', 'Hepatic Hemorrhage', 'Corneal Ulcer', 'Alanine Aminotransferase Increased', 'Blood and Lymphatic System Disorders Other', 'Pain of Skin', 'Edema Face', 'Vagus Nerve Disorder', 'Catheter Related Infection', 'Tracheal Fistula', 'Urinary Tract Obstruction', 'Dysesthesia', 'Bullous Dermatitis', 'Eyelid Function Disorder', '']",,FollowUp -Recist Targeted Regions Number,Recist Targeted Regions Number,RecistTargetedRegionsNumber,"Numeric value that represents the number of baseline target lesions, as described by the Response Evaluation Criteria in Solid Tumours (RECIST) criteria",False,,,,FollowUp -Comorbidity,Comorbidity,Comorbidity,"The text term used to describe a comorbidity disease, which coexists with the patient's malignant disease.",False,,"['Depression', 'Adrenocortical Insufficiency', 'Familial Adenomatous Polyposis', 'Human Papillomavirus Infection', 'Adenomatous Polyposis Coli', 'Ischemic Heart Disease', 'Other Cancer Within 5 Years', 'Denys-Drash Syndrome', 'Glycogen Storage Disease', 'Epstein-Barr Virus', 'Sleep apnea', 'Diet Controlled Diabetes', ""Hashimoto's Thyroiditis"", 'Coronary Artery Disease', 'Iron Overload', 'Wagr Syndrome', 'Obesity', 'Insulin Controlled Diabetes', 'Congestive Heart Failure (CHF)', 'Osteoporosis or Osteopenia', 'Not Reported', 'Renal Dialysis', 'Rheumatologic Disease', 'Blood Clots', 'Chronic Hepatitis', 'Rubinstein-Taybi Syndrome', 'Diverticulitis', 'Transient Ischemic Attack', 'HIV / AIDS', 'Other', 'Psoriasis', 'H. pylori Infection', ""Crohn's Disease"", 'Tyrosinemia', 'Peutz-Jeghers Disease', 'Asthma', 'Hemihypertrophy', 'Hypothyroidism', 'Gout', 'COPD', 'Atrial Fibrillation', 'Myasthenia Gravis', 'Unknown', 'Glaucoma', 'Cholelithiasis', 'Myocardial Infarction', 'Deep Vein Thrombosis / Thromboembolism', 'Tuberculosis', 'Gorlin Syndrome', 'Arrhythmia', 'Sarcoidosis', 'MAI', 'Steatosis', 'Renal Failure (Requiring Dialysis)', 'Hyperlipidemia', 'Common Variable Immunodeficiency', 'Pulmonary Fibrosis', 'Liver Cirrhosis (Liver Disease)', 'Cryptogenic Organizing Pneumonia', 'Avascular Necrosis', 'unknown Etiology', 'Cerebrovascular Disease', 'Heart Disease', 'Kidney Disease', 'Fanconi Anemia', 'Peptic Ulcer (Ulcer)', 'Chronic Renal Failure', 'Basal Cell Carcinoma', ""Behcet's Disease"", 'Seizure', 'Hypospadias', 'Rheumatoid Arthritis', 'Diabetes', 'Renal Insufficiency', 'Osteoarthritis', 'Beckwith-Wiedemann', 'Colon Polyps', 'Hepatitis', 'High Grade Liver Dysplastic Nodule', 'Adenocarcinoma', 'Biliary Disorder', 'DVT/PE', 'Eczema', 'Hepatitis B Infection', 'Liver Toxicity (Non-Infectious)', 'Connective Tissue Disorder', 'Headache', 'Interstitial Pneumontis or ARDS', 'Li-Fraumeni Syndrome', 'Anxiety', 'Nonalcoholic Steatohepatitis', 'Joint Replacement', 'Low Grade Liver Dysplastic Nodule', 'Hyperglycemia', 'Other Nonmalignant Systemic Disease', 'Lupus', 'Intraductal Papillary Mucinous Neoplasm', 'Pregnancy in Patient or Partner', 'Cirrhosis', 'Bronchitis', 'Calcium Channel Blockers', 'Fibrosis', 'Peripheral Vascular Disease', 'Diabetic Neuropathy', 'Acute Renal Failure', 'Other Pulmonary Complications', 'Alpha-1 Antitrypsin', 'ITP', 'Gonadal Dysfunction', 'Cancer', 'Herpes', 'Bone Fracture(s)', 'Epilepsy', 'Anemia', 'Hereditary Non-polyposis Colon Cancer', 'Pancreatitis', 'Hepatitis C Infection', 'Arthritis', 'Organ transplant (site)', 'Hemorrhagic Cystitis', 'Pain (Various)', 'Cataracts', 'Lynch Syndrome', 'Type II', 'Pulmonary Hemorrhage', 'Peripheral Neuropathy', 'Stroke', 'Neuroendocrine Tumor', 'Smoking', 'Hypercholesterolemia', 'GERD', 'Ulcerative Colitis', ""Barrett's Esophagus"", 'Dyslipidemia', 'Turcot Syndrome', 'Allergies', 'Celiac Disease', 'Hepatitis A Infection', 'Gastroesophageal Reflux Disease', 'Hypertension', 'Hypercalcemia', 'HUS/TTP', 'Primary Sclerosing Cholangitis', 'Inflammatory Bowel Disease', '']",,FollowUp -AIDS Risk Factors,AIDS Risk Factors,AIDSRiskFactors,The text term used to describe a risk factor of the acquired immunodeficiency syndrome (AIDS) that the patient either had at time time of the study or experienced in the past.,False,,"['Mycobacterium tuberculosis', 'Cytomegalovirus', 'Mycobacterium avium Complex', 'Pneumonia', 'Mycobacterium', 'Herpes Simplex Virus', 'Candidiasis', 'Histoplasmosis', 'Wasting Syndrome', 'Cryptococcosis', 'Isosporiasis', 'Salmonella Septicemia', 'NOS', 'Coccidioidomycosis', 'Pneumocystis Pneumonia', 'Toxoplasmosis', 'Encephalopathy', 'Nocardiosis', 'Progressive Multifocal Leukoencephalopathy', '']",,FollowUp -Weight,Weight,Weight,The weight of the patient measured in kilograms.,False,,,,FollowUp -Pancreatitis Onset Year,Pancreatitis Onset Year,PancreatitisOnsetYear,TBD,False,,,,FollowUp -Reflux Treatment Type,Reflux Treatment Type,RefluxTreatmentType,Text term used to describe the types of treatment used to manage gastroesophageal reflux disease (GERD).,False,,"['Not Reported', 'Proton Pump Inhibitors', 'Not Applicable', 'Medically Treated', 'Surgically Treated', 'Antacids', 'Unknown', 'No Treatment', 'H2 Blockers', '']",,FollowUp -Adverse Event Grade,Adverse Event Grade,AdverseEventGrade,"The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.",False,,"['Grade 3', 'Grade 5', 'Grade 2', 'Grade 1', 'Grade 4', '']",,FollowUp -DLCO Ref Predictive Percent,DLCO Ref Predictive Percent,DLCORefPredictivePercent,"The value, as a percentage of predicted lung volume, measuring the amount of carbon monoxide detected in a patient's lungs.",False,,,,FollowUp -Days to Imaging,Days to Imaging,DaystoImaging,Number of days between the date used for index and the date the imaging or scan was performed on the patient.,False,,,,FollowUp -Menopause Status,Menopause Status,MenopauseStatus,Text term used to describe the patient's menopause status.,False,,"['Not Reported', 'Perimenopausal', 'Postmenopausal', 'Unknown', 'Premenopausal', '']",,FollowUp -Scan Tracer Used,Scan Tracer Used,ScanTracerUsed,The text term used to describe the type of tracer used during the imaging or scan of the patient.,False,,"['Sodium Fluoride', 'Axumin', 'PSMA', 'Acetate', 'Choline', '']",,FollowUp -Disease Response,Disease Response,DiseaseResponse,Code assigned to describe the patient's response or outcome to the disease.,False,,"['DU-Disease Unchanged', 'PDM-Persistent Distant Metastasis', 'MX-Mixed Response', 'PSR-Pseudoresponse', 'CRU-Complete Response Unconfirmed', 'PPD-Pseudoprogression', 'CPD-Clinical Progression', 'IMR-Immunoresponse', 'BED-Biochemical Evidence of Disease', 'SD-Stable Disease', 'SPD-Surgical Progression', 'PB-Palliative Benefit', 'WT-With Tumor', 'PA-Palliative Therapy', 'VGPR-Very Good Partial Response', 'Unknown', 'CR-Complete Response', 'NR-No Response', 'RPD-Radiographic Progressive Disease', 'sCR-Stringent Complete Response', 'MR-Minimal/Marginal response', 'NPB-No Palliative Benefit', 'Not Reported', 'RP-Response', 'TE-Too Early', 'PLD-Persistent Locoregional Disease', 'TF-Tumor Free', 'PR-Partial Response', 'AJ-Adjuvant Therapy', 'Non-CR/Non-PD-Non-CR/Non-PD', 'PD-Progressive Disease', 'RD-Responsive Disease', 'IPD-Immunoprogression', '']",,FollowUp -Viral Hepatitis Serologies,Viral Hepatitis Serologies,ViralHepatitisSerologies,Text term that describes the kind of serological laboratory test used to determine the patient's hepatitus status.,False,,"['Hepatitis C Antibody', 'Not Reported', 'HBV Surface Antibody', 'HBV Core Antibody', 'Hepatitis C Virus RNA', 'HCV Genotype', 'Unknown', 'HBV Genotype', 'HBV DNA', 'Hepatitis B Surface Antigen', '']",,FollowUp -Body Surface Area,Body Surface Area,BodySurfaceArea,Numeric value used to represent the 2-dimensional extent of the body surface relating height to weight.,False,,,,FollowUp -HIV Viral Load,HIV Viral Load,HIVViralLoad,"Numeric value that represents the concentration of an analyte or aliquot extracted from the sample or sample portion, measured in milligrams per milliliter.",False,,,,FollowUp -Risk Factor,Risk Factor,RiskFactor,The text term used to describe a risk factor the patient had at the time of or prior to their diagnosis.,False,,"['Diet', 'HIV', 'Familial Adenomatous Polyposis', 'Common variable immune deficiency (CVID)', 'Human Papillomavirus Infection', 'Gastric Polyp(s)', 'Denys-Drash Syndrome', 'Epstein-Barr Virus', 'Allergy Mold or Dust', ""Hashimoto's Thyroiditis"", 'Iron Overload', 'Thyroid Nodular Hyperplasia', 'Wagr Syndrome', 'Obesity', 'Not Reported', 'Helicobacter Pylori-Associated Gastritis', ""Gilbert's Syndrome"", 'Rubinstein-Taybi Syndrome', 'Chronic Hepatitis', 'Diverticulitis', 'Endometriosis', 'Parasitic Disease of Biliary Tract', 'Endosalpingiosis', 'Lymphocytic Thyroiditis', 'Autoimmune Atrophic Chronic Gastritis', 'Allergy Dog', 'Hemihypertrophy', 'Nonalcoholic Fatty Liver Disease', 'Tobacco Smokeless', 'Tattoo', 'Allergy Meat', 'Allergy Bee', 'Diabetes Type II', 'Myasthenia Gravis', 'Serous tubal intraepithelial carcinoma (STIC)', 'Unknown', 'Allergy Eggs', 'Intestinal Metaplasia', 'Cholelithiasis', 'Tobacco Smoking', 'Gorlin Syndrome', 'Sarcoidosis', 'Alcohol Consumption', 'Oral Contraceptives', 'Steatosis', 'Tobacco NOS', 'Allergy Cat', 'Low Grade Dysplasia', 'High Grade Dysplasia', 'Allergy Animal NOS', 'Allergy Nuts', 'Fanconi Anemia', 'Alcoholic Liver Disease', 'Diabetes NOS', ""Behcet's Disease"", 'Seizure', 'Hypospadias', 'Rheumatoid Arthritis', 'Beckwith-Wiedemann', 'Colon Polyps', 'Eczema', 'Hepatitis B Infection', 'Hepatic Encephalopathy', 'Allergy Wasp', 'Headache', 'Li-Fraumeni Syndrome', 'Vision Changes', 'Nonalcoholic Steatohepatitis', 'Hemochromatosis', 'Allergy Dairy or Lactose', 'Sensory Changes', 'Hay Fever', 'Reflux Disease', 'Cirrhosis', 'Allergy Fruit', 'Fibrosis', 'Hematologic Disorder NOS', 'Allergy Ant', 'Allergy Processed Foods', 'Cancer', 'Diabetes Type I', 'Pancreatitis', 'Hepatitis C Infection', 'Allergy Seafood', 'Lynch Syndrome', 'Allergy Food NOS', ""Barrett's Esophagus"", 'Turcot Syndrome', 'Undescended Testis', 'Hepatitis NOS', 'Alpha-1 Antitrypsin Deficiency', 'Primary Sclerosing Cholangitis', 'Recurrent Pyogenic Cholangitis', '']",,FollowUp -FEV1 Ref Post Bronch Percent,FEV1 Ref Post Bronch Percent,FEV1RefPostBronchPercent,The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second post-bronchodilator.,False,,,,FollowUp -ECOG Performance Status,ECOG Performance Status,ECOGPerformanceStatus,The ECOG functional performance status of the patient/participant.,False,,"['3.0', '4', '4.0', '1', '1.0', '5', '5.0', '0.0', '2.0', '2', '3', '0', '']",,FollowUp -HAART Treatment Indicator,HAART Treatment Indicator,HAARTTreatmentIndicator,The text term used to indicate whether the patient received Highly Active Antiretroviral Therapy (HAART).,False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,FollowUp -Days to Adverse Event,Days to Adverse Event,DaystoAdverseEvent,Number of days between the date used for index and the date of the patient's adverse event.,False,,,,FollowUp -FEV1 Ref Pre Bronch Percent,FEV1 Ref Pre Bronch Percent,FEV1RefPreBronchPercent,The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second pre-bronchodilator.,False,,,,FollowUp -Cause of Response,Cause of Response,CauseofResponse,The text term used to describe the suspected cause or reason for the patient disease response.,False,,,,FollowUp -FEV 1 FVC Pre Bronch Percent,FEV 1 FVC Pre Bronch Percent,FEV1FVCPreBronchPercent,Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) pre-bronchodilator.,False,,,,FollowUp -Risk Factor Treatment,Risk Factor Treatment,RiskFactorTreatment,The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.,False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,FollowUp -Progression or Recurrence,Progression or Recurrence,ProgressionorRecurrence,Yes/No/unknown indicator to identify whether a patient has had a new tumor event after initial treatment.,True,,"['No', 'Yes - Progression or Recurrence', 'Unknown', 'Not Reported']",,FollowUp -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,FollowUp -CD4 Count,CD4 Count,CD4Count,The text term used to describe the outcome of the procedure to determine the amount of the CD4 expressing cells in a sample.,False,,,,FollowUp -Diabetes Treatment Type,Diabetes Treatment Type,DiabetesTreatmentType,Text term used to describe the types of treatment used to manage diabetes.,False,,"['Alpha-Glucosidase Inhibitor', 'Diet', 'Sulfonylurea', 'Oral Hypoglycemic', 'Not Reported', 'Injected Insulin', 'Thiazolidinedione', 'Other', 'Unknown', 'Biguanide', 'Insulin', '']",,FollowUp -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,FollowUp -FEV1 FVC Post Bronch Percent,FEV1 FVC Post Bronch Percent,FEV1FVCPostBronchPercent,Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) post-bronchodilator.,False,,,,FollowUp -Nadir CD4 Count,Nadir CD4 Count,NadirCD4Count,Numeric value that represents the lowest point to which the CD4 count has dropped (nadir).,False,,,,FollowUp -Recist Targeted Regions Sum,Recist Targeted Regions Sum,RecistTargetedRegionsSum,"Numeric value that represents the sum of baseline target lesions, as described by the Response Evaluation Criteria in Solid Tumours (RECIST) criteria.",False,,,,FollowUp -Evidence of Recurrence Type,Evidence of Recurrence Type,EvidenceofRecurrenceType,The text term used to describe the type of evidence used to determine whether the patient's disease recurred,False,,"['Biopsy with Histologic Confirmation', 'Positive Biomarkers', 'Convincing Image Source', '']",,FollowUp -Comorbidity Method of Diagnosis,Comorbidity Method of Diagnosis,ComorbidityMethodofDiagnosis,The text term used to describe the method used to diagnose the patient's comorbidity disease.,False,,"['Radiology', 'Not Reported', 'Pathology', 'Histology', 'Unknown', '']",,FollowUp -Imaging Type,Imaging Type,ImagingType,The text term used to describe the type of imaging or scan performed on the patient.,False,,"['99mTc Bone Scintigraphy', 'MRI', 'CT Scan', 'PET', '']",,FollowUp -Hysterectomy Margins Involved,Hysterectomy Margins Involved,HysterectomyMarginsInvolved,The text term used to indicate whether the patient's disease was determined to be involved based on the surgical margins of the hysterectomy.,False,,"['None', 'Not Reported', 'Macroscopic Parametrium', 'Microscopic Parametrium', 'Unknown', 'Bladder', 'Vagina', '']",,FollowUp -HPV Positive Type,HPV Positive Type,HPVPositiveType,Text classification to represent the strain or type of human papillomavirus identified in an individual.,False,,"['58', '26', '51', '82', '59', '73', '33', '18', '53', '63', '66', '31', '39', '16', '45', '52', '70', '56', '35', '68', '']",,FollowUp -Hepatitis Sustained Virological Response,Hepatitis Sustained Virological Response,HepatitisSustainedVirologicalResponse,The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.,False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,FollowUp -BMI,BMI,BMI,A calculated numerical quantity that represents an individual's weight to height ratio.,False,,,,FollowUp -Days to Comorbidity,Days to Comorbidity,DaystoComorbidity,Number of days between the date used for index and the date the patient was diagnosed with a comorbidity.,False,,,,FollowUp -Height,Height,Height,The height of the patient in centimeters.,False,,,,FollowUp -Hormonal Contraceptive Use,Hormonal Contraceptive Use,HormonalContraceptiveUse,The text term used to indicate whether the patient used hormonal contraceptives.,False,,"['Current User', 'Not Reported', 'Former User', 'Unknown', 'Never Used', '']",,FollowUp -Days to Recurrence,Days to Recurrence,DaystoRecurrence,Number of days between the date used for index and the date the patient's disease recurred.,False,True,," If Progression or Recurrence is ""Yes - Progression or Recurrence"" then ""Days to Recurrence"" is required",FollowUp -Days to Progression,Days to Progression,DaystoProgression,Number of days between the date used for index and the date the patient's disease progressed.,False,True,," If Progression or Recurrence is ""Yes - Progression or Recurrence"" then ""Days to Progression"" is required",FollowUp -Progression or Recurrence Type,Progression or Recurrence Type,ProgressionorRecurrenceType,The text term used to describe the type of progressive or recurrent disease or relapsed disease.,False,True,"['Distant', 'Not Reported', 'Unknown', 'Biochemical', 'Regional', 'Local', '']"," If Progression or Recurrence is ""Yes - Progression or Recurrence"" then ""Progression or Recurrence Type"" is required",FollowUp -Progression or Recurrence Anatomic Site,Progression or Recurrence Anatomic Site,ProgressionorRecurrenceAnatomicSite,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,False,True,"['Paraurethral gland', 'Colon NOS', 'Frontal sinus', 'Overlapping lesion of tongue', 'Overlapping lesion of palate', 'Scrotum NOS', 'Bone marrow', 'Axillary tail of breast', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'unknown primary site', 'Broad ligament', 'Lateral floor of mouth', 'Overlapping lesion of vulva', 'Trigone of bladder', 'Lacrimal gland', 'Thorax NOS', 'Ampulla of Vater', 'Myometrium', 'Penis NOS', 'Female genital tract NOS', 'Submandibular gland', 'Anterior 2/3 of tongue NOS', 'Posterior wall of bladder', 'Thymus', 'Endocrine gland NOS', 'Stomach NOS', 'Unknown', 'Cerebrum', 'Splenic flexure of colon', 'Urachus', 'Skin of lip NOS', 'Mucosa of lip NOS', 'Accessory sinus NOS', 'Cortex of adrenal gland', 'Other ill-defined sites', 'Middle lobe lung', 'Pelvis NOS', 'Anus NOS', 'Upper-inner quadrant of breast', 'Posterior mediastinum', 'Esophagus NOS', 'Duodenum', 'Cervical esophagus', 'Optic nerve', 'Long bones of lower limb and associated joints', 'Middle ear', 'Breast NOS', 'Dorsal surface of tongue NOS', 'Lesser curvature of stomach NOS', 'Overlapping lesion of floor of mouth', 'Overlapping lesion of heart mediastinum and pleura', 'Eye NOS', 'Overlapping lesion of esophagus', 'Ciliary body', 'Ureteric orifice', 'Postcricoid region', 'External ear', 'Base of tongue NOS', 'Liver', 'Commissure of lip', 'Cloacogenic zone', 'Lower lobe lung', 'Transverse colon', 'Acoustic nerve', 'Supraglottis', 'Fallopian tube', 'Upper third of esophagus', 'Skin of scalp and neck', 'Choroid', 'Long bones of upper limb scapula and associated joints', 'Overlapping lesion of brain', 'Upper gum', 'Skin NOS', 'Hard palate', 'Ileum', 'Overlapping lesion of colon', 'Ascending colon', 'Lower gum', 'Pelvic bones sacrum coccyx and associated joints', 'Hepatic flexure of colon', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Vestibule of mouth', 'Cervix uteri', 'Bones of skull and face and associated joints', 'Overlapping lesion of lip oral cavity and pharynx', 'Endometrium', 'Sphenoid sinus', 'Overlapping lesion of ill-defined sites', 'Sigmoid colon', 'Peritoneum NOS', 'Specified parts of peritoneum', 'Meckel diverticulum', 'Rectosigmoid junction', 'Kidney NOS', 'Reticuloendothelial system NOS', 'Rectum NOS', 'Pylorus', 'Overlapping lesion of tonsil', 'Pleura NOS', 'Jejunum', 'Vallecula', 'Skin of lower limb and hip', 'Pelvic lymph nodes', 'External lower lip', 'Overlapping lesion of skin', 'Mucosa of upper lip', 'Ovary', 'Cauda equina', 'Lower limb NOS', 'Body of stomach', 'Overlapping lesion of larynx', 'Pancreas NOS', 'Overlapping lesion of lung', 'Overlapping lesion of major salivary glands', 'Uvula', 'Overlapping lesion of hypopharynx', 'Round ligament', 'Corpus uteri', 'Biliary tract NOS', 'Male genital organs NOS', 'Parametrium', 'External lip NOS', 'Overlapping lesion of accessory sinuses', 'Cardia NOS', 'Islets of Langerhans', 'Carotid body', 'Ventral surface of tongue NOS', 'Autonomic nervous system NOS', 'Overlapping lesion of corpus uteri', 'Spinal meninges', 'Posterior wall of nasopharynx', 'Placenta', 'Intrahepatic bile duct', 'Overlapping lesion of digestive system', 'Mediastinum NOS', 'Hematopoietic system NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Major salivary gland NOS', 'Cerebellum NOS', 'Overlapping lesion of stomach', 'Vulva NOS', 'Craniopharyngeal duct', 'Lung NOS', 'Greater curvature of stomach NOS', 'Upper-outer quadrant of breast', 'Gallbladder', 'Thoracic esophagus', 'Lymph nodes of axilla or arm', 'Ventricle NOS', 'Overlapping lesion of biliary tract', 'Hypopharynx NOS', 'Clitoris', 'Exocervix', 'Parietal lobe', 'Waldeyer ring', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Head face or neck NOS', 'Anterior wall of nasopharynx', 'Urethra', 'Overlapping lesion of nasopharynx', 'Maxillary sinus', 'Lymph nodes of inguinal region or leg', 'Ureter', 'Tonsillar pillar', 'Sublingual gland', 'Pituitary gland', 'Gastrointestinal tract NOS', 'Pineal gland', 'Meninges NOS', 'Lingual tonsil', 'Trachea', 'Pyriform sinus', 'Mucosa of lower lip', 'Not Reported', 'Posterior wall of hypopharynx', 'Urinary system NOS', 'Orbit NOS', 'Short bones of lower limb and associated joints', 'Connective subcutaneous and other soft tissues of thorax', 'Upper limb NOS', 'Gastric antrum', 'Lymph node NOS', 'Peripheral nerves and autonomic nervous system of thorax', 'Ill-defined sites within respiratory system', 'Other specified parts of male genital organs', 'Rib sternum clavicle and associated joints', 'Overlapping lesion of bladder', 'Appendix', 'Prostate gland', 'Lymph nodes of multiple regions', 'Lateral wall of nasopharynx', 'Branchial cleft', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Floor of mouth NOS', 'Connective subcutaneous and other soft tissues NOS', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Bladder neck', 'Border of tongue', 'Connective subcutaneous and other soft tissues of abdomen', 'Overlapping lesion of small intestine', 'Lateral wall of bladder', 'Soft palate NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Isthmus uteri', 'Nasal cavity', 'Endocervix', 'Tonsil NOS', 'Glottis', 'Retroperitoneum', 'Peripheral nerves and autonomic nervous system of pelvis', 'Frontal lobe', 'Vagina NOS', 'Undescended testis', 'Laryngeal cartilage', 'Eyelid', 'Hypopharyngeal aspect of aryepiglottic fold', 'Overlapping lesion of other and unspecified parts of mouth', 'Upper lobe lung', 'Lip NOS', 'Lymph nodes of head face and neck', 'Overlapping lesion of brain and central nervous system', 'Overlapping lesion of penis', 'Overlapping lesion of retroperitoneum and peritoneum', 'Parotid gland', 'Dome of bladder', 'Bone of limb NOS', 'Descended testis', 'Vertebral column', 'Fundus uteri', 'Connective subcutaneous and other soft tissues of pelvis', 'Epididymis', 'Intra-abdominal lymph nodes', 'Prepuce', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Pharynx NOS', 'Overlapping lesion of endocrine glands and related structures', 'Gum NOS', 'Spinal cord', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Skin of upper limb and shoulder', 'Nasopharynx NOS', 'Parathyroid gland', 'Bone NOS', 'Mouth NOS', 'Abdomen NOS', 'Conjunctiva', 'Spermatic cord', 'External upper lip', 'Labium minus', 'Renal pelvis', 'Overlapping lesion of lip', 'Short bones of upper limb and associated joints', 'Main bronchus', 'Upper respiratory tract NOS', 'Body of penis', 'Small intestine NOS', 'Central portion of breast', 'Lower-inner quadrant of breast', 'Labium majus', 'Tonsillar fossa', 'Cecum', 'Glans penis', 'Tail of pancreas', 'Lower third of esophagus', 'Body of pancreas', 'Intestinal tract NOS', 'Brain stem', 'Overlapping lesion of rectum anus and anal canal', 'Posterior wall of oropharynx', 'Pancreatic duct', 'Blood', 'Temporal lobe', 'Anterior floor of mouth', 'Nervous system NOS', 'Cornea NOS', 'Palate NOS', 'Occipital lobe', 'Abdominal esophagus', 'Overlapping lesion of pancreas', 'Overlapping lesion of female genital organs', 'Cheek mucosa', 'Retina', 'Overlapping lesion of male genital organs', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Larynx NOS', 'Skin of other and unspecified parts of face', 'Spleen', 'Oropharynx NOS', 'Anal canal', 'Subglottis', 'Cerebral meninges', 'Lateral wall of oropharynx', 'Middle third of esophagus', 'Nipple', 'Medulla of adrenal gland', 'Overlapping lesion of eye and adnexa', 'Olfactory nerve', 'Ethmoid sinus', 'Overlapping lesion of cervix uteri', 'Descending colon', 'Brain NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Anterior wall of bladder', 'Mandible', 'Other specified parts of pancreas', 'Skin of trunk', 'Other specified parts of female genital organs', 'Uterus NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Intrathoracic lymph nodes', 'Heart', 'Adrenal gland NOS', 'Aortic body and other paraganglia', 'Extrahepatic bile duct', 'Overlapping lesion of breast', 'Superior wall of nasopharynx', 'Fundus of stomach', 'Anterior mediastinum', 'Tongue NOS', 'Cranial nerve NOS', 'Head of pancreas', 'Overlapping lesions of oropharynx', 'Overlapping lesion of bones joints and articular cartilage', 'Retromolar area', 'Testis NOS', 'Connective subcutaneous and other soft tissues of head face and neck', 'Bladder NOS', 'Overlapping lesion of urinary organs', 'Lower-outer quadrant of breast', 'Thyroid gland', 'Anterior surface of epiglottis', 'Uterine adnexa', '']"," If Progression or Recurrence is ""Yes - Progression or Recurrence"" then ""Progression or Recurrence Anatomic Site"" is required",FollowUp -Days to Progression Free,Days to Progression Free,DaystoProgressionFree,Number of days between the date used for index and the date the patient's disease was formally confirmed as progression-free.,False,True,," If Progression or Recurrence is ""Yes - Progression or Recurrence"" then ""Days to Progression Free"" is required",FollowUp -Anaplasia Present,Anaplasia Present,AnaplasiaPresent,Yes/no/unknown/Not Reported indicator used to describe whether anaplasia was present at the time of diagnosis.,False,,"['No', 'Yes - Anaplasia Present', 'Unknown', 'Not Reported', '']",,Diagnosis -Cog Neuroblastoma Risk Group,Cog Neuroblastoma Risk Group,CogNeuroblastomaRiskGroup,Text term that represents the categorization of patients on the basis of prognostic factors per a system developed by Children's Oncology Group (COG). Risk level is used to assign treatment intensity.,False,,"['Not Reported', 'High Risk', 'Intermediate Risk', 'Unknown', 'Low Risk', '']",,Diagnosis -Days to Last Known Disease Status,Days to Last Known Disease Status,DaystoLastKnownDiseaseStatus,"Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days.",True,,,,Diagnosis -Tissue or Organ of Origin,Tissue or Organ of Origin,TissueorOrganofOrigin,"The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",True,,"['Paraurethral gland', 'Colon NOS', 'Frontal sinus', 'Overlapping lesion of tongue', 'Overlapping lesion of palate', 'Scrotum NOS', 'Bone marrow', 'Axillary tail of breast', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'unknown primary site', 'Broad ligament', 'Lateral floor of mouth', 'Overlapping lesion of vulva', 'Trigone of bladder', 'Lacrimal gland', 'Thorax NOS', 'Ampulla of Vater', 'Myometrium', 'Penis NOS', 'Female genital tract NOS', 'Submandibular gland', 'Anterior 2/3 of tongue NOS', 'Posterior wall of bladder', 'Thymus', 'Endocrine gland NOS', 'Stomach NOS', 'Unknown', 'Cerebrum', 'Splenic flexure of colon', 'Urachus', 'Skin of lip NOS', 'Mucosa of lip NOS', 'Accessory sinus NOS', 'Cortex of adrenal gland', 'Other ill-defined sites', 'Middle lobe lung', 'Pelvis NOS', 'Anus NOS', 'Upper-inner quadrant of breast', 'Posterior mediastinum', 'Esophagus NOS', 'Duodenum', 'Cervical esophagus', 'Optic nerve', 'Long bones of lower limb and associated joints', 'Middle ear', 'Breast NOS', 'Dorsal surface of tongue NOS', 'Lesser curvature of stomach NOS', 'Overlapping lesion of floor of mouth', 'Overlapping lesion of heart mediastinum and pleura', 'Eye NOS', 'Overlapping lesion of esophagus', 'Ciliary body', 'Ureteric orifice', 'Postcricoid region', 'External ear', 'Base of tongue NOS', 'Liver', 'Commissure of lip', 'Cloacogenic zone', 'Lower lobe lung', 'Transverse colon', 'Acoustic nerve', 'Supraglottis', 'Fallopian tube', 'Upper third of esophagus', 'Skin of scalp and neck', 'Choroid', 'Long bones of upper limb scapula and associated joints', 'Overlapping lesion of brain', 'Upper gum', 'Skin NOS', 'Hard palate', 'Ileum', 'Overlapping lesion of colon', 'Ascending colon', 'Lower gum', 'Pelvic bones sacrum coccyx and associated joints', 'Hepatic flexure of colon', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Vestibule of mouth', 'Cervix uteri', 'Bones of skull and face and associated joints', 'Overlapping lesion of lip oral cavity and pharynx', 'Endometrium', 'Sphenoid sinus', 'Overlapping lesion of ill-defined sites', 'Sigmoid colon', 'Peritoneum NOS', 'Specified parts of peritoneum', 'Meckel diverticulum', 'Rectosigmoid junction', 'Kidney NOS', 'Reticuloendothelial system NOS', 'Rectum NOS', 'Pylorus', 'Overlapping lesion of tonsil', 'Pleura NOS', 'Jejunum', 'Vallecula', 'Skin of lower limb and hip', 'Pelvic lymph nodes', 'External lower lip', 'Overlapping lesion of skin', 'Mucosa of upper lip', 'Ovary', 'Cauda equina', 'Lower limb NOS', 'Body of stomach', 'Overlapping lesion of larynx', 'Pancreas NOS', 'Overlapping lesion of lung', 'Overlapping lesion of major salivary glands', 'Uvula', 'Overlapping lesion of hypopharynx', 'Round ligament', 'Corpus uteri', 'Biliary tract NOS', 'Male genital organs NOS', 'Parametrium', 'External lip NOS', 'Overlapping lesion of accessory sinuses', 'Cardia NOS', 'Islets of Langerhans', 'Carotid body', 'Ventral surface of tongue NOS', 'Autonomic nervous system NOS', 'Overlapping lesion of corpus uteri', 'Spinal meninges', 'Posterior wall of nasopharynx', 'Placenta', 'Intrahepatic bile duct', 'Overlapping lesion of digestive system', 'Mediastinum NOS', 'Hematopoietic system NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Major salivary gland NOS', 'Cerebellum NOS', 'Overlapping lesion of stomach', 'Vulva NOS', 'Craniopharyngeal duct', 'Lung NOS', 'Greater curvature of stomach NOS', 'Upper-outer quadrant of breast', 'Gallbladder', 'Thoracic esophagus', 'Lymph nodes of axilla or arm', 'Ventricle NOS', 'Overlapping lesion of biliary tract', 'Hypopharynx NOS', 'Clitoris', 'Exocervix', 'Parietal lobe', 'Waldeyer ring', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Head face or neck NOS', 'Anterior wall of nasopharynx', 'Urethra', 'Overlapping lesion of nasopharynx', 'Maxillary sinus', 'Lymph nodes of inguinal region or leg', 'Ureter', 'Tonsillar pillar', 'Sublingual gland', 'Pituitary gland', 'Gastrointestinal tract NOS', 'Pineal gland', 'Meninges NOS', 'Lingual tonsil', 'Trachea', 'Pyriform sinus', 'Mucosa of lower lip', 'Not Reported', 'Posterior wall of hypopharynx', 'Urinary system NOS', 'Orbit NOS', 'Short bones of lower limb and associated joints', 'Connective subcutaneous and other soft tissues of thorax', 'Upper limb NOS', 'Gastric antrum', 'Lymph node NOS', 'Peripheral nerves and autonomic nervous system of thorax', 'Ill-defined sites within respiratory system', 'Other specified parts of male genital organs', 'Rib sternum clavicle and associated joints', 'Overlapping lesion of bladder', 'Appendix', 'Prostate gland', 'Lymph nodes of multiple regions', 'Lateral wall of nasopharynx', 'Branchial cleft', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Floor of mouth NOS', 'Connective subcutaneous and other soft tissues NOS', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Bladder neck', 'Border of tongue', 'Connective subcutaneous and other soft tissues of abdomen', 'Overlapping lesion of small intestine', 'Lateral wall of bladder', 'Soft palate NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Isthmus uteri', 'Nasal cavity', 'Endocervix', 'Tonsil NOS', 'Glottis', 'Retroperitoneum', 'Peripheral nerves and autonomic nervous system of pelvis', 'Frontal lobe', 'Vagina NOS', 'Undescended testis', 'Laryngeal cartilage', 'Eyelid', 'Hypopharyngeal aspect of aryepiglottic fold', 'Overlapping lesion of other and unspecified parts of mouth', 'Upper lobe lung', 'Lip NOS', 'Lymph nodes of head face and neck', 'Overlapping lesion of brain and central nervous system', 'Overlapping lesion of penis', 'Overlapping lesion of retroperitoneum and peritoneum', 'Parotid gland', 'Dome of bladder', 'Bone of limb NOS', 'Descended testis', 'Vertebral column', 'Fundus uteri', 'Connective subcutaneous and other soft tissues of pelvis', 'Epididymis', 'Intra-abdominal lymph nodes', 'Paraspinal', 'Prepuce', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Pharynx NOS', 'Overlapping lesion of endocrine glands and related structures', 'Gum NOS', 'Spinal cord', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Skin of upper limb and shoulder', 'Nasopharynx NOS', 'Parathyroid gland', 'Bone NOS', 'Mouth NOS', 'Abdomen NOS', 'Conjunctiva', 'Spermatic cord', 'External upper lip', 'Labium minus', 'Renal pelvis', 'Overlapping lesion of lip', 'Short bones of upper limb and associated joints', 'Main bronchus', 'Upper respiratory tract NOS', 'Body of penis', 'Small intestine NOS', 'Central portion of breast', 'Lower-inner quadrant of breast', 'Labium majus', 'Tonsillar fossa', 'Cecum', 'Glans penis', 'Tail of pancreas', 'Lower third of esophagus', 'Body of pancreas', 'Intestinal tract NOS', 'Brain stem', 'Overlapping lesion of rectum anus and anal canal', 'Posterior wall of oropharynx', 'Pancreatic duct', 'Blood', 'Temporal lobe', 'Anterior floor of mouth', 'Nervous system NOS', 'Cornea NOS', 'Palate NOS', 'Occipital lobe', 'Abdominal esophagus', 'Overlapping lesion of pancreas', 'Overlapping lesion of female genital organs', 'Cheek mucosa', 'Retina', 'Overlapping lesion of male genital organs', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Larynx NOS', 'Skin of other and unspecified parts of face', 'Spleen', 'Oropharynx NOS', 'Anal canal', 'Subglottis', 'Cerebral meninges', 'Lateral wall of oropharynx', 'Middle third of esophagus', 'Nipple', 'Medulla of adrenal gland', 'Overlapping lesion of eye and adnexa', 'Olfactory nerve', 'Ethmoid sinus', 'Overlapping lesion of cervix uteri', 'Descending colon', 'Brain NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Anterior wall of bladder', 'Mandible', 'Other specified parts of pancreas', 'Skin of trunk', 'Other specified parts of female genital organs', 'Uterus NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Intrathoracic lymph nodes', 'Heart', 'Adrenal gland NOS', 'Aortic body and other paraganglia', 'Extrahepatic bile duct', 'Overlapping lesion of breast', 'Superior wall of nasopharynx', 'Fundus of stomach', 'Anterior mediastinum', 'Tongue NOS', 'Cranial nerve NOS', 'Head of pancreas', 'Overlapping lesions of oropharynx', 'Overlapping lesion of bones joints and articular cartilage', 'Retromolar area', 'Testis NOS', 'Connective subcutaneous and other soft tissues of head face and neck', 'Bladder NOS', 'Overlapping lesion of urinary organs', 'Lower-outer quadrant of breast', 'Thyroid gland', 'Anterior surface of epiglottis', 'Uterine adnexa']",,Diagnosis -Primary Gleason Grade,Primary Gleason Grade,PrimaryGleasonGrade,"The text term used to describe the primary Gleason score, which describes the pattern of cells making up the largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.",False,,"['Pattern 2', 'Pattern 3', 'Pattern 5', 'Pattern 1', 'Pattern 4', '']",,Diagnosis -Mitosis Karyorrhexis Index,Mitosis Karyorrhexis Index,MitosisKaryorrhexisIndex,Text term that represents the component of the International Neuroblastoma Pathology Classification (INPC) for mitosis-karyorrhexis index (MKI).,False,,"['Not Reported', 'Low', 'Intermediate', 'Unknown', 'High', '']",,Diagnosis -IRS Stage,IRS Stage,IRSStage,"The text term used to describe the classification of rhabdomyosarcoma tumors, as defined by the Intergroup Rhabdomyosarcoma Study (IRS).",False,,"['4', '1', 'Not Reported', 'Unknown', '2', '3', '']",,Diagnosis -Anaplasia Present Type,Anaplasia Present Type,AnaplasiaPresentType,"The text term used to describe the morphologic findings indicating the presence of a malignant cellular infiltrate characterized by the presence of large pleomorphic cells, necrosis, and high mitotic activity in a tissue sample.",False,,"['Equivocal', 'Not Reported', 'Absent', 'Unknown', 'Focal', 'Sclerosis', 'Diffuse', 'Present', '']",,Diagnosis -International Prognostic Index,International Prognostic Index,InternationalPrognosticIndex,"The text term used to describe the International Prognostic Index, which classifies the prognosis of patients with aggressive non-Hodgkin's lymphoma.",False,,"['High Risk', 'High-Intermediate Risk', 'Low-Intermediate Risk', 'Low Risk', '']",,Diagnosis -Days to Last Follow up,Days to Last Follow up,DaystoLastFollowup,"Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days.",True,,,,Diagnosis -AJCC Pathologic M,AJCC Pathologic M,AJCCPathologicM,"Code to represent the defined absence or presence of distant spread or metastases (M) to locations via vascular channels or lymphatics beyond the regional lymph nodes, using criteria established by the American Joint Committee on Cancer (AJCC).",False,,"['M1c', 'M1', 'Not Reported', 'Unknown', 'M1b', 'M0', 'M1a', 'cM0 (i+)', 'MX', '']",,Diagnosis -Ovarian Specimen Status,Ovarian Specimen Status,OvarianSpecimenStatus,The text term used to describe the physical condition of the involved ovary.,False,,"['Ovarian Capsule Ruptured', 'Not Reported', 'Ovarian Capsule Intact', 'Unknown', 'Ovarian Capsule Fragmented', '']",,Diagnosis -AJCC Pathologic Stage,AJCC Pathologic Stage,AJCCPathologicStage,"The extent of a cancer, especially whether the disease has spread from the original site to other parts of the body based on AJCC staging criteria.",False,,"['Stage IC', 'Stage IIA', 'Stage IIC', 'Stage IVB', 'Stage IIIA', 'Stage IB', 'Stage IIIC2', 'Stage IS', 'Stage I', 'Stage IVC', 'Stage 0', 'Stage IB2', 'Stage IIC1', 'Unknown', 'Stage 0is', 'Stage IVA', 'Stage IA', 'Not Reported', 'Stage 0a', 'Stage Tis', 'Stage X', 'Stage IB1', 'Stage IIB', 'Stage II', 'Stage IA2', 'Stage III', 'Stage IIIC1', 'Stage IV', 'Stage IIIB', 'Stage IIA1', 'Stage IA1', 'Stage IIIC', 'Stage IIA2', '']",,Diagnosis -Gleason Grade Tertiary,Gleason Grade Tertiary,GleasonGradeTertiary,The text term used to describe the tertiary pattern as described by the Gleason Grading System.,False,,"['Pattern 5', 'Pattern 4', '']",,Diagnosis -Lymph Nodes Positive,Lymph Nodes Positive,LymphNodesPositive,The number of lymph nodes involved with disease as determined by pathologic examination.,False,,,,Diagnosis -Micropapillary Features,Micropapillary Features,MicropapillaryFeatures,The yes/no/unknown indicator used to describe whether micropapillary features were determined to be present.,False,,"['Absent', 'Unknown', 'Not Reported', 'Present', '']",,Diagnosis -AJCC Clinical N,AJCC Clinical N,AJCCClinicalN,Extent of the regional lymph node involvement for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.,False,,"['N3', 'N0 (i-)', 'N3c', 'N1b', 'N1a', 'N2c', 'N4', 'N0 (mol+)', 'N1bII', 'N1bIV', 'Unknown', 'N2b', 'N1c', 'Not Reported', 'N3a', 'N1', 'N1bI', 'N3b', 'N0', 'N1mi', 'N0 (i+)', 'N2a', 'N0 (mol-)', 'N1bIII', 'N2', 'NX', '']",,Diagnosis -Tumor Largest Dimension Diameter,Tumor Largest Dimension Diameter,TumorLargestDimensionDiameter,"Numeric value used to describe the maximum diameter or dimension of the primary tumor, measured in centimeters.",False,,,,Diagnosis -WHO NTE Grade,WHO NTE Grade,WHONTEGrade,WHO NTE Grade,False,,"['Not Reported', 'GX', 'G2', 'Unknown', 'G3', 'G1', '']",,Diagnosis -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Diagnosis -Year of Diagnosis,Year of Diagnosis,YearofDiagnosis,Numeric value to represent the year of an individual's initial pathologic diagnosis of cancer.,False,,,,Diagnosis -Last Known Disease Status,Last Known Disease Status,LastKnownDiseaseStatus,Text term that describes the last known state or condition of an individual's neoplasm.,True,,"['With tumor', 'Not Reported', 'Not Applicable', 'unknown tumor status', 'Distant met recurrence/progression', 'Loco-regional recurrence/progression', 'Tumor free', 'Biochemical evidence of disease without structural correlate', 'Not Allowed To Collect']",,Diagnosis -IGCCCG Stage,IGCCCG Stage,IGCCCGStage,"The text term used to describe the International Germ Cell Cancer Collaborative Group (IGCCCG), a grouping used to further classify metastatic testicular tumors.",False,,"['Good Prognosis', 'Intermediate Prognosis', 'Not Reported', 'Poor Prognosis', 'Unknown', '']",,Diagnosis -Residual Disease,Residual Disease,ResidualDisease,Text terms to describe the status of a tissue margin following surgical resection.,False,,"['Not Reported', 'R1', 'RX', 'R0', 'Unknown', 'R2', '']",,Diagnosis -Best Overall Response,Best Overall Response,BestOverallResponse,The best improvement achieved throughout the entire course of protocol treatment.,False,,"['DU-Disease Unchanged', 'MX-Mixed Response', 'PSR-Pseudoresponse', 'CRU-Complete Response Unconfirmed', 'PPD-Pseudoprogression', 'CPD-Clinical Progression', 'IMR-Immunoresponse', 'SD-Stable Disease', 'SPD-Surgical Progression', 'PB-Palliative Benefit', 'PA-Palliative Therapy', 'VGPR-Very Good Partial Response', 'CR-Complete Response', 'NR-No Response', 'RPD-Radiographic Progressive Disease', 'sCR-Stringent Complete Response', 'NPB-No Palliative Benefit', 'MR-Minimal/Marginal Response', 'RP-Response', 'TE-Too Early', 'PR-Partial Response', 'AJ-Adjuvant Therapy', 'Non-CR/Non-PD-Non-CR/Non-PD', 'PD-Progressive Disease', 'RD-Responsive Disease', 'IPD-Immunoprogression', '']",,Diagnosis -AJCC Clinical Stage,AJCC Clinical Stage,AJCCClinicalStage,"Stage group determined from clinical information on the tumor (T), regional node (N) and metastases (M) and by grouping cases with similar prognosis for cancer.",False,,"['Stage IC', 'Stage IIA', 'Stage IIC', 'Stage IVB', 'Stage IIIA', 'Stage IB', 'Stage IIIC2', 'Stage IS', 'Stage I', 'Stage IVC', 'Stage 0', 'Stage IB2', 'Stage IIC1', 'Unknown', 'Stage 0is', 'Stage IVA', 'Stage IA', 'Not Reported', 'Stage 0a', 'Stage Tis', 'Stage X', 'Stage IB1', 'Stage IIB', 'Stage II', 'Stage IA2', 'Stage III', 'Stage IIIC1', 'Stage IV', 'Stage IIIB', 'Stage IIA1', 'Stage IA1', 'Stage IIIC', 'Stage IIA2', '']",,Diagnosis -Synchronous Malignancy,Synchronous Malignancy,SynchronousMalignancy,"A yes/no/unknown indicator used to describe whether the patient had an additional malignant diagnosis at the same time the tumor used for sequencing was diagnosed. If both tumors were sequenced, both tumors would have synchronous malignancies.",False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,Diagnosis -Classification of Tumor,Classification of Tumor,ClassificationofTumor,Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint.,False,,"['Not Reported', 'primary', 'Other', 'Unknown', 'Metastasis', 'Recurrence', 'Not Allowed To Collect', '']",,Diagnosis -Medulloblastoma Molecular Classification,Medulloblastoma Molecular Classification,MedulloblastomaMolecularClassification,The text term used to describe the classification of medulloblastoma tumors based on molecular features.,False,,"['SHH-Activated', 'Not Reported', 'Not Determined', 'WNT-Activated', 'Non-WNT/non-SHH Activated', 'Unknown', '']",,Diagnosis -Supratentorial Localization,Supratentorial Localization,SupratentorialLocalization,Text term to specify the location of the supratentorial tumor.,False,,"['Not Reported', 'Spinal Cord', 'Unknown', 'Cerebral Cortex', 'White Matter', 'Deep Gray', '']",,Diagnosis -Non Nodal Regional Disease,Non Nodal Regional Disease,NonNodalRegionalDisease,The text term used to describe whether the patient had non-nodal regional disease.,False,,"['Not Reported', 'Absent', 'Unknown', 'Indeterminate', 'Present', '']",,Diagnosis -Tumor Focality,Tumor Focality,TumorFocality,The text term used to describe whether the patient's disease originated in a single location or multiple locations.,False,,"['Unknown', 'Unifocal', 'Not Reported', 'Multifocal', '']",,Diagnosis -AJCC Clinical M,AJCC Clinical M,AJCCClinicalM,Extent of the distant metastasis for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.,False,,"['M1c', 'M1', 'Not Reported', 'Unknown', 'M1b', 'M0', 'M1a', 'cM0 (i+)', 'MX', '']",,Diagnosis -First Symptom Prior to Diagnosis,First Symptom Prior to Diagnosis,FirstSymptomPriortoDiagnosis,Text term used to describe the patient's first symptom experienced prior to diagnosis and thought to be related to the disease.,False,,"['Visual Changes', 'Not Reported', 'Altered Mental Status', 'Headaches', 'Motor or Movement Changes', 'Unknown', 'Sensory Changes', 'Seizures', '']",,Diagnosis -Greatest Tumor Dimension,Greatest Tumor Dimension,GreatestTumorDimension,Numeric value that represents the measurement of the widest portion of the tumor in centimeters.,False,,,,Diagnosis -AJCC Pathologic N,AJCC Pathologic N,AJCCPathologicN,The codes that represent the stage of cancer based on the nodes present (N stage) according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.,False,,"['N3', 'N0 (i-)', 'N3c', 'N1b', 'N1a', 'N2c', 'N4', 'N0 (mol+)', 'N1bII', 'N1bIV', 'Unknown', 'N2b', 'N1c', 'Not Reported', 'N3a', 'N1', 'N1bI', 'N3b', 'N0', 'N1mi', 'N0 (i+)', 'N2a', 'N0 (mol-)', 'N1bIII', 'N2', 'NX', '']",,Diagnosis -Metastasis at Diagnosis,Metastasis at Diagnosis,MetastasisatDiagnosis,The text term used to describe the extent of metastatic disease present at diagnosis.,False,,"['Not Reported', 'Regional Metastasis', 'Distant Metastasis', 'Metastasis NOS', 'Unknown', 'No Metastasis', '']",,Diagnosis -Gross Tumor Weight,Gross Tumor Weight,GrossTumorWeight,"Numeric value used to describe the gross pathologic tumor weight, measured in grams.",False,,,,Diagnosis -Breslow Thickness,Breslow Thickness,BreslowThickness,"The number that describes the distance, in millimeters, between the upper layer of the epidermis and the deepest point of tumor penetration.",False,,,,Diagnosis -Lymph Node Involved Site,Lymph Node Involved Site,LymphNodeInvolvedSite,The text term used to describe the anatomic site of lymph node involvement.,False,,"['Epitrochlear', 'Splenic', 'Retroperitoneal', 'Iliac-external', 'Femoral', 'Axillary', 'None', 'Cervical', 'Unknown', 'Paraaortic', 'Mesenteric', 'Not Reported', 'Popliteal', 'Hilar', 'Supraclavicular', 'Inguinal', 'Iliac-common', 'Occipital', 'Iliac', 'Submandibular', 'NOS', 'Parotid', 'Mediastinal', '']",,Diagnosis -Progression or Recurrence,Progression or Recurrence,ProgressionorRecurrence,Yes/No/unknown indicator to identify whether a patient has had a new tumor event after initial treatment.,True,,"['No', 'Yes - Progression or Recurrence', 'Unknown', 'Not Reported']",,Diagnosis -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,Diagnosis -Gleason Patterns Percent,Gleason Patterns Percent,GleasonPatternsPercent,"Numeric value that represents the percentage of Patterns 4 and 5, which is used when the Gleason score is greater than 7 to predict prognosis.",False,,,,Diagnosis -Vascular Invasion Present,Vascular Invasion Present,VascularInvasionPresent,The yes/no indicator to ask if large vessel or venous invasion was detected by surgery or presence in a tumor specimen.,False,,"['Yes - Vascular Invasion Present', 'Not Reported', 'No', 'Unknown', 'Not Allowed To Collect', '']",,Diagnosis -Mitotic Count,Mitotic Count,MitoticCount,"The number of mitoses identified under the microscope in tumors. The method of counting varies, according to the specific tumor examined. Usually, the mitotic count is determined based on the number of mitoses per high power field (40X) or 10 high power fields.",False,,,,Diagnosis -Perineural Invasion Present,Perineural Invasion Present,PerineuralInvasionPresent,A yes/no indicator to ask if perineural invasion or infiltration of tumor or cancer is present.,False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,Diagnosis -Secondary Gleason Grade,Secondary Gleason Grade,SecondaryGleasonGrade,"The text term used to describe the secondary Gleason score, which describes the pattern of cells making up the second largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.",False,,"['Pattern 2', 'Pattern 3', 'Pattern 5', 'Pattern 1', 'Pattern 4', '']",,Diagnosis -ISS Stage,ISS Stage,ISSStage,The multiple myeloma disease stage at diagnosis.,False,,"['Not Reported', 'III', 'Unknown', 'I', 'II', '']",,Diagnosis -Margins Involved Site,Margins Involved Site,MarginsInvolvedSite,The text term used to describe the anatomic sites that were involved in the survival margins.,False,,"['Renal Sinus', 'Gerota Fascia', 'Renal Vein', 'Ureter', 'Renal', 'Parenchyma', 'Perinephric Fat', 'Renal Capsule', '']",,Diagnosis -INPC Grade,INPC Grade,INPCGrade,"Text term used to describe the classification of neuroblastic differentiation within neuroblastoma tumors, as defined by the International Neuroblastoma Pathology Classification (INPC).",False,,"['Differentiating', 'Poorly Differentiated', 'Not Reported', 'Unknown', 'Undifferentiated', '']",,Diagnosis -Morphology,Morphology,Morphology,"The third edition of the International Classification of Diseases for Oncology, published in 2000 used principally in tumor and cancer registries for coding the site (topography) and the histology (morphology) of neoplasms. The study of the structure of the cells and their arrangement to constitute tissues and, finally, the association among these to form organs. In pathology, the microscopic process of identifying normal and abnormal morphologic characteristics in tissues, by employing various cytochemical and immunocytochemical stains. A system of numbered categories for representation of data.",True,,,,Diagnosis -Tumor Grade,Tumor Grade,TumorGrade,"Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.",True,,"['Low Grade', 'Not Reported', 'High Grade', 'Intermediate Grade', 'Not Applicable', 'GX', 'G2', 'Unknown', 'GB', 'G3', 'G4', 'G1']",,Diagnosis -Ovarian Surface Involvement,Ovarian Surface Involvement,OvarianSurfaceInvolvement,The text term that describes whether the surface tissue (outer boundary) of the ovary shows evidence of involvement or presence of cancer.,False,,"['Not Reported', 'Absent', 'Unknown', 'Indeterminate', 'Present', '']",,Diagnosis -AJCC Staging System Edition,AJCC Staging System Edition,AJCCStagingSystemEdition,"The text term used to describe the version or edition of the American Joint Committee on Cancer Staging Handbooks, a publication by the group formed for the purpose of developing a system of staging for cancer that is acceptable to the American medical profession and is compatible with other accepted classifications.",False,,"['6th', 'Not Reported', '5th', '7th', '1st', 'Unknown', '4th', '8th', '2nd', '3rd', '']",,Diagnosis -Primary Diagnosis,Primary Diagnosis,PrimaryDiagnosis,"Text term used to describe the patient's histologic diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",True,,"['Adenocarcinoma in tubular adenoma', 'Tumor cells NOS', 'Malignant lymphoma mixed cell type follicular', 'T-cell large granular lymphocytic leukemia', 'Kaposi sarcoma', 'Carcinoma in adenomatous polyp', 'Adenocarcinoma in situ in tubular adenoma', 'Mixed medullary-papillary carcinoma', 'Liposarcoma NOS', 'Carcinoma intestinal type', 'Classical Hodgkin lymphoma nodular sclerosis grade 1', 'Bile duct adenoma', 'Inflammatory carcinoma', 'Carcinoma in situ in a polyp NOS', 'Intravascular B-cell lymphoma', 'Melanotic psammomatous MPNST', 'Acinar cell carcinoma', 'Papillary renal cell carcinoma', 'Papillary serous cystadenoma NOS', 'Papillary adenoma NOS', 'Interstitial cell tumor benign', 'Mixed small cell carcinoma', 'Rhabdoid sarcoma', 'Malignant lymphoma mixed cell type diffuse', 'Chronic leukemia NOS', 'Intraductal papillary carcinoma', 'Intraductal tubular-papillary neoplasm high grade', 'Central neurocytoma', 'Undifferentiated spindle cell sarcoma', 'Bronchiolo-alveolar carcinoma indeterminate type', 'Pancreatic endocrine tumor NOS', 'Tubulocystic renal cell carcinoma', 'Basophil adenocarcinoma', 'Intraductal carcinoma solid type', 'Papillotubular adenoma', 'Undifferentiated epithelioid sarcoma', 'Renal medullary carcinoma', 'Chronic granulocytic leukemia Philadelphia chromosome (Ph1) positive', 'Unclassified tumor benign', 'Bronchial adenoma cylindroid', 'Classical Hodgkin lymphoma mixed cellularity NOS', 'Pigmented adenoma', 'Infiltrating duct and colloid carcinoma', 'Bronchial-associated lymphoid tissue lymphoma', 'Epidermoid carcinoma in situ NOS', 'Unknown', 'Carcinoma NOS', 'Malignancy', 'Undifferentiated leukaemia', 'Unclassified tumor borderline malignancy', 'Hodgkin lymphoma NOS', 'Papillary cystadenoma NOS', 'Medullary carcinoma NOS', 'Myeloma NOS', 'Acute basophilic leukaemia', 'Renal cell carcinoma NOS', 'Neoplasm secondary', 'Primary amyloidosis', 'Acute lymphoblastic leukemia NOS', 'Malignant melanoma in junctional nevus', 'Nevus NOS', 'Tumor malignant NOS', 'Basal cell adenoma', 'Bronchio-alveolar carcinoma mucinous', 'Mucosal-associated lymphoid tissue lymphoma', 'Pleomorphic lobular carcinoma in situ', 'Small cell carcinoma NOS', 'Dermal nevus', 'Liver cell adenoma', 'Malignant lymphoma lymphocytic diffuse NOS', 'Cerebellar liponeurocytoma', 'Acute lymphoblastic leukemia mature B-cell type', 'Adenocarcinoma combined with other types of carcinoma', 'Adenocarcinoma metastatic NOS', 'Carcinoma in a polyp NOS', 'Pleomorphic adenoma', 'Osteosarcoma NOS', 'Carcinosarcoma NOS', 'Lymphoblastic leukemia NOS', 'Unclassified tumor uncertain whether benign or malignant', 'Renal cell carcinoma unclassified', 'Neoplasm NOS', 'Acute lymphoblastic leukemia precursor cell type', 'Cerebellar sarcoma NOS', 'Renal cell carcinoma spindle cell', 'Small cell sarcoma', 'Bronchiolo-alveolar carcinoma goblet cell type', 'Combined small cell-adenocarcinoma', 'Precancerous melanosis NOS', 'Tumor NOS', 'Neoplasm malignant', 'Melanoma in situ', 'Melanotic neuroectodermal tumor', 'Intraductal carcinoma NOS', 'Lymphoma NOS', 'Tumor cells malignant', 'Hepatocholangiocarcinoma', 'Preleukemic syndrome', 'Papillomatosis glandular', 'Small congenital nevus', 'c-ALL', 'Hodgkin lymphoma nodular sclerosis NOS', 'Bronchiolo-alveolar adenocarcinoma NOS', 'Pancreatic microadenoma', 'Tubular carcinoid', 'Gastrinoma NOS', 'Papillary urothelial carcinoma', 'Carcinoma in situ in adenomatous polyp', 'Pancreatobiliary-type carcinoma', 'Small cell osteosarcoma', 'Adenocarcinoma of anal glands', 'Gastrointestinal stromal tumor malignant', 'Acute myeloid leukemia minimal differentiation', 'Ductal carcinoma NOS', 'Malignant melanoma in Hutchinson melanotic freckle', 'Malignant lymphoma nodular NOS', 'B-cell lymphocytic leukemia/small lymphocytic lymphoma', 'Malignant lymphoma NOS', 'Combined hepatocellular carcinoma and cholangiocarcinoma', 'Combined small cell-large carcinoma', 'Epithelial tumor malignant', 'Intraepidermal carcinoma NOS', 'Endometrioid carcinoma NOS', 'Acute leukemia Burkitt type', 'Pituitary adenoma NOS', 'Adenocarcinoma NOS', 'Papillary epidermoid carcinoma', 'Teratoma NOS', 'Combined small cell-squamous cell carcinoma', 'Lobular carcinoma NOS', 'Basophil carcinoma', 'Serous cystadenocarcinoma NOS', 'Glioma malignant', 'Diffuse astrocytoma IDH-wildtype', 'Renal cell carcinoma sarcomatoid', 'Hepatoid adenocarcinoma', 'Intraductal and lobular carcinoma', 'Malignant melanoma NOS', 'Peripheral T-cell lymphoma large cell', 'Chronic myelomonocytic leukemia Type 1', 'Combined/mixed carcinoid and adenocarcinoma', 'Intraductal carcinoma and lobular carcinoma in situ', 'Pancreatic endocrine tumor nonfunctioning', 'Tubulovillous adenoma NOS', 'Intraductal carcinoma noninfiltrating NOS', 'Tumorlet benign', 'Basal cell epithelioma', 'Endometrioid adenocarcinoma NOS', 'Large cell carcinoma NOS', 'Burkitt tumor', 'Papillary microcarcinoma', 'Melanotic neurofibroma', 'Paget disease and intraductal carcinoma of breast', 'Precursor B-cell lymphoblastic lymphoma', 'Pleomorphic carcinoma', 'Dysplastic nevus', 'Undifferentiated high-grade pleomorphic sarcoma', 'Acute myeloid leukemia NOS', 'Esophageal glandular dysplasia (intraepithelial neoplasia) low grade', 'Unclassified tumor malignant uncertain whether primary or metastatic', 'Mixed pineal tumor', 'Bile duct adenocarcinoma', 'Adenocarcinoma in adenomatous polyp', 'Lymphatic leukemic NOS', 'Papillotubular adenocarcinoma', 'Lobular adenocarcinoma', 'Melanocytoma eyeball', 'Melanoma malignant of soft parts', 'Therapy related myeloid neoplasm', 'Oat cell carcinoma', 'Duct carcinoma desmoplastic type', 'Melanotic MPNST', 'Neurofibromatosis NOS', 'Melanotic medulloblastoma', 'Skin appendage carcinoma', 'Hodgkin disease NOS', 'Diffuse melanocytosis', 'Preleukemia', 'Tumor cells benign', 'Chronic myelomonocytic leukemia Type II', 'Cervical intraepithelial neoplasia low grade', 'Tubulo-papillary adenoma', 'Adenocarcinoma of anal ducts', 'Papillary carcinoma in situ', 'Acute lymphocytic leukemia', 'Myeloid leukemia NOS', 'T-cell large granular lymphocytosis', 'Bronchial adenoma NOS', 'Pulmonary blastoma', 'Intraductal carcinoma clinging', 'Adult T-cell lymphoma/leukemia', 'Intraductal adenocarcinoma noninfiltrating NOS', 'Acute lymphatic leukemia', 'Infiltrating duct and cribriform carcinoma', 'Neoplasm metastatic', 'Basal cell tumor', 'Papilloma of bladder', 'Teratoma malignant NOS', 'Pancreatoblastoma', 'Infiltrating duct carcinoma NOS', 'Precursor T-cell lymphoblastic lymphoma', 'Basal cell carcinoma NOS', 'Malignant melanoma in precancerous melanosis', 'Inflammatory adenocarcinoma', 'Splenic B-cell lymphoma/leukemia unclassifiable', 'Squamous cell carcinoma adenoid', 'T-cell lymphoma NOS', 'Tubular adenoma NOS', 'Papillary adenocarcinoma NOS', 'Esophageal intraepithelial neoplasia high grade', 'Papillary squamous cell carcinoma', 'Pulmonary adenomatosis', 'Bile duct cystadenoma', 'Combined large cell neuroendocrine carcinoma', 'Neoplasm uncertain whether benign or malignant', 'Mammary carcinoma in situ', 'Melanoma NOS', 'Spindle cell melanoma NOS', 'Esophageal glandular dysplasia (intraepithelial neoplasia) high grade', 'Neuroendocrine carcinoma NOS', 'Meningeal melanoma', 'Burkitt-like lymphoma', 'Precursor cell lymphoblastic leukemia NOS', 'Acute lymphoid leukemia', 'Chondrosarcoma grade 2/3', 'Tubulopapillary adenocarcinoma', 'B lymphoblastic leukemia/lymphoma NOS', 'Non-lymphocytic leukemia NOS', 'Pleomorphic liposarcoma', 'Mixed medullary-follicular carcinoma', 'Bronchiolo-alveolar carcinoma NOS', 'Myelocytic leukemia NOS', 'Splenic lymphoma with villous lymphocytes', 'Transitional carcinoma', 'Melanocytic nevus', 'Liposarcoma well differentiated', 'Eosinophilic leukemia', 'Chronic myeloproliferative disease NOS', 'Adenocarcinoma in situ in a polyp NOS', 'Hodgkin lymphoma mixed cellularity NOS', 'Classical Hodgkin lymphoma nodular sclerosis grade 2', 'Eosinophilic granuloma', 'Tumor embolus', 'Mixed tumor NOS', 'Carcinoma diffuse type', 'Precursor T-cell lymphoblastic leukemia', 'Neurofibrosarcoma', 'Melanocytoma NOS', 'B-ALL', 'Bronchio-alveolar carcinoma mixed mucinous and non-mucinous', 'Acute myeloid leukemia MLL', 'Adenocarcinoma in situ non-mucinous', 'Malignant lymphoma lymphoblastic NOS', 'Papillary adenocarcinoma follicular variant', 'Tumor cells uncertain whether benign or malignant', 'Pleomorphic lipoma', 'Lymphocytic leukemia NOS', 'Astrocytoma anaplastic', 'Non-Hodgkin lymphoma NOS', 'Papillary serous adenocarcinoma', 'Meningioma malignant', 'Chronic lymphoid leukemia', 'Ductal carcinoma in situ NOS', 'Neuroepithelioma NOS', 'Melanotic progonoma', 'Melanotic schwannoma', 'Diffuse astrocytoma IDH-mutant', 'Small cell neuroendocrine carcinoma', 'Esophageal squamous intraepithelial neoplasia (dysplasia) high grade', 'Paget disease extramammary', 'Prostatic intraepithelial neoplasia grade III', 'Ewing sarcoma', 'Micropapillary carcinoma NOS', 'Epithelial tumor benign', 'Hepatocellular adenoma', 'Cementoma NOS', 'Malignant lymphoma mixed cell type nodular', 'Acute leukemia NOS', 'Bile duct carcinoma', 'Nephroblastoma NOS', 'Pagetoid reticulosis', 'Hepatocarcinoma', 'Not Reported', 'Neoplasm malignant uncertain whether primary or metastatic', 'Malignant melanoma regressing', 'Bronchiolo-alveolar carcinoma Clara cell and goblet cell type', 'Dermatofibroma NOS', 'Interstitial cell tumor malignant', 'Adenocarcinoma in situ NOS', 'Adenocarcinoma endocervical type', 'Meningioma anaplastic', 'B lymphoblastic leukemia/lymphoma with hypodiploidy (Hypodiploid ALL)', 'Intraductal tubulopapillary neoplasm', 'Tumor secondary', 'Chronic myelogenous leukemia Philadelphia chromosome (Ph 1) positive', 'Sclerosing hemangioma', 'Papillary transitional cell carcinoma', 'Tubular androblastoma NOS', 'Ependymoma NOS', 'Papillary tumor of the pineal region', 'Chronic myelocytic leukemia NOS', 'Papillary serous cystadenocarcinoma', 'Haemangiosarcoma', 'Papillary and follicular carcinoma', 'Chronic myelomonocytic leukemia in transformation', 'Carcinoma anaplastic NOS', 'Paget disease mammary', 'Liver cell carcinoma', 'Eosinophil adenocarcinoma', 'Sclerosing hepatic carcinoma', 'Tumor metastatic', 'Endometrial sarcoma NOS', 'Gastrin cell tumor', 'Chronic myeloproliferative disorder', 'Acute promyelocytic leukemia NOS', 'Malignant lymphoma Hodgkin', 'Classical Hodgkin lymphoma lymphocyte depletion NOS', 'Lobular carcinoma noninfiltrating', 'Mixed pancreatic endocrine and exocrine tumor malignant', 'Unclassified tumor malignant', 'Chondroma NOS', 'Basophil adenoma', 'Transitional cell carcinoma', 'Carcinoma metastatic NOS', 'Medullary adenocarcinoma', 'Adenocarcinoma in villous adenoma', 'Ganglioglioma NOS', 'Intradermal nevus', 'Osteoblastoma malignant', 'Papillary squamous cell carcinoma in situ', 'Undifferentiated pleomorphic sarcoma', 'Bronchiolar carcinoma', 'Pancreatic endocrine tumor benign', 'Malignant melanoma in congenital melanocytic nevus', 'Malignant lymphoma diffuse NOS', 'Composite Hodgkin and non-Hodgkin lymphoma', 'Monocytic leukemia NOS', 'Paraganglioma malignant', 'Splenic diffuse red pulp small B-cell lymphoma', 'B lymphoblastic leukemia/lymphoma with hyperdiploidy', 'Rodent ulcer', 'Hodgkin sarcoma', 'Familial adenomatous polyposis', 'Duct cell carcinoma', 'Rhabdomyosarcoma NOS', 'Eosinophil carcinoma', 'Pulmonary artery intimal sarcoma', 'Capillary hemangioma', 'Adult rhabdomyoma', 'Tubular carcinoma', 'Burkitt cell leukemia', 'Bronchiolo-alveolar carcinoma Clara cell', 'Papillary glioneuronal tumor', 'T lymphoblastic leukemia/lymphoma', 'Neuroblastoma NOS', 'Meningioma NOS', 'Adenocarcinoid tumor', 'Malignant lymphoma large cell NOS', 'Combined small cell carcinoma', 'Mucous adenocarcinoma', 'Peripheral T-cell lymphoma NOS', 'Renal carcinoma collecting duct type', 'Bile duct cystadenocarcinoma', 'Chronic myelogenous leukemia BCR-ABL positive', 'Intraductal tubular-papillary neoplasm low grade', 'Tumor benign', 'Adenocarcinoma intestinal type', 'Pro-B ALL', 'Malignant lymphoma large B-cell diffuse NOS', 'Secondary carcinoma', 'Gastrinoma malignant', 'Intracystic papilloma', 'Cancer', 'Intraductal papillary adenocarcinoma with invasion', 'Mixed squamous cell and glandular papilloma', 'Sarcoma NOS', 'Non-invasive low grade serous carcinoma', 'Serous surface papillary carcinoma', 'Pro-T ALL', 'Neurofibroma NOS', 'Pancreatobiliary neoplasm non-invasive', 'Bronchial adenoma carcinoid', 'Precursor B-cell lymphoblastic leukemia', 'Melanoameloblastoma', 'Mixed adenocarcinoma and epidermoid carcinoma', 'Splenic marginal zone lymphoma NOS', 'Intraepidermal squamous cell carcinoma Bowen type', 'Carcinoma undifferentiated NOS', 'Capillary lymphangioma', 'Chronic myelomonocytic leukemia NOS', 'Adenocarcinoma in a polyp NOS', 'Astrocytoma NOS', 'Glioblastoma', 'Adult T-cell lymphoma', 'Transitional cell carcinoma in situ', 'Carcinoma in pleomorphic adenoma', 'Renal cell adenocarcinoma', 'Medulloblastoma NOS', 'Papillomatosis NOS', 'Acute myelomonocytic leukemia', 'Malignant lymphoma immunoblastic NOS', 'Chronic lymphocytic leukemia B-cell type (includes all variants of BCLL)', 'Malignant lymphoma lymphocytic NOS', 'Nonpigmented nevus', 'Squamous cell carcinoma clear cell type', 'Mixed adenocarcinoma and squamous cell carcinoma', 'Diffuse large B-cell lymphoma NOS', 'Paraganglioma benign', 'Malignant lymphoma non-Hodgkin NOS', 'Classical Hodgkin lymphoma lymphocyte-rich', 'Intraductal micropapillary carcinoma', 'Secretory carcinoma of breast', 'Gastrin cell tumor malignant', 'Papilloma NOS', 'Infiltrating basal cell carcinoma NOS', 'Adenocarcinoma in polypoid adenoma', 'Chronic neutrophilic leukemia', 'Undifferentiated sarcoma', 'Neurosarcoma', 'Medullary osteosarcoma', 'Papillary carcinoma NOS', 'Chronic lymphocytic leukemia', 'Undifferentiated uterine sarcoma', 'Malignant lymphoma lymphocytic nodular NOS', 'Adenocarcinoma in situ mucinous', 'Multiple myeloma', 'Lobular and ductal carcinoma', 'Undifferentiated round cell sarcoma', 'Chronic lymphatic leukemia', 'Endometrioid adenofibroma NOS', 'Malignant lymphoma large B-cell NOS', 'Pancreatic endocrine tumor malignant', 'Cervical intraepithelial neoplasia grade III', 'Glioma NOS', 'Papillary adenofibroma', 'Classical Hodgkin lymphoma nodular sclerosis NOS', 'Non-small cell carcinoma', 'Squamous cell carcinoma NOS', 'Haemangioblastoma', 'Paraganglioma NOS', 'Bronchiolar adenocarcinoma', 'Liposarcoma differentiated', 'Mixed tumor malignant NOS', 'Burkitt lymphoma NOS (Includes all variants)', 'Renal cell carcinoma chromophobe type', 'Malignant melanoma in giant pigmented nevus', 'Chronic monocytic leukemia', 'Carcinoma in situ NOS', 'Lymphoblastoma', 'Tubulolobular carcinoma', 'Rhabdoid tumor NOS', 'Hepatocellular carcinoma NOS', 'Adenocarcinoma in situ in adenomatous polyp', 'Classical Hodgkin lymphoma nodular sclerosis cellular phase', 'Paget disease of breast', 'Squamous cell carcinoma in situ NOS', 'Classical Hodgkin lymphoma lymphocyte depletion diffuse fibrosis', 'Bronchiolo-alveolar carcinoma non-mucinous', 'Rhabdosarcoma', 'Astrocytoma low grade', 'Chronic myeloid leukemia NOS', 'Chronic granulocytic leukemia NOS', 'Endometrioid adenoma NOS', 'Typical carcinoid', 'Rhabdoid meningioma', 'Hodgkin paragranuloma NOS', 'Hodgkin granuloma', 'Duct adenocarcinoma NOS', 'Juvenile myelomonocytic leukemia', 'Adenocarcinoma diffuse type', 'Osteoblastoma NOS', 'Rhabdomyosarcoma with ganglionic differentiation', 'Eosinophil adenoma', 'Interstitial cell tumor NOS', 'Tubular adenocarcinoma', 'Myoepithelioma', 'Pigmented nevus NOS', 'Duct carcinoma NOS', 'Neoplasm benign', 'Rhabdomyoma NOS', 'Spindle cell carcinoma NOS', 'Pleomorphic lobular carcinoma', 'Lobular carcinoma in situ NOS', 'Central neuroblastoma', 'Adenocarcinoma pancreatobiliary type', 'Chronic granulocytic leukemia BCR/ABL', 'Pigmented basal cell carcinoma', 'Paget disease and infiltrating duct carcinoma of breast', 'Acute lymphoblastic leukemia-lymphoma NOS', 'Epidermoid carcinoma NOS', 'Hepatoid carcinoma', 'Papillary meningioma', 'High-grade serous carcinoma', 'Basal cell adenocarcinoma', 'Esophageal squamous intraepithelial neoplasia (dysplasia) low grade', 'Malignant lymphoma small B lymphocytic NOS', 'Pituitary carcinoma NOS', 'Tubular androblastoma with lipid storage', 'Meningeal melanocytoma', 'Duct adenoma NOS', 'Diffuse astrocytoma low grade', 'Intraductal papillary adenocarcinoma NOS', 'Splenic marginal zone B-cell lymphoma', 'Classical Hodgkin lymphoma lymphocyte depletion reticular', 'B cell lymphoma NOS']",,Diagnosis -Lymphatic Invasion Present,Lymphatic Invasion Present,LymphaticInvasionPresent,"A yes/no indicator to ask if small or thin-walled vessel invasion is present, indicating lymphatic involvement",False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,Diagnosis -Site of Resection or Biopsy,Site of Resection or Biopsy,SiteofResectionorBiopsy,"The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",True,,"['Paraurethral gland', 'Colon NOS', 'Frontal sinus', 'Overlapping lesion of tongue', 'Overlapping lesion of palate', 'Scrotum NOS', 'Bone marrow', 'Axillary tail of breast', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'unknown primary site', 'Broad ligament', 'Lateral floor of mouth', 'Overlapping lesion of vulva', 'Trigone of bladder', 'Lacrimal gland', 'Thorax NOS', 'Ampulla of Vater', 'Myometrium', 'Penis NOS', 'Female genital tract NOS', 'Submandibular gland', 'Anterior 2/3 of tongue NOS', 'Posterior wall of bladder', 'Thymus', 'Endocrine gland NOS', 'Stomach NOS', 'Unknown', 'Cerebrum', 'Splenic flexure of colon', 'Urachus', 'Skin of lip NOS', 'Mucosa of lip NOS', 'Accessory sinus NOS', 'Cortex of adrenal gland', 'Other ill-defined sites', 'Middle lobe lung', 'Pelvis NOS', 'Anus NOS', 'Upper-inner quadrant of breast', 'Posterior mediastinum', 'Esophagus NOS', 'Duodenum', 'Cervical esophagus', 'Optic nerve', 'Long bones of lower limb and associated joints', 'Middle ear', 'Breast NOS', 'Dorsal surface of tongue NOS', 'Lesser curvature of stomach NOS', 'Overlapping lesion of floor of mouth', 'Overlapping lesion of heart mediastinum and pleura', 'Eye NOS', 'Overlapping lesion of esophagus', 'Ciliary body', 'Ureteric orifice', 'Postcricoid region', 'External ear', 'Base of tongue NOS', 'Liver', 'Commissure of lip', 'Cloacogenic zone', 'Lower lobe lung', 'Transverse colon', 'Acoustic nerve', 'Supraglottis', 'Fallopian tube', 'Upper third of esophagus', 'Skin of scalp and neck', 'Choroid', 'Long bones of upper limb scapula and associated joints', 'Overlapping lesion of brain', 'Upper gum', 'Skin NOS', 'Hard palate', 'Ileum', 'Overlapping lesion of colon', 'Ascending colon', 'Lower gum', 'Pelvic bones sacrum coccyx and associated joints', 'Hepatic flexure of colon', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Vestibule of mouth', 'Cervix uteri', 'Bones of skull and face and associated joints', 'Overlapping lesion of lip oral cavity and pharynx', 'Endometrium', 'Sphenoid sinus', 'Overlapping lesion of ill-defined sites', 'Sigmoid colon', 'Peritoneum NOS', 'Specified parts of peritoneum', 'Meckel diverticulum', 'Rectosigmoid junction', 'Kidney NOS', 'Reticuloendothelial system NOS', 'Rectum NOS', 'Pylorus', 'Overlapping lesion of tonsil', 'Pleura NOS', 'Jejunum', 'Vallecula', 'Skin of lower limb and hip', 'Pelvic lymph nodes', 'External lower lip', 'Overlapping lesion of skin', 'Mucosa of upper lip', 'Ovary', 'Cauda equina', 'Lower limb NOS', 'Body of stomach', 'Overlapping lesion of larynx', 'Pancreas NOS', 'Overlapping lesion of lung', 'Overlapping lesion of major salivary glands', 'Uvula', 'Overlapping lesion of hypopharynx', 'Round ligament', 'Corpus uteri', 'Biliary tract NOS', 'Male genital organs NOS', 'Parametrium', 'External lip NOS', 'Overlapping lesion of accessory sinuses', 'Cardia NOS', 'Islets of Langerhans', 'Carotid body', 'Ventral surface of tongue NOS', 'Autonomic nervous system NOS', 'Overlapping lesion of corpus uteri', 'Spinal meninges', 'Posterior wall of nasopharynx', 'Placenta', 'Intrahepatic bile duct', 'Overlapping lesion of digestive system', 'Mediastinum NOS', 'Hematopoietic system NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Major salivary gland NOS', 'Cerebellum NOS', 'Overlapping lesion of stomach', 'Vulva NOS', 'Craniopharyngeal duct', 'Lung NOS', 'Greater curvature of stomach NOS', 'Upper-outer quadrant of breast', 'Gallbladder', 'Thoracic esophagus', 'Lymph nodes of axilla or arm', 'Ventricle NOS', 'Overlapping lesion of biliary tract', 'Hypopharynx NOS', 'Clitoris', 'Exocervix', 'Parietal lobe', 'Waldeyer ring', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Head face or neck NOS', 'Anterior wall of nasopharynx', 'Urethra', 'Overlapping lesion of nasopharynx', 'Maxillary sinus', 'Lymph nodes of inguinal region or leg', 'Ureter', 'Tonsillar pillar', 'Sublingual gland', 'Pituitary gland', 'Gastrointestinal tract NOS', 'Pineal gland', 'Meninges NOS', 'Lingual tonsil', 'Trachea', 'Pyriform sinus', 'Mucosa of lower lip', 'Not Reported', 'Posterior wall of hypopharynx', 'Urinary system NOS', 'Orbit NOS', 'Short bones of lower limb and associated joints', 'Connective subcutaneous and other soft tissues of thorax', 'Upper limb NOS', 'Gastric antrum', 'Lymph node NOS', 'Peripheral nerves and autonomic nervous system of thorax', 'Ill-defined sites within respiratory system', 'Other specified parts of male genital organs', 'Rib sternum clavicle and associated joints', 'Overlapping lesion of bladder', 'Appendix', 'Prostate gland', 'Lymph nodes of multiple regions', 'Lateral wall of nasopharynx', 'Branchial cleft', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Floor of mouth NOS', 'Connective subcutaneous and other soft tissues NOS', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Bladder neck', 'Border of tongue', 'Connective subcutaneous and other soft tissues of abdomen', 'Overlapping lesion of small intestine', 'Lateral wall of bladder', 'Soft palate NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Isthmus uteri', 'Nasal cavity', 'Endocervix', 'Tonsil NOS', 'Glottis', 'Retroperitoneum', 'Peripheral nerves and autonomic nervous system of pelvis', 'Frontal lobe', 'Vagina NOS', 'Undescended testis', 'Laryngeal cartilage', 'Eyelid', 'Hypopharyngeal aspect of aryepiglottic fold', 'Overlapping lesion of other and unspecified parts of mouth', 'Upper lobe lung', 'Lip NOS', 'Lymph nodes of head face and neck', 'Overlapping lesion of brain and central nervous system', 'Overlapping lesion of penis', 'Overlapping lesion of retroperitoneum and peritoneum', 'Parotid gland', 'Dome of bladder', 'Bone of limb NOS', 'Descended testis', 'Vertebral column', 'Fundus uteri', 'Connective subcutaneous and other soft tissues of pelvis', 'Epididymis', 'Intra-abdominal lymph nodes', 'Paraspinal', 'Prepuce', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Pharynx NOS', 'Overlapping lesion of endocrine glands and related structures', 'Gum NOS', 'Spinal cord', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Skin of upper limb and shoulder', 'Nasopharynx NOS', 'Parathyroid gland', 'Bone NOS', 'Mouth NOS', 'Abdomen NOS', 'Conjunctiva', 'Spermatic cord', 'External upper lip', 'Labium minus', 'Renal pelvis', 'Overlapping lesion of lip', 'Short bones of upper limb and associated joints', 'Main bronchus', 'Upper respiratory tract NOS', 'Body of penis', 'Small intestine NOS', 'Central portion of breast', 'Lower-inner quadrant of breast', 'Labium majus', 'Tonsillar fossa', 'Cecum', 'Glans penis', 'Tail of pancreas', 'Lower third of esophagus', 'Body of pancreas', 'Intestinal tract NOS', 'Brain stem', 'Overlapping lesion of rectum anus and anal canal', 'Posterior wall of oropharynx', 'Pancreatic duct', 'Blood', 'Temporal lobe', 'Anterior floor of mouth', 'Nervous system NOS', 'Cornea NOS', 'Palate NOS', 'Occipital lobe', 'Abdominal esophagus', 'Overlapping lesion of pancreas', 'Overlapping lesion of female genital organs', 'Cheek mucosa', 'Retina', 'Overlapping lesion of male genital organs', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Larynx NOS', 'Skin of other and unspecified parts of face', 'Spleen', 'Oropharynx NOS', 'Anal canal', 'Subglottis', 'Cerebral meninges', 'Lateral wall of oropharynx', 'Middle third of esophagus', 'Nipple', 'Medulla of adrenal gland', 'Overlapping lesion of eye and adnexa', 'Olfactory nerve', 'Ethmoid sinus', 'Overlapping lesion of cervix uteri', 'Descending colon', 'Brain NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Anterior wall of bladder', 'Mandible', 'Other specified parts of pancreas', 'Skin of trunk', 'Other specified parts of female genital organs', 'Uterus NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Intrathoracic lymph nodes', 'Heart', 'Adrenal gland NOS', 'Aortic body and other paraganglia', 'Extrahepatic bile duct', 'Overlapping lesion of breast', 'Superior wall of nasopharynx', 'Fundus of stomach', 'Anterior mediastinum', 'Tongue NOS', 'Cranial nerve NOS', 'Head of pancreas', 'Overlapping lesions of oropharynx', 'Overlapping lesion of bones joints and articular cartilage', 'Retromolar area', 'Testis NOS', 'Connective subcutaneous and other soft tissues of head face and neck', 'Bladder NOS', 'Overlapping lesion of urinary organs', 'Lower-outer quadrant of breast', 'Thyroid gland', 'Anterior surface of epiglottis', 'Uterine adnexa']",,Diagnosis -Tumor Depth,Tumor Depth,TumorDepth,"Numeric value that represents the depth of tumor invasion, measured in millimeters (mm).",False,,,,Diagnosis -Margin Distance,Margin Distance,MarginDistance,Numeric value (in centimeters) that represents the distance between the tumor and the surgical margin.,False,,,,Diagnosis -Vascular Invasion Type,Vascular Invasion Type,VascularInvasionType,Text term that represents the type of vascular tumor invasion.,False,,"['Not Reported', 'Intramural', 'Micro', 'Unknown', 'No Vascular Invasion', 'Macro', 'Extramural', '']",,Diagnosis -IRS Group,IRS Group,IRSGroup,"Text term used to describe the classification of rhabdomyosarcoma tumors, as defined by the Intergroup Rhabdomyosarcoma Study (IRS).",False,,"['Group Ia', 'Group II', 'Group IIc', 'Group IIIa', 'Not Reported', 'Group Ib', 'Group III', 'Unknown', 'Group I', 'Group IV', 'Group IIa', 'Group IIIb', '']",,Diagnosis -Non Nodal Tumor Deposits,Non Nodal Tumor Deposits,NonNodalTumorDeposits,The yes/no/unknown indicator used to describe the presence of tumor deposits in the pericolic or perirectal fat or in adjacent mesentery away from the leading edge of the tumor.,False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,Diagnosis -Days to Diagnosis,Days to Diagnosis,DaystoDiagnosis,Number of days between the date used for index and the date the patient was diagnosed with the malignant disease.,False,,,,Diagnosis -Prior Malignancy,Prior Malignancy,PriorMalignancy,The yes/no/unknown indicator used to describe the patient's history of prior cancer diagnosis.,False,,"['Not Reported', 'Yes', 'No', 'Unknown', 'Not Allowed To Collect', '']",,Diagnosis -Gleason Grade Group,Gleason Grade Group,GleasonGradeGroup,"The text term used to describe the overall grouping of grades defined by the Gleason grading classification, which is used to determine the aggressiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.",False,,"['Group 1', 'Group 4', 'Group 2', 'Group 3', 'Group 5', '']",,Diagnosis -Age at Diagnosis,Age at Diagnosis,AgeatDiagnosis,Age at the time of diagnosis expressed in number of days since birth.,True,,,,Diagnosis -INRG Stage,INRG Stage,INRGStage,"The text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Risk Group (INRG).",False,,"['Not Reported', 'L2', 'Ms', 'Unknown', 'm', 'L1', '']",,Diagnosis -AJCC Clinical T,AJCC Clinical T,AJCCClinicalT,Extent of the primary cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.,False,,"['T2', 'T4a', 'T3a', 'T2b', 'Tis (DCIS)', 'T3c', ""Tis (Paget's)"", 'T4', 'T1b2', 'T2a1', 'T1a2', 'T1b', 'T1b1', 'T1a1', 'Tis', 'TX', 'Unknown', 'T1mi', 'T4d', 'Tis (LCIS)', 'Not Reported', 'T3b', 'T2c', 'T1', 'T4b', 'T1a', 'T2a', 'T3d', 'T2a2', 'T2d', 'T4e', 'T0', 'T1c', 'Ta', 'T4c', 'T3', '']",,Diagnosis -Metastasis at Diagnosis Site,Metastasis at Diagnosis Site,MetastasisatDiagnosisSite,Text term to identify an anatomic site in which metastatic disease involvement is found.,False,,"['Adrenal Gland', 'Lung', 'Soft Tissue', 'Pleura', 'Scalp', 'Brain', 'Liver', 'Groin', 'Small Intestine', 'Axillary', 'Distant Organ', 'Bone', 'Peritoneal Cavity', 'Central Nervous System', 'Unknown', 'Abdomen', 'Ovary', 'Kidney', 'Not Reported', 'Colon', 'Mediastinum', 'Pelvis', 'Inguinal', 'Spinal Cord', 'Bone Marrow', 'Ascites', 'Peritoneum', 'Skin', 'Lymph Node NOS', 'Lymph Node', 'Cerebrospinal Fluid', 'Omentum', 'Distant Nodes', '']",,Diagnosis -Prior Treatment,Prior Treatment,PriorTreatment,A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received before the body specimen was collected.,False,,"['Not Reported', 'Yes', 'No', 'Unknown', 'Not Allowed To Collect', '']",,Diagnosis -Cog Rhabdomyosarcoma Risk Group,Cog Rhabdomyosarcoma Risk Group,CogRhabdomyosarcomaRiskGroup,"Text term used to describe the classification of rhabdomyosarcoma, as defined by the Children's Oncology Group (COG).",False,,"['Not Reported', 'High Risk', 'Intermediate Risk', 'Unknown', 'Low Risk', '']",,Diagnosis -Percent Tumor Invasion,Percent Tumor Invasion,PercentTumorInvasion,The percentage of tumor cells spread locally in a malignant neoplasm through infiltration or destruction of adjacent tissue.,False,,,,Diagnosis -INSS Stage,INSS Stage,INSSStage,"Text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Staging System (INSS).",False,,"['Stage 1', 'Not Reported', 'Stage 4', 'Stage 3', 'Unknown', 'Stage 2B', 'Stage 2A', 'Stage 4S', '']",,Diagnosis -Laterality,Laterality,Laterality,"For tumors in paired organs, designates the side on which the cancer originates.",False,,"['Not Reported', 'Bilateral', 'Midline', 'Unilateral', 'Unknown', 'Left', 'Right', '']",,Diagnosis -Pregnant at Diagnosis,Pregnant at Diagnosis,PregnantatDiagnosis,The text term used to indicate whether the patient was pregnant at the time they were diagnosed.,False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,Diagnosis -Tumor Confined to Organ of Origin,Tumor Confined to Organ of Origin,TumorConfinedtoOrganofOrigin,The yes/no/unknown indicator used to describe whether the tumor is confined to the organ where it originated and did not spread to a proximal or distant location within the body.,False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,Diagnosis -Lymph Nodes Tested,Lymph Nodes Tested,LymphNodesTested,The number of lymph nodes tested to determine whether lymph nodes were involved with disease as determined by a pathologic examination.,False,,,,Diagnosis -AJCC Pathologic T,AJCC Pathologic T,AJCCPathologicT,"Code of pathological T (primary tumor) to define the size or contiguous extension of the primary tumor (T), using staging criteria from the American Joint Committee on Cancer (AJCC).",False,,"['T2', 'T4a', 'T3a', 'T2b', 'Tis (DCIS)', 'T3c', ""Tis (Paget's)"", 'T4', 'T1b2', 'T2a1', 'T1a2', 'T1b', 'T1b1', 'T1a1', 'Tis', 'TX', 'Unknown', 'T1mi', 'T4d', 'Tis (LCIS)', 'Not Reported', 'T3b', 'T2c', 'T1', 'T4b', 'T1a', 'T2a', 'T3d', 'T2a2', 'T2d', 'T4e', 'T0', 'T1c', 'Ta', 'T4c', 'T3', '']",,Diagnosis -WHO CNS Grade,WHO CNS Grade,WHOCNSGrade,WHO CNS Grade,False,,"['Not Reported', 'Grade II', 'Grade IV', 'Grade Not Assigned', 'Unknown', 'Grade III', 'Grade I', '']",,Diagnosis -Method of Diagnosis,Method of Diagnosis,MethodofDiagnosis,Text term used to describe the method used to confirm the patients malignant diagnosis.,False,,"['Pap Smear', 'Bone Marrow Aspirate', 'Blood Draw', 'Enucleation', 'Incisional Biopsy', 'Cystoscopy', 'Biopsy', 'Fine Needle Aspiration', 'Ultrasound Guided Biopsy', 'Unknown', 'Cytology', 'Physical Exam', 'Debulking', 'Not Reported', 'Excisional Biopsy', 'Laparotomy', 'Pathologic Review', 'Surgical Resection', 'Core Biopsy', 'Diagnostic Imaging', 'Other', 'Dilation and Curettage Procedure', 'Laparoscopy', 'Autopsy', 'Thoracentesis', '']",,Diagnosis -INPC Histologic Group,INPC Histologic Group,INPCHistologicGroup,"The text term used to describe the classification of neuroblastomas distinguishing between favorable and unfavorable histologic groups. The histologic score, defined by the International Neuroblastoma Pathology Classification (INPC), is based on age, mitosis-karyorrhexis index (MKI), stromal content and degree of tumor cell differentiation.",False,,"['Unknown', 'Favorable', 'Not Reported', 'Unfavorable', '']",,Diagnosis -Peritoneal Fluid Cytological Status,Peritoneal Fluid Cytological Status,PeritonealFluidCytologicalStatus,The text term used to describe the malignant status of the peritoneal fluid determined by cytologic testing.,False,,"['Atypical', 'Not Reported', 'Unsatisfactory', 'Non-Malignant', 'Unknown', 'Malignant', '']",,Diagnosis -Days to Recurrence,Days to Recurrence,DaystoRecurrence,Number of days between the date used for index and the date the patient's disease recurred.,False,True,," If Progression or Recurrence is ""Yes - Progression or Recurrence"" then ""Days to Recurrence"" is required",Diagnosis -Days to Progression,Days to Progression,DaystoProgression,Number of days between the date used for index and the date the patient's disease progressed.,False,True,," If Progression or Recurrence is ""Yes - Progression or Recurrence"" then ""Days to Progression"" is required",Diagnosis -Progression or Recurrence Type,Progression or Recurrence Type,ProgressionorRecurrenceType,The text term used to describe the type of progressive or recurrent disease or relapsed disease.,False,True,"['Distant', 'Not Reported', 'Unknown', 'Biochemical', 'Regional', 'Local', '']"," If Progression or Recurrence is ""Yes - Progression or Recurrence"" then ""Progression or Recurrence Type"" is required",Diagnosis -Progression or Recurrence Anatomic Site,Progression or Recurrence Anatomic Site,ProgressionorRecurrenceAnatomicSite,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,False,True,"['Paraurethral gland', 'Colon NOS', 'Frontal sinus', 'Overlapping lesion of tongue', 'Overlapping lesion of palate', 'Scrotum NOS', 'Bone marrow', 'Axillary tail of breast', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'unknown primary site', 'Broad ligament', 'Lateral floor of mouth', 'Overlapping lesion of vulva', 'Trigone of bladder', 'Lacrimal gland', 'Thorax NOS', 'Ampulla of Vater', 'Myometrium', 'Penis NOS', 'Female genital tract NOS', 'Submandibular gland', 'Anterior 2/3 of tongue NOS', 'Posterior wall of bladder', 'Thymus', 'Endocrine gland NOS', 'Stomach NOS', 'Unknown', 'Cerebrum', 'Splenic flexure of colon', 'Urachus', 'Skin of lip NOS', 'Mucosa of lip NOS', 'Accessory sinus NOS', 'Cortex of adrenal gland', 'Other ill-defined sites', 'Middle lobe lung', 'Pelvis NOS', 'Anus NOS', 'Upper-inner quadrant of breast', 'Posterior mediastinum', 'Esophagus NOS', 'Duodenum', 'Cervical esophagus', 'Optic nerve', 'Long bones of lower limb and associated joints', 'Middle ear', 'Breast NOS', 'Dorsal surface of tongue NOS', 'Lesser curvature of stomach NOS', 'Overlapping lesion of floor of mouth', 'Overlapping lesion of heart mediastinum and pleura', 'Eye NOS', 'Overlapping lesion of esophagus', 'Ciliary body', 'Ureteric orifice', 'Postcricoid region', 'External ear', 'Base of tongue NOS', 'Liver', 'Commissure of lip', 'Cloacogenic zone', 'Lower lobe lung', 'Transverse colon', 'Acoustic nerve', 'Supraglottis', 'Fallopian tube', 'Upper third of esophagus', 'Skin of scalp and neck', 'Choroid', 'Long bones of upper limb scapula and associated joints', 'Overlapping lesion of brain', 'Upper gum', 'Skin NOS', 'Hard palate', 'Ileum', 'Overlapping lesion of colon', 'Ascending colon', 'Lower gum', 'Pelvic bones sacrum coccyx and associated joints', 'Hepatic flexure of colon', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Vestibule of mouth', 'Cervix uteri', 'Bones of skull and face and associated joints', 'Overlapping lesion of lip oral cavity and pharynx', 'Endometrium', 'Sphenoid sinus', 'Overlapping lesion of ill-defined sites', 'Sigmoid colon', 'Peritoneum NOS', 'Specified parts of peritoneum', 'Meckel diverticulum', 'Rectosigmoid junction', 'Kidney NOS', 'Reticuloendothelial system NOS', 'Rectum NOS', 'Pylorus', 'Overlapping lesion of tonsil', 'Pleura NOS', 'Jejunum', 'Vallecula', 'Skin of lower limb and hip', 'Pelvic lymph nodes', 'External lower lip', 'Overlapping lesion of skin', 'Mucosa of upper lip', 'Ovary', 'Cauda equina', 'Lower limb NOS', 'Body of stomach', 'Overlapping lesion of larynx', 'Pancreas NOS', 'Overlapping lesion of lung', 'Overlapping lesion of major salivary glands', 'Uvula', 'Overlapping lesion of hypopharynx', 'Round ligament', 'Corpus uteri', 'Biliary tract NOS', 'Male genital organs NOS', 'Parametrium', 'External lip NOS', 'Overlapping lesion of accessory sinuses', 'Cardia NOS', 'Islets of Langerhans', 'Carotid body', 'Ventral surface of tongue NOS', 'Autonomic nervous system NOS', 'Overlapping lesion of corpus uteri', 'Spinal meninges', 'Posterior wall of nasopharynx', 'Placenta', 'Intrahepatic bile duct', 'Overlapping lesion of digestive system', 'Mediastinum NOS', 'Hematopoietic system NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Major salivary gland NOS', 'Cerebellum NOS', 'Overlapping lesion of stomach', 'Vulva NOS', 'Craniopharyngeal duct', 'Lung NOS', 'Greater curvature of stomach NOS', 'Upper-outer quadrant of breast', 'Gallbladder', 'Thoracic esophagus', 'Lymph nodes of axilla or arm', 'Ventricle NOS', 'Overlapping lesion of biliary tract', 'Hypopharynx NOS', 'Clitoris', 'Exocervix', 'Parietal lobe', 'Waldeyer ring', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Head face or neck NOS', 'Anterior wall of nasopharynx', 'Urethra', 'Overlapping lesion of nasopharynx', 'Maxillary sinus', 'Lymph nodes of inguinal region or leg', 'Ureter', 'Tonsillar pillar', 'Sublingual gland', 'Pituitary gland', 'Gastrointestinal tract NOS', 'Pineal gland', 'Meninges NOS', 'Lingual tonsil', 'Trachea', 'Pyriform sinus', 'Mucosa of lower lip', 'Not Reported', 'Posterior wall of hypopharynx', 'Urinary system NOS', 'Orbit NOS', 'Short bones of lower limb and associated joints', 'Connective subcutaneous and other soft tissues of thorax', 'Upper limb NOS', 'Gastric antrum', 'Lymph node NOS', 'Peripheral nerves and autonomic nervous system of thorax', 'Ill-defined sites within respiratory system', 'Other specified parts of male genital organs', 'Rib sternum clavicle and associated joints', 'Overlapping lesion of bladder', 'Appendix', 'Prostate gland', 'Lymph nodes of multiple regions', 'Lateral wall of nasopharynx', 'Branchial cleft', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Floor of mouth NOS', 'Connective subcutaneous and other soft tissues NOS', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Bladder neck', 'Border of tongue', 'Connective subcutaneous and other soft tissues of abdomen', 'Overlapping lesion of small intestine', 'Lateral wall of bladder', 'Soft palate NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Isthmus uteri', 'Nasal cavity', 'Endocervix', 'Tonsil NOS', 'Glottis', 'Retroperitoneum', 'Peripheral nerves and autonomic nervous system of pelvis', 'Frontal lobe', 'Vagina NOS', 'Undescended testis', 'Laryngeal cartilage', 'Eyelid', 'Hypopharyngeal aspect of aryepiglottic fold', 'Overlapping lesion of other and unspecified parts of mouth', 'Upper lobe lung', 'Lip NOS', 'Lymph nodes of head face and neck', 'Overlapping lesion of brain and central nervous system', 'Overlapping lesion of penis', 'Overlapping lesion of retroperitoneum and peritoneum', 'Parotid gland', 'Dome of bladder', 'Bone of limb NOS', 'Descended testis', 'Vertebral column', 'Fundus uteri', 'Connective subcutaneous and other soft tissues of pelvis', 'Epididymis', 'Intra-abdominal lymph nodes', 'Prepuce', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Pharynx NOS', 'Overlapping lesion of endocrine glands and related structures', 'Gum NOS', 'Spinal cord', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Skin of upper limb and shoulder', 'Nasopharynx NOS', 'Parathyroid gland', 'Bone NOS', 'Mouth NOS', 'Abdomen NOS', 'Conjunctiva', 'Spermatic cord', 'External upper lip', 'Labium minus', 'Renal pelvis', 'Overlapping lesion of lip', 'Short bones of upper limb and associated joints', 'Main bronchus', 'Upper respiratory tract NOS', 'Body of penis', 'Small intestine NOS', 'Central portion of breast', 'Lower-inner quadrant of breast', 'Labium majus', 'Tonsillar fossa', 'Cecum', 'Glans penis', 'Tail of pancreas', 'Lower third of esophagus', 'Body of pancreas', 'Intestinal tract NOS', 'Brain stem', 'Overlapping lesion of rectum anus and anal canal', 'Posterior wall of oropharynx', 'Pancreatic duct', 'Blood', 'Temporal lobe', 'Anterior floor of mouth', 'Nervous system NOS', 'Cornea NOS', 'Palate NOS', 'Occipital lobe', 'Abdominal esophagus', 'Overlapping lesion of pancreas', 'Overlapping lesion of female genital organs', 'Cheek mucosa', 'Retina', 'Overlapping lesion of male genital organs', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Larynx NOS', 'Skin of other and unspecified parts of face', 'Spleen', 'Oropharynx NOS', 'Anal canal', 'Subglottis', 'Cerebral meninges', 'Lateral wall of oropharynx', 'Middle third of esophagus', 'Nipple', 'Medulla of adrenal gland', 'Overlapping lesion of eye and adnexa', 'Olfactory nerve', 'Ethmoid sinus', 'Overlapping lesion of cervix uteri', 'Descending colon', 'Brain NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Anterior wall of bladder', 'Mandible', 'Other specified parts of pancreas', 'Skin of trunk', 'Other specified parts of female genital organs', 'Uterus NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Intrathoracic lymph nodes', 'Heart', 'Adrenal gland NOS', 'Aortic body and other paraganglia', 'Extrahepatic bile duct', 'Overlapping lesion of breast', 'Superior wall of nasopharynx', 'Fundus of stomach', 'Anterior mediastinum', 'Tongue NOS', 'Cranial nerve NOS', 'Head of pancreas', 'Overlapping lesions of oropharynx', 'Overlapping lesion of bones joints and articular cartilage', 'Retromolar area', 'Testis NOS', 'Connective subcutaneous and other soft tissues of head face and neck', 'Bladder NOS', 'Overlapping lesion of urinary organs', 'Lower-outer quadrant of breast', 'Thyroid gland', 'Anterior surface of epiglottis', 'Uterine adnexa', '']"," If Progression or Recurrence is ""Yes - Progression or Recurrence"" then ""Progression or Recurrence Anatomic Site"" is required",Diagnosis -Days to Progression Free,Days to Progression Free,DaystoProgressionFree,Number of days between the date used for index and the date the patient's disease was formally confirmed as progression-free.,False,True,," If Progression or Recurrence is ""Yes - Progression or Recurrence"" then ""Days to Progression Free"" is required",Diagnosis -Treatment Outcome,Treatment Outcome,TreatmentOutcome,Text term that describes the patient's final outcome after the treatment was administered.,False,,"['Progressive Disease', 'Stable Disease', 'Very Good Partial Response', 'Not Reported', 'Treatment Ongoing', 'Complete Response', 'No Response', 'Persistent Disease', 'Partial Response', 'Mixed Response', 'Treatment Stopped Due to Toxicity', 'Unknown', 'No Measurable Disease', '']",,Therapy -Chemo Concurrent to Radiation,Chemo Concurrent to Radiation,ChemoConcurrenttoRadiation,The text term used to describe whether the patient was receiving chemotherapy concurrent to radiation.,False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,Therapy -Treatment Arm,Treatment Arm,TreatmentArm,Text term used to describe the treatment arm assigned to a patient at the time eligibility is determined.,False,,"['E4512', 'EA5142', 'A081105', '']",,Therapy -Treatment Effect Indicator,Treatment Effect Indicator,TreatmentEffectIndicator,The text term used to indicate whether the treatment had an effect on the patient.,False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,Therapy -Treatment Dose,Treatment Dose,TreatmentDose,The numeric value used to describe the dose of an agent the patient received.,False,,,,Therapy -Initial Disease Status,Initial Disease Status,InitialDiseaseStatus,The text term used to describe the status of the patient's malignancy when the treatment began.,False,,"['Progressive Disease', 'Initial Diagnosis', 'Not Reported', 'Recurrent Disease', 'Residual Disease', 'Unknown', '']",,Therapy -Days to Treatment End,Days to Treatment End,DaystoTreatmentEnd,Number of days between the date used for index and the date the treatment ended.,False,,,,Therapy -Regimen or Line of Therapy,Regimen or Line of Therapy,RegimenorLineofTherapy,The text term used to describe the regimen or line of therapy.,False,,,,Therapy -Treatment Frequency,Treatment Frequency,TreatmentFrequency,The text term used to describe the frequency the patient received an agent or regimen.,False,,"['Once Weekly', 'Not Reported', 'Every Hour', 'Three Times Daily', 'Five Times Daily', 'Twice Weekly', 'Four Times Daily', 'Unknown', 'Every Other Day', 'Every 24 Hours', 'Twice Daily', '']",,Therapy -Treatment Dose Units,Treatment Dose Units,TreatmentDoseUnits,The text term used to describe the dose units of an agent the patient received.,False,,"['cGy', 'Gy', '']",,Therapy -Therapeutic Agents,Therapeutic Agents,TherapeuticAgents,Text identification of the individual agent(s) used as part of a treatment regimen.,False,,,,Therapy -Treatment Type,Treatment Type,TreatmentType,Text term that describes the kind of treatment administered.,False,,,,Therapy -Reason Treatment Ended,Reason Treatment Ended,ReasonTreatmentEnded,The text term used to describe the reason a specific treatment or regimen ended.,False,,"['Adverse Therapy Event', 'Disease Progression', 'Other', 'Death', 'Withdrawal by Subject', 'Course of Therapy Completed', '']",,Therapy -Treatment Effect,Treatment Effect,TreatmentEffect,The text term used to describe the pathologic effect a treatment(s) had on the tumor.,False,,"['Not Reported', 'Unknown', 'Complete Necrosis (No Viable Tumor)', 'Incomplete Necrosis (Viable Tumor Present)', 'No Necrosis', '']",,Therapy -Treatment or Therapy,Treatment or Therapy,TreatmentorTherapy,A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received.,False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,Therapy -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,Therapy -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Therapy -Treatment Anatomic Site,Treatment Anatomic Site,TreatmentAnatomicSite,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,False,,"['Paraurethral gland', 'Colon NOS', 'Frontal sinus', 'Overlapping lesion of tongue', 'Overlapping lesion of palate', 'Scrotum NOS', 'Bone marrow', 'Axillary tail of breast', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'unknown primary site', 'Broad ligament', 'Lateral floor of mouth', 'Overlapping lesion of vulva', 'Trigone of bladder', 'Lacrimal gland', 'Thorax NOS', 'Ampulla of Vater', 'Myometrium', 'Penis NOS', 'Female genital tract NOS', 'Submandibular gland', 'Anterior 2/3 of tongue NOS', 'Posterior wall of bladder', 'Thymus', 'Endocrine gland NOS', 'Stomach NOS', 'Unknown', 'Cerebrum', 'Splenic flexure of colon', 'Urachus', 'Skin of lip NOS', 'Mucosa of lip NOS', 'Accessory sinus NOS', 'Cortex of adrenal gland', 'Other ill-defined sites', 'Middle lobe lung', 'Pelvis NOS', 'Anus NOS', 'Upper-inner quadrant of breast', 'Posterior mediastinum', 'Esophagus NOS', 'Duodenum', 'Cervical esophagus', 'Optic nerve', 'Long bones of lower limb and associated joints', 'Middle ear', 'Breast NOS', 'Dorsal surface of tongue NOS', 'Lesser curvature of stomach NOS', 'Overlapping lesion of floor of mouth', 'Overlapping lesion of heart mediastinum and pleura', 'Eye NOS', 'Overlapping lesion of esophagus', 'Ciliary body', 'Ureteric orifice', 'Postcricoid region', 'External ear', 'Base of tongue NOS', 'Liver', 'Commissure of lip', 'Cloacogenic zone', 'Lower lobe lung', 'Transverse colon', 'Acoustic nerve', 'Supraglottis', 'Fallopian tube', 'Upper third of esophagus', 'Skin of scalp and neck', 'Choroid', 'Long bones of upper limb scapula and associated joints', 'Overlapping lesion of brain', 'Upper gum', 'Skin NOS', 'Hard palate', 'Ileum', 'Overlapping lesion of colon', 'Ascending colon', 'Lower gum', 'Pelvic bones sacrum coccyx and associated joints', 'Hepatic flexure of colon', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Vestibule of mouth', 'Cervix uteri', 'Bones of skull and face and associated joints', 'Overlapping lesion of lip oral cavity and pharynx', 'Endometrium', 'Sphenoid sinus', 'Overlapping lesion of ill-defined sites', 'Sigmoid colon', 'Peritoneum NOS', 'Specified parts of peritoneum', 'Meckel diverticulum', 'Rectosigmoid junction', 'Kidney NOS', 'Reticuloendothelial system NOS', 'Rectum NOS', 'Pylorus', 'Overlapping lesion of tonsil', 'Pleura NOS', 'Jejunum', 'Vallecula', 'Skin of lower limb and hip', 'Pelvic lymph nodes', 'External lower lip', 'Overlapping lesion of skin', 'Mucosa of upper lip', 'Ovary', 'Cauda equina', 'Lower limb NOS', 'Body of stomach', 'Overlapping lesion of larynx', 'Pancreas NOS', 'Overlapping lesion of lung', 'Overlapping lesion of major salivary glands', 'Uvula', 'Overlapping lesion of hypopharynx', 'Round ligament', 'Corpus uteri', 'Biliary tract NOS', 'Male genital organs NOS', 'Parametrium', 'External lip NOS', 'Overlapping lesion of accessory sinuses', 'Cardia NOS', 'Islets of Langerhans', 'Carotid body', 'Ventral surface of tongue NOS', 'Autonomic nervous system NOS', 'Overlapping lesion of corpus uteri', 'Spinal meninges', 'Posterior wall of nasopharynx', 'Placenta', 'Intrahepatic bile duct', 'Overlapping lesion of digestive system', 'Mediastinum NOS', 'Hematopoietic system NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Major salivary gland NOS', 'Cerebellum NOS', 'Overlapping lesion of stomach', 'Vulva NOS', 'Craniopharyngeal duct', 'Lung NOS', 'Greater curvature of stomach NOS', 'Upper-outer quadrant of breast', 'Gallbladder', 'Thoracic esophagus', 'Lymph nodes of axilla or arm', 'Ventricle NOS', 'Overlapping lesion of biliary tract', 'Hypopharynx NOS', 'Clitoris', 'Exocervix', 'Parietal lobe', 'Waldeyer ring', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Head face or neck NOS', 'Anterior wall of nasopharynx', 'Urethra', 'Overlapping lesion of nasopharynx', 'Maxillary sinus', 'Lymph nodes of inguinal region or leg', 'Ureter', 'Tonsillar pillar', 'Sublingual gland', 'Pituitary gland', 'Gastrointestinal tract NOS', 'Pineal gland', 'Meninges NOS', 'Lingual tonsil', 'Trachea', 'Pyriform sinus', 'Mucosa of lower lip', 'Not Reported', 'Posterior wall of hypopharynx', 'Urinary system NOS', 'Orbit NOS', 'Short bones of lower limb and associated joints', 'Connective subcutaneous and other soft tissues of thorax', 'Upper limb NOS', 'Gastric antrum', 'Lymph node NOS', 'Peripheral nerves and autonomic nervous system of thorax', 'Ill-defined sites within respiratory system', 'Other specified parts of male genital organs', 'Rib sternum clavicle and associated joints', 'Overlapping lesion of bladder', 'Appendix', 'Prostate gland', 'Lymph nodes of multiple regions', 'Lateral wall of nasopharynx', 'Branchial cleft', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Floor of mouth NOS', 'Connective subcutaneous and other soft tissues NOS', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Bladder neck', 'Border of tongue', 'Connective subcutaneous and other soft tissues of abdomen', 'Overlapping lesion of small intestine', 'Lateral wall of bladder', 'Soft palate NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Isthmus uteri', 'Nasal cavity', 'Endocervix', 'Tonsil NOS', 'Glottis', 'Retroperitoneum', 'Peripheral nerves and autonomic nervous system of pelvis', 'Frontal lobe', 'Vagina NOS', 'Undescended testis', 'Laryngeal cartilage', 'Eyelid', 'Hypopharyngeal aspect of aryepiglottic fold', 'Overlapping lesion of other and unspecified parts of mouth', 'Upper lobe lung', 'Lip NOS', 'Lymph nodes of head face and neck', 'Overlapping lesion of brain and central nervous system', 'Overlapping lesion of penis', 'Overlapping lesion of retroperitoneum and peritoneum', 'Parotid gland', 'Dome of bladder', 'Bone of limb NOS', 'Descended testis', 'Vertebral column', 'Fundus uteri', 'Connective subcutaneous and other soft tissues of pelvis', 'Epididymis', 'Intra-abdominal lymph nodes', 'Prepuce', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Pharynx NOS', 'Overlapping lesion of endocrine glands and related structures', 'Gum NOS', 'Spinal cord', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Skin of upper limb and shoulder', 'Nasopharynx NOS', 'Parathyroid gland', 'Bone NOS', 'Mouth NOS', 'Abdomen NOS', 'Conjunctiva', 'Spermatic cord', 'External upper lip', 'Labium minus', 'Renal pelvis', 'Overlapping lesion of lip', 'Short bones of upper limb and associated joints', 'Main bronchus', 'Upper respiratory tract NOS', 'Body of penis', 'Small intestine NOS', 'Central portion of breast', 'Lower-inner quadrant of breast', 'Labium majus', 'Tonsillar fossa', 'Cecum', 'Glans penis', 'Tail of pancreas', 'Lower third of esophagus', 'Body of pancreas', 'Intestinal tract NOS', 'Brain stem', 'Overlapping lesion of rectum anus and anal canal', 'Posterior wall of oropharynx', 'Pancreatic duct', 'Blood', 'Temporal lobe', 'Anterior floor of mouth', 'Nervous system NOS', 'Cornea NOS', 'Palate NOS', 'Occipital lobe', 'Abdominal esophagus', 'Overlapping lesion of pancreas', 'Overlapping lesion of female genital organs', 'Cheek mucosa', 'Retina', 'Overlapping lesion of male genital organs', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Larynx NOS', 'Skin of other and unspecified parts of face', 'Spleen', 'Oropharynx NOS', 'Anal canal', 'Subglottis', 'Cerebral meninges', 'Lateral wall of oropharynx', 'Middle third of esophagus', 'Nipple', 'Medulla of adrenal gland', 'Overlapping lesion of eye and adnexa', 'Olfactory nerve', 'Ethmoid sinus', 'Overlapping lesion of cervix uteri', 'Descending colon', 'Brain NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Anterior wall of bladder', 'Mandible', 'Other specified parts of pancreas', 'Skin of trunk', 'Other specified parts of female genital organs', 'Uterus NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Intrathoracic lymph nodes', 'Heart', 'Adrenal gland NOS', 'Aortic body and other paraganglia', 'Extrahepatic bile duct', 'Overlapping lesion of breast', 'Superior wall of nasopharynx', 'Fundus of stomach', 'Anterior mediastinum', 'Tongue NOS', 'Cranial nerve NOS', 'Head of pancreas', 'Overlapping lesions of oropharynx', 'Overlapping lesion of bones joints and articular cartilage', 'Retromolar area', 'Testis NOS', 'Connective subcutaneous and other soft tissues of head face and neck', 'Bladder NOS', 'Overlapping lesion of urinary organs', 'Lower-outer quadrant of breast', 'Thyroid gland', 'Anterior surface of epiglottis', 'Uterine adnexa', '']",,Therapy -Number of Cycles,Number of Cycles,NumberofCycles,The numeric value used to describe the number of cycles of a specific treatment or regimen the patient received.,False,,,,Therapy -Treatment Intent Type,Treatment Intent Type,TreatmentIntentType,Text term to identify the reason for the administration of a treatment regimen. [Manually-curated],False,,"['Palliative', 'Cure', 'Not Reported', 'Cancer Control', 'Unknown', 'Prevention', 'Neoadjuvant', 'Adjuvant', '']",,Therapy -Days to Treatment Start,Days to Treatment Start,DaystoTreatmentStart,Number of days between the date used for index and the date the treatment started.,False,,,,Therapy -Loci Count,Loci Count,LociCount,Numeric value used to describe the number of loci tested.,False,,,,MolecularTest -Loci Abnormal Count,Loci Abnormal Count,LociAbnormalCount,Numeric value used to describe the number of loci determined to be abnormal.,False,,,,MolecularTest -Mismatch Repair Mutation,Mismatch Repair Mutation,MismatchRepairMutation,The yes/no/unknown indicator used to describe whether the mutation included in molecular testing was known to have an affect on the mismatch repair process. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,MolecularTest -Locus,Locus,Locus,Alphanumeric value used to describe the locus of a specific genetic variant. Example: NM_001126114.,False,,,,MolecularTest -Second Exon,Second Exon,SecondExon,"The second exon number involved in molecular variation. If a specific genetic variant is being reported, this property can be used to capture the second exon where that variant is located. This property is typically used for a translocation where two different locations are involved in the variation.",False,,,,MolecularTest -Second Gene Symbol,Second Gene Symbol,SecondGeneSymbol,"The text term used to describe a secondary gene targeted or included in molecular analysis. For rearrangements, this is should represent the location of the variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,,,MolecularTest -Specialized Molecular Test,Specialized Molecular Test,SpecializedMolecularTest,Text term used to describe a specific test that is not covered in the list of molecular analysis methods. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,,,MolecularTest -Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,MolecularTest -Gene Symbol,Gene Symbol,GeneSymbol,"The text term used to describe a gene targeted or included in molecular analysis. For rearrangements, this is should be used to represent the reference gene. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",True,,,,MolecularTest -Antigen,Antigen,Antigen,The text term used to describe an antigen included in molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['CD33', 'CD138', 'CD15', 'CD25', 'Mesothelin', 'CD14', 'CD20', 'CD79A', 'CD3', 'CCND1', 'NSE', 'CD23', 'CD34', 'CD22', 'Unknown', 'CD56', 'CD45', 'CA19-9', 'CD117', 'HLA-DR', 'CD30', 'Not Reported', 'CD5', 'CD7', 'Squamous Cell Carcinoma Antigen', 'CD10', 'BCL6', 'CD19', 'CA-125', 'CEA', '']",,MolecularTest -Histone Family,Histone Family,HistoneFamily,"The text term used to describe the family, or classification of a group of basic proteins found in chromatin, called histones.",False,,"['Not Reported', 'H3', 'H2A', 'H4', 'H1', 'Unknown', 'H2B', '']",,MolecularTest -Test Value,Test Value,TestValue,The text term or numeric value used to describe a specific result of a molecular test. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here,False,,,,MolecularTest -Exon,Exon,Exon,"Exon number targeted or included in a molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the exon where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,,,MolecularTest -Molecular Analysis Method,Molecular Analysis Method,MolecularAnalysisMethod,The text term used to describe the method used for molecular analysis. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,True,,"['Not Applicable', 'WGS', 'Targeted Sequencing', 'FISH', 'IHC', 'Unknown', 'Microarray', 'Cytogenetics NOS', 'Nuclear Staining', 'Microsatellite Analysis', 'Sequencing NOS', 'Comparative Genomic Hybridization', 'Not Reported', 'Flow Cytometry', 'Southern Blotting', 'ISH', 'RNA Sequencing', 'Other', 'RT-PCR', 'WXS', 'Karyotype']",,MolecularTest -Variant Origin,Variant Origin,VariantOrigin,The text term used to describe the biological origin of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Unknown', 'Germline', 'Somatic', '']",,MolecularTest -Test Result,Test Result,TestResult,The text term used to describe the result of the molecular test. If the test result was a numeric value see test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,True,,"['Equivocal', 'Copy Number Reported', 'Abnormal NOS', 'Not Reported', 'Low', 'Overexpressed', 'Test Value Reported', 'Intermediate', 'Not Applicable', 'Positive', 'Unknown', 'High', 'Normal', 'Negative', 'Loss of Expression']",,MolecularTest -Histone Variant,Histone Variant,HistoneVariant,"The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.",False,,"['H2A.Z', 'H2A.Z.1', 'H3t (H3.4)', 'mH2A.2', 'H2A-Bbd', 'Unknown', 'H3.5', 'H3.2', 'mH2A.1', 'Not Reported', 'H2A.Z.2.2', 'mH2A', 'H2A.Z.2', 'H3.Y', 'H3.X', 'H3.1', 'H3.3', 'CENP-A', 'H2A.X', '']",,MolecularTest -Molecular Consequence,Molecular Consequence,MolecularConsequence,The text term used to describe the molecular consequence of genetic variation. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Start Lost', 'Stop Lost', 'Splice Region Variant', 'Mature miRNA Variant', 'Intron Variant', 'Missense Variant', 'TFBS Amplification', 'Feature Elongation', 'Non-coding Transcript Variant', '3 Prime UTR Variant', 'Regulatory Region Ablation', 'Splice Acceptor Variant', 'Frameshift Variant', 'Inframe Insertion', 'Intergenic Variant', 'Regulatory Region Variant', 'Feature Truncation', 'Protein Altering Variant', 'Upstream Gene Variant', 'Transcript Amplification', 'Stop Retained Variant', 'NMD Transcript Variant', 'Regulatory Region Amplification', 'Splice Donor Variant', 'Inframe Deletion', 'Non-coding Transcript Exon Variant', 'Coding Sequence Variant', 'TF Binding Site Variant', 'TFBS Ablation', 'Stop Gain', 'Downstream Gene Variant', 'Transcript Ablation', '5 Prime UTR Variant', 'Synonymous Variant', 'Incomplete Terminal Codon Variant', '']",,MolecularTest -Blood Test Normal Range Upper,Blood Test Normal Range Upper,BloodTestNormalRangeUpper,Numeric value used to describe the upper limit of the normal range used to describe a healthy individual at the institution where the test was completed.,False,,,,MolecularTest -Stop Days from Index,Stop Days from Index,StopDaysfromIndex,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'",False,,,,MolecularTest -Test Units,Test Units,TestUnits,The text term used to describe the units of the test value for a molecular test. This property is used in conjunction with test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,,,MolecularTest -Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,MolecularTest -Copy Number,Copy Number,CopyNumber,"Numeric value used to describe the number of times a section of the genome is repeated or copied within an insertion, duplication or deletion variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,,,MolecularTest -Variant Type,Variant Type,VariantType,The text term used to describe the type of genetic variation.,False,,"['Chrimerism', 'Inversion', 'Extension', 'Loss', 'Splice', 'Unknown', 'Substitution', 'Insertion', 'Partial Methylation', 'Translocation', 'Amplification', 'Duplication', 'Not Reported', 'Mosaicism', 'Conversion', 'Hypermethylation', 'Methylation', 'Repeated Sequences', 'Alleles', 'Deletion-Insertion', 'Gain', 'Other', 'Rearrangement', 'Deletion', '']",,MolecularTest -Ploidy,Ploidy,Ploidy,Text term used to describe the number of sets of homologous chromosomes.,False,,"['Not Reported', 'Diploid', 'Hypodiploid', 'Unknown', 'Near Diploid', 'Hyperdiploid', 'Aneuploid', 'Tetraploid', '']",,MolecularTest -Pathogenicity,Pathogenicity,Pathogenicity,The text used to describe a variant's level of involvement in the cause of the patient's disease according to the standards outlined by the American College of Medical Genetics and Genomics (ACMG).,False,,"['Benign', 'Uncertain Significance', 'Likely Pathogenic', 'Pathogenic', 'Likely Benign', '']",,MolecularTest -Transcript,Transcript,Transcript,Alphanumeric value used to describe the transcript of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,,,MolecularTest -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,MolecularTest -Zygosity,Zygosity,Zygosity,The text term used to describe the zygosity of a specific genetic variant.,False,,"['Hemizygous', 'Homozygous', 'Not Reported', 'Heterozygous', 'Nullizygous', 'Unknown', '']",,MolecularTest -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MolecularTest -Cell Count,Cell Count,CellCount,Numeric value used to describe the number of cells used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,,,MolecularTest -Cytoband,Cytoband,Cytoband,"Alphanumeric value used to describe the cytoband or chromosomal location targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the cytoband where the variant is located. Format: [chromosome][chromosome arm].[band+sub-bands]. Example: 17p13.1. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,,,MolecularTest -AA Change,AA Change,AAChange,Alphanumeric value used to describe the amino acid change for a specific genetic variant. Example: R116Q. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,,,MolecularTest -Intron,Intron,Intron,"Intron number targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the intron where that variant is located.",False,,,,MolecularTest -Blood Test Normal Range Lower,Blood Test Normal Range Lower,BloodTestNormalRangeLower,Numeric value used to describe the lower limit of the normal range used to describe a healthy individual at the institution where the test was completed.,False,,,,MolecularTest -Test Analyte Type,Test Analyte Type,TestAnalyteType,The text term used to describe the type of analyte used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Protein Analyte', 'Not Reported', 'Total RNA', 'Unknown', 'miRNA', 'mRNA', 'DNA', '']",,MolecularTest -Clonality,Clonality,Clonality,The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Clonal', 'Non-clonal', '']",,MolecularTest -Clinical Biospecimen Type,Clinical Biospecimen Type,ClinicalBiospecimenType,"The text term used to describe the biological material used for testing, diagnostic, treatment or research purposes. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,"['Serum', 'Granulocyte', 'Pleural Fluid', 'Soft Tissue', 'Connective Tissue', 'Muscle Tissue', 'Blood', 'Feces', 'Buccal Mucosa', 'Embryonic Fluid', 'Nerve Tissue', 'Unknown', 'Not Reported', 'Embryonic Tissue', 'Urine', 'Bone Marrow', 'Peritoneal Fluid', 'Buffy Coat', 'Skin', 'Plasma', 'Saliva', 'Tissue NOS', 'Cerebrospinal Fluid', 'Uninvolved Tissue NOS', '']",,MolecularTest -Chromosome,Chromosome,Chromosome,"The text term used to describe a chromosome targeted or included in molecular testing. If a specific genetic variant is being reported, this property can be used to capture the chromosome where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,"['chr4', 'chrX', 'chr3', 'chr13', 'chr1', 'chr19', 'chr5', 'Unknown', 'chr16', 'chr7', 'chr10', 'chr12', 'Not Reported', 'chrM', 'chrY', 'chr2', 'chr21', 'chr23', 'chr17', 'chr11', 'chr15', 'chr9', 'chr22', 'chr6', 'chr14', 'chr8', 'chr20', 'chr18', '']",,MolecularTest -Laboratory Test,Laboratory Test,LaboratoryTest,"The text term used to describe the medical testing used to diagnose, treat or further understand a patient's disease.",False,,"['Blood Urea Nitrogen', 'Hemoglobin', 'Lymphocytes', 'Calcium', 'C-Reactive Protein', 'Human Papillomavirus', 'Kappa', 'Lambda', 'Total Bilirubin', 'Beta 2 Microglobulin', 'Cellularity', 'Eosinophil', 'M Protein', 'Immunoglobulin M', 'Epstein-Barr Virus', 'Leukocytes', 'Unknown', 'Metamyelocytes', 'Myeloblasts', 'Circulating Tumor Cells', 'Prolymphocytes', 'Alpha Fetoprotein', 'Basophil', 'Not Reported', 'Segmented Neutrophil', 'Testosterone', 'Immunoglobulin G', 'Total Protein', 'Creatinine', 'Glucose', 'Serum Free Immunoglobulin Light Chain', 'HPV-E6/E7', 'Hematocrit', 'Lymphoblasts', 'Promonocytes', 'B-cell genotyping', 'Myelocytes', 'Neutrophil Bands', 'NOS', 'Luteinizing Hormone', 'Immunoglobulin A', 'Absolute Neutrophil', 'Albumin', 'Promyelocytes', 'Lactate Dehydrogenase', 'Human Chorionic Gonadotropin', 'Platelets', '']",,MolecularTest -Lysis Buffer,Lysis Buffer,LysisBuffer,scRNA-seq specific: Type of lysis buffer used,False,,,,Biospecimen -Dysplasia Fraction,Dysplasia Fraction,DysplasiaFraction,Resulting value to represent the number of pieces of dysplasia divided by the total number of pieces. [Text: max length 5],False,,,,Biospecimen -Method of Nucleic Acid Isolation,Method of Nucleic Acid Isolation,MethodofNucleicAcidIsolation,"Bulk RNA & DNA-seq specific: method used for nucleic acid isolation. E.g. Qiagen Allprep, Qiagen miRNAeasy. [Text - max length 100]",False,,,,Biospecimen -Fixative Type,Fixative Type,FixativeType,Text term to identify the type of fixative used to preserve a tissue specimen,True,,"['95% Ethanol', 'Dimidoester', 'Acetone', 'RNAlater', 'Polaxamer', 'Glutaraldehyde', 'Cryo-store', 'Carbodiimide', 'OCT media', 'None', 'Formalin', 'Methacarn', 'Unknown', 'NP40 lysis buffer', 'PAXgene tissue', 'Para-benzoquinone', 'Alcohol', 'TCL lysis buffer', 'Dimethylacetamide', 'Saline', 'Other', ""Carnoy's Fixative""]",,Biospecimen -Histology Assessment By,Histology Assessment By,HistologyAssessmentBy,Text term describing who (in what role) made the histological assessments of the sample,False,,"['Unknown', 'Research Scientist', 'Pathologist', 'Other', '']",,Biospecimen -Biospecimen Type,Biospecimen Type,BiospecimenType,Biospecimen Type,True,,"['Bone Marrow Biospecimen Type', 'Tissue Biospecimen Type', 'Stool Biospecimen Type', 'Fluids Biospecimen Type', 'Cells Biospecimen Type', 'Urine Biospecimen Type', 'Blood Biospecimen Type', 'Ascites Biospecimen Type', 'Analyte Biospecimen Type', 'Mouth Rinse Biospecimen Type', 'Sputum Biospecimen Type']",,Biospecimen -Degree of Dysplasia,Degree of Dysplasia,DegreeofDysplasia,Information related to the presence of cells that look abnormal under a microscope but are not cancer. Records the degree of dysplasia for the cyst or lesion under consideration.,False,,"['Normal or basal cell hyperplasia or metaplasia', 'Carcinoma in Situ', 'Unknown', 'Severe dysplasia', 'Mild dysplasia', 'Moderate dysplasia', '']",,Biospecimen -Slicing Method,Slicing Method,SlicingMethod,Imaging specific: the method by which the tissue was sliced.,False,,"['Tissue molds', 'Not Reported', 'Vibratome', 'Sectioning', 'Other', 'Unknown', 'Sliding microtome', 'Cryosectioning', '']",,Biospecimen -Percent Monocyte Infiltration,Percent Monocyte Infiltration,PercentMonocyteInfiltration,Numeric value to represent the percentage of monocyte infiltration in a sample or specimen.,False,,,,Biospecimen -HTAN Parent ID,HTAN Parent ID,HTANParentID,HTAN ID of parent from which the biospecimen was obtained. Parent could be another biospecimen or a research participant.,True,,,,Biospecimen -Percent Eosinophil Infiltration,Percent Eosinophil Infiltration,PercentEosinophilInfiltration,Numeric value to represent the percentage of infiltration by eosinophils in a tumor sample or specimen.,False,,,,Biospecimen -Percent Tumor Nuclei,Percent Tumor Nuclei,PercentTumorNuclei,Numeric value to represent the percentage of tumor nuclei in a malignant neoplasm sample or specimen.,False,,,,Biospecimen -Percent Necrosis,Percent Necrosis,PercentNecrosis,Numeric value to represent the percentage of cell death in a malignant tumor sample or specimen.,False,,,,Biospecimen -Percent Granulocyte Infiltration,Percent Granulocyte Infiltration,PercentGranulocyteInfiltration,Numeric value to represent the percentage of infiltration by granulocytes in a tumor sample or specimen.,False,,,,Biospecimen -Percent Stromal Cells,Percent Stromal Cells,PercentStromalCells,"Numeric value to represent the percentage of reactive cells that are present in a malignant tumor sample or specimen but are not malignant such as fibroblasts, vascular structures, etc.",False,,,,Biospecimen -Source HTAN Biospecimen ID,Source HTAN Biospecimen ID,SourceHTANBiospecimenID,This is the HTAN ID that may have been assigned to the biospecimen at the site of biospecimen origin (e.g. BU).,False,,,,Biospecimen -HTAN Biospecimen ID,HTAN Biospecimen ID,HTANBiospecimenID,HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,Biospecimen -Collection Days from Index,Collection Days from Index,CollectionDaysfromIndex,Number of days from the research participant's index date that the biospecimen was obtained.,True,,,,Biospecimen -Site Data Source,Site Data Source,SiteDataSource,"Text to identify the data source for the specimen/sample from within the HTAN center, if applicable. Any identifier used within the center to identify data sources. No PHI/PII is allowed.",False,,,,Biospecimen -Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,Biospecimen -Number Proliferating Cells,Number Proliferating Cells,NumberProliferatingCells,Numeric value that represents the count of proliferating cells determined during pathologic review of the sample slide(s).,False,,,,Biospecimen -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,Biospecimen -Preinvasive Morphology,Preinvasive Morphology,PreinvasiveMorphology,"Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the HTAN",False,,"['Melanoma in situ - superficial spreading', 'Invasive melanoma - other', 'Benign tumor NOS', 'No diagnosis possible', 'Melanoma in situ - lentigo maligna type', 'Normal WDA', 'Persistent melanoma in situ', 'Atypical adenomatous hyperplasia', 'Squamous Carcinoma in situ', 'Invasive melanoma - nevoid', 'Invasive melanoma - nodular type', 'Severe dysplasia', 'Reserve cell hyperplasia', 'Melanocytic hyperplasia', 'Squamous metaplasia - immature', 'Melanoma in situ - acral-lentiginous', 'Melanoma in situ - arising in a giant congenital nevus', 'Atypical melanocytic proliferation', 'Carcinoma NOS', 'Mild dysplasia', 'Squamous metaplasia - mature', 'Moderate dysplasia', 'Invasive melanoma - acral lentiginous', 'Melanoma in situ - not otherwise classified', 'Adenocarcinoma in situ - mucinous', 'Invasive melanoma - desmoplastic', 'Hamartoma', 'Scar - no residual melanoma', 'Invasive melanoma - superficial spreading', 'Adenocarcinoma in situ - non mucinous', 'Invasive melanoma - lentigo maligna', '']",,Biospecimen -Storage Method,Storage Method,StorageMethod,The method by which a biomaterial was stored after preservation or before another protocol was used.,True,,"['RNAlater at 25C', '4C in vacuum chamber', 'RNAlater at 4C', 'Frozen at -80C', 'Cut slide', 'Frozen at -70C', 'Fresh', 'Frozen in vapor phase', 'Not Applicable', 'Ambient temperature', 'Refrigerated at 4 degrees', 'Unknown', 'Paraffin block', 'Refrigerated vacuum chamber', 'Frozen in liquid nitrogen', 'Desiccant at 4C', 'RNAlater at -20C', 'Frozen at -150C']",,Biospecimen -Processing Days from Index,Processing Days from Index,ProcessingDaysfromIndex,Number of days from the research participant's index date that the biospecimen was processed,True,,,,Biospecimen -Percent Inflam Infiltration,Percent Inflam Infiltration,PercentInflamInfiltration,"Numeric value to represent local response to cellular injury, marked by capillary dilatation, edema and leukocyte infiltration; clinically, inflammation is manifest by redness, heat, pain, swelling and loss of function, with the need to heal damaged tissue.",False,,,,Biospecimen -Fiducial Marker,Fiducial Marker,FiducialMarker,Imaging specific: fiducial markers for the alignment of images taken across multiple rounds of imaging.,False,,"['Grid Slides - Hemocytometer', 'Not Reported', 'Nuclear Stain - DAPI', 'Other', 'Unknown', 'Fluorescent Beads', 'Adhesive Markers', '']",,Biospecimen -Acquisition Method Type,Acquisition Method Type,AcquisitionMethodType,Records the method of acquisition or source for the specimen under consideration.,True,,"['Blood draw', 'Core needle biopsy', 'Lymphadenectomy - Regional Nodes', 'Biopsy', 'Endoscopic biopsy', 'Shave Biopsy', 'Other Acquisition Method', 'Re-excision', 'BAL (bronchial alveolar lavage)', 'Not specified', 'Induced sputum', 'Cytobrush', 'Sentinel Node Biopsy', 'Surgical Resection', 'Excision', 'Fine Needle Aspirate', 'Punch Biopsy', 'Non induced sputum', 'Fluid collection', 'Forceps biopsy', 'Autopsy']",,Biospecimen -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Biospecimen -Adjacent Biospecimen IDs,Adjacent Biospecimen IDs,AdjacentBiospecimenIDs,"List of HTAN Identifiers (separated by commas) of adjacent biospecimens cut from the same sample; for example HTA3_3000_3, HTA3_3000_4, ...",False,,,,Biospecimen -Tumor Infiltrating Lymphocytes,Tumor Infiltrating Lymphocytes,TumorInfiltratingLymphocytes,Measure of Tumor-Infiltrating Lymphocytes [Number],False,,,,Biospecimen -Percent Normal Cells,Percent Normal Cells,PercentNormalCells,Numeric value to represent the percentage of normal cell content in a malignant tumor sample or specimen.,False,,,,Biospecimen -Percent Tumor Cells,Percent Tumor Cells,PercentTumorCells,Numeric value that represents the percentage of infiltration by tumor cells in a sample.,False,,,,Biospecimen -Mounting Medium,Mounting Medium,MountingMedium,"The solution in which the specimen is embedded, generally under a cover glass. It may be liquid, gum or resinous, soluble in water, alcohol or other solvents and be sealed from the external atmosphere by non-soluble ringing media",False,,"['Antifade with DAPI', 'Not Reported', 'Non-Aqueous Solvent based', 'Antifade without DAPI', 'PBS', 'Xylene', 'Unknown', 'Aqueous water based', 'Toluene', '']",,Biospecimen -Collection Media,Collection Media,CollectionMedia,Material Specimen is collected into post procedure,False,,"['None', 'PBS', 'PBS+Serum', 'RPMI', 'DMEM+Serum', 'RPMI+Serum', 'DMEM', '']",,Biospecimen -Processing Location,Processing Location,ProcessingLocation,"Site with an HTAN center where specimen processing occurs, if applicable. Any identifier used within the center to identify processing location. No PHI/PII is allowed.",False,,,,Biospecimen -Percent Lymphocyte Infiltration,Percent Lymphocyte Infiltration,PercentLymphocyteInfiltration,Numeric value to represent the percentage of infiltration by lymphocytes in a solid tissue normal sample or specimen.,False,,,,Biospecimen -Percent Neutrophil Infiltration,Percent Neutrophil Infiltration,PercentNeutrophilInfiltration,Numeric value to represent the percentage of infiltration by neutrophils in a tumor sample or specimen.,False,,,,Biospecimen -Histology Assessment Medium,Histology Assessment Medium,HistologyAssessmentMedium,The method of assessment used to characterize histology,False,,"['Unknown', 'Microscopy', 'Digital', 'Other', '']",,Biospecimen -Biospecimen Dimension 3,Biospecimen Dimension 3,BiospecimenDimension3,"Third dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,," If Biospecimen is ""Bone"" OR ""Tissue"" then ""Biospecimen Dimension 3"" is required",Biospecimen -Preservation Method,Preservation Method,PreservationMethod,Text term that represents the method used to preserve the sample.,False,True,"['Negative 80 Deg C', 'Formalin fixed-unbuffered', 'Formalin fixed-buffered', 'Formalin fixed paraffin embedded - FFPE', 'Fresh dissociated and single cell sorted', 'Fresh', 'Frozen', 'Cryopreservation in liquid nitrogen - dead tissue', 'Unknown', 'Liquid Nitrogen', 'OCT', 'Cryopreserved', 'Methacarn fixed paraffin embedded - MFPE', 'Not Reported', 'Cryopreservation in dry ice - dead tissue', 'Snap Frozen', 'Fresh dissociated and single cell sorted into plates', 'Fresh dissociated and single cell sorted into plates in NP40 buffer', 'Fresh dissociated', 'Cryopreservation in liquid nitrogen - live cells', '']"," If Biospecimen is ""Bone"" OR ""Tissue"" OR ""Urine"" then ""Preservation Method"" is required",Biospecimen -Portion Weight,Portion Weight,PortionWeight,"Numeric value that represents the sample portion weight, measured in milligrams.",False,True,," If Biospecimen is ""Bone"" OR ""Tissue"" OR ""Urine"" then ""Portion Weight"" is required",Biospecimen -Site of Resection or Biopsy,Site of Resection or Biopsy,SiteofResectionorBiopsy,"The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",False,True,"['Paraurethral gland', 'Colon NOS', 'Frontal sinus', 'Overlapping lesion of tongue', 'Overlapping lesion of palate', 'Scrotum NOS', 'Bone marrow', 'Axillary tail of breast', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'unknown primary site', 'Broad ligament', 'Lateral floor of mouth', 'Overlapping lesion of vulva', 'Trigone of bladder', 'Lacrimal gland', 'Thorax NOS', 'Ampulla of Vater', 'Myometrium', 'Penis NOS', 'Female genital tract NOS', 'Submandibular gland', 'Anterior 2/3 of tongue NOS', 'Posterior wall of bladder', 'Thymus', 'Endocrine gland NOS', 'Stomach NOS', 'Unknown', 'Cerebrum', 'Splenic flexure of colon', 'Urachus', 'Skin of lip NOS', 'Mucosa of lip NOS', 'Accessory sinus NOS', 'Cortex of adrenal gland', 'Other ill-defined sites', 'Middle lobe lung', 'Pelvis NOS', 'Anus NOS', 'Upper-inner quadrant of breast', 'Posterior mediastinum', 'Esophagus NOS', 'Duodenum', 'Cervical esophagus', 'Optic nerve', 'Long bones of lower limb and associated joints', 'Middle ear', 'Breast NOS', 'Dorsal surface of tongue NOS', 'Lesser curvature of stomach NOS', 'Overlapping lesion of floor of mouth', 'Overlapping lesion of heart mediastinum and pleura', 'Eye NOS', 'Overlapping lesion of esophagus', 'Ciliary body', 'Ureteric orifice', 'Postcricoid region', 'External ear', 'Base of tongue NOS', 'Liver', 'Commissure of lip', 'Cloacogenic zone', 'Lower lobe lung', 'Transverse colon', 'Acoustic nerve', 'Supraglottis', 'Fallopian tube', 'Upper third of esophagus', 'Skin of scalp and neck', 'Choroid', 'Long bones of upper limb scapula and associated joints', 'Overlapping lesion of brain', 'Upper gum', 'Skin NOS', 'Hard palate', 'Ileum', 'Overlapping lesion of colon', 'Ascending colon', 'Lower gum', 'Pelvic bones sacrum coccyx and associated joints', 'Hepatic flexure of colon', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Vestibule of mouth', 'Cervix uteri', 'Bones of skull and face and associated joints', 'Overlapping lesion of lip oral cavity and pharynx', 'Endometrium', 'Sphenoid sinus', 'Overlapping lesion of ill-defined sites', 'Sigmoid colon', 'Peritoneum NOS', 'Specified parts of peritoneum', 'Meckel diverticulum', 'Rectosigmoid junction', 'Kidney NOS', 'Reticuloendothelial system NOS', 'Rectum NOS', 'Pylorus', 'Overlapping lesion of tonsil', 'Pleura NOS', 'Jejunum', 'Vallecula', 'Skin of lower limb and hip', 'Pelvic lymph nodes', 'External lower lip', 'Overlapping lesion of skin', 'Mucosa of upper lip', 'Ovary', 'Cauda equina', 'Lower limb NOS', 'Body of stomach', 'Overlapping lesion of larynx', 'Pancreas NOS', 'Overlapping lesion of lung', 'Overlapping lesion of major salivary glands', 'Uvula', 'Overlapping lesion of hypopharynx', 'Round ligament', 'Corpus uteri', 'Biliary tract NOS', 'Male genital organs NOS', 'Parametrium', 'External lip NOS', 'Overlapping lesion of accessory sinuses', 'Cardia NOS', 'Islets of Langerhans', 'Carotid body', 'Ventral surface of tongue NOS', 'Autonomic nervous system NOS', 'Overlapping lesion of corpus uteri', 'Spinal meninges', 'Posterior wall of nasopharynx', 'Placenta', 'Intrahepatic bile duct', 'Overlapping lesion of digestive system', 'Mediastinum NOS', 'Hematopoietic system NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Major salivary gland NOS', 'Cerebellum NOS', 'Overlapping lesion of stomach', 'Vulva NOS', 'Craniopharyngeal duct', 'Lung NOS', 'Greater curvature of stomach NOS', 'Upper-outer quadrant of breast', 'Gallbladder', 'Thoracic esophagus', 'Lymph nodes of axilla or arm', 'Ventricle NOS', 'Overlapping lesion of biliary tract', 'Hypopharynx NOS', 'Clitoris', 'Exocervix', 'Parietal lobe', 'Waldeyer ring', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Head face or neck NOS', 'Anterior wall of nasopharynx', 'Urethra', 'Overlapping lesion of nasopharynx', 'Maxillary sinus', 'Lymph nodes of inguinal region or leg', 'Ureter', 'Tonsillar pillar', 'Sublingual gland', 'Pituitary gland', 'Gastrointestinal tract NOS', 'Pineal gland', 'Meninges NOS', 'Lingual tonsil', 'Trachea', 'Pyriform sinus', 'Mucosa of lower lip', 'Not Reported', 'Posterior wall of hypopharynx', 'Urinary system NOS', 'Orbit NOS', 'Short bones of lower limb and associated joints', 'Connective subcutaneous and other soft tissues of thorax', 'Upper limb NOS', 'Gastric antrum', 'Lymph node NOS', 'Peripheral nerves and autonomic nervous system of thorax', 'Ill-defined sites within respiratory system', 'Other specified parts of male genital organs', 'Rib sternum clavicle and associated joints', 'Overlapping lesion of bladder', 'Appendix', 'Prostate gland', 'Lymph nodes of multiple regions', 'Lateral wall of nasopharynx', 'Branchial cleft', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Floor of mouth NOS', 'Connective subcutaneous and other soft tissues NOS', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Bladder neck', 'Border of tongue', 'Connective subcutaneous and other soft tissues of abdomen', 'Overlapping lesion of small intestine', 'Lateral wall of bladder', 'Soft palate NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Isthmus uteri', 'Nasal cavity', 'Endocervix', 'Tonsil NOS', 'Glottis', 'Retroperitoneum', 'Peripheral nerves and autonomic nervous system of pelvis', 'Frontal lobe', 'Vagina NOS', 'Undescended testis', 'Laryngeal cartilage', 'Eyelid', 'Hypopharyngeal aspect of aryepiglottic fold', 'Overlapping lesion of other and unspecified parts of mouth', 'Upper lobe lung', 'Lip NOS', 'Lymph nodes of head face and neck', 'Overlapping lesion of brain and central nervous system', 'Overlapping lesion of penis', 'Overlapping lesion of retroperitoneum and peritoneum', 'Parotid gland', 'Dome of bladder', 'Bone of limb NOS', 'Descended testis', 'Vertebral column', 'Fundus uteri', 'Connective subcutaneous and other soft tissues of pelvis', 'Epididymis', 'Intra-abdominal lymph nodes', 'Paraspinal', 'Prepuce', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Pharynx NOS', 'Overlapping lesion of endocrine glands and related structures', 'Gum NOS', 'Spinal cord', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Skin of upper limb and shoulder', 'Nasopharynx NOS', 'Parathyroid gland', 'Bone NOS', 'Mouth NOS', 'Abdomen NOS', 'Conjunctiva', 'Spermatic cord', 'External upper lip', 'Labium minus', 'Renal pelvis', 'Overlapping lesion of lip', 'Short bones of upper limb and associated joints', 'Main bronchus', 'Upper respiratory tract NOS', 'Body of penis', 'Small intestine NOS', 'Central portion of breast', 'Lower-inner quadrant of breast', 'Labium majus', 'Tonsillar fossa', 'Cecum', 'Glans penis', 'Tail of pancreas', 'Lower third of esophagus', 'Body of pancreas', 'Intestinal tract NOS', 'Brain stem', 'Overlapping lesion of rectum anus and anal canal', 'Posterior wall of oropharynx', 'Pancreatic duct', 'Blood', 'Temporal lobe', 'Anterior floor of mouth', 'Nervous system NOS', 'Cornea NOS', 'Palate NOS', 'Occipital lobe', 'Abdominal esophagus', 'Overlapping lesion of pancreas', 'Overlapping lesion of female genital organs', 'Cheek mucosa', 'Retina', 'Overlapping lesion of male genital organs', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Larynx NOS', 'Skin of other and unspecified parts of face', 'Spleen', 'Oropharynx NOS', 'Anal canal', 'Subglottis', 'Cerebral meninges', 'Lateral wall of oropharynx', 'Middle third of esophagus', 'Nipple', 'Medulla of adrenal gland', 'Overlapping lesion of eye and adnexa', 'Olfactory nerve', 'Ethmoid sinus', 'Overlapping lesion of cervix uteri', 'Descending colon', 'Brain NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Anterior wall of bladder', 'Mandible', 'Other specified parts of pancreas', 'Skin of trunk', 'Other specified parts of female genital organs', 'Uterus NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Intrathoracic lymph nodes', 'Heart', 'Adrenal gland NOS', 'Aortic body and other paraganglia', 'Extrahepatic bile duct', 'Overlapping lesion of breast', 'Superior wall of nasopharynx', 'Fundus of stomach', 'Anterior mediastinum', 'Tongue NOS', 'Cranial nerve NOS', 'Head of pancreas', 'Overlapping lesions of oropharynx', 'Overlapping lesion of bones joints and articular cartilage', 'Retromolar area', 'Testis NOS', 'Connective subcutaneous and other soft tissues of head face and neck', 'Bladder NOS', 'Overlapping lesion of urinary organs', 'Lower-outer quadrant of breast', 'Thyroid gland', 'Anterior surface of epiglottis', 'Uterine adnexa', '']"," If Biospecimen is ""Bone"" OR ""Tissue"" OR ""Urine"" then ""Site of Resection or Biopsy"" is required",Biospecimen -Specimen Laterality,Specimen Laterality,SpecimenLaterality,"For tumors in paired organs, designates the side on which the specimen was obtained.",False,True,"['Not Reported', 'Bilateral', 'Not Applicable', 'Unknown', 'Left', 'Right', '']"," If Biospecimen is ""Bone"" OR ""Tissue"" OR ""Urine"" then ""Specimen Laterality"" is required",Biospecimen -Ischemic Temperature,Ischemic Temperature,IschemicTemperature,Specify whether specimen experienced warm or cold ischemia.,False,True,"['4C wet ice', 'Ambient air', 'Cold Ischemia', 'Warm Ischemia', 'Unknown', 'Liquid Nitrogen', 'Negative -20C', 'Dry Ice', '']"," If Biospecimen is ""Bone"" OR ""Tissue"" OR ""Urine"" OR ""Analyte"" then ""Ischemic Temperature"" is required",Biospecimen -Tumor Tissue Type,Tumor Tissue Type,TumorTissueType,Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint (add rows to select multiple values along with timepoints),False,True,"['Not analyzed', 'Local recurrence', 'Metastatic', 'Premalignant - in situ', 'primary', 'Post therapy neoadjuvant', 'Normal adjacent', 'Post therapy', 'Normal', 'Recurrent', 'Not Otherwise Specified', 'Premalignant', 'Normal distant', 'Additional Primary', 'Post therapy adjuvant', 'Atypia - hyperplasia', '']"," If Biospecimen is ""Bone"" OR ""Tissue"" OR ""Urine"" then ""Tumor Tissue Type"" is required",Biospecimen -Histologic Morphology Code,Histologic Morphology Code,HistologicMorphologyCode,"Histologic Morphology Code, based on ICD-O-3. Any valid ICD-O-3 morphology code. See https://seer.cancer.gov/icd-o-3/ and https://seer.cancer.gov/icd-o-3/sitetype.icdo3.20200629.xlsx. Examples: 80510",False,True,," If Biospecimen is ""Bone"" OR ""Tissue"" OR ""Urine"" then ""Histologic Morphology Code"" is required",Biospecimen -Biospecimen Dimension 1,Biospecimen Dimension 1,BiospecimenDimension1,"First dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,," If Biospecimen is ""Bone"" OR ""Tissue"" then ""Biospecimen Dimension 1"" is required",Biospecimen -Total Volume,Total Volume,TotalVolume,Numeric value for the total amount of sample or specimen,False,True,," If Biospecimen is ""Bone"" OR ""Tissue"" OR ""Urine"" then ""Total Volume"" is required",Biospecimen -Section Number in Sequence,Section Number in Sequence,SectionNumberinSequence,"Numeric value (integer, including ranges) provided to a sample in a series of sections (list all adjacent sections in the Adjacent Biospecimen IDs field)",False,True,," If Biospecimen is ""Bone"" OR ""Tissue"" then ""Section Number in Sequence"" is required",Biospecimen -Ischemic Time,Ischemic Time,IschemicTime,"Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value.",False,True,," If Biospecimen is ""Bone"" OR ""Tissue"" OR ""Urine"" OR ""Analyte"" then ""Ischemic Time"" is required",Biospecimen -Biospecimen Dimension 2,Biospecimen Dimension 2,BiospecimenDimension2,"Second dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,," If Biospecimen is ""Bone"" OR ""Tissue"" then ""Biospecimen Dimension 2"" is required",Biospecimen -Shipping Condition Type,Shipping Condition Type,ShippingConditionType,Text descriptor of the shipping environment of a biospecimen.,False,True,"['Ambient Pack', 'Other Shipping Environment', 'Ice Pack', 'Cold Pack', 'Liquid Nitrogen', 'Not Shipped', 'Dry Ice', 'Specimen at Room Temperature', '']"," If Biospecimen is ""Blood"" OR ""Analyte"" then ""Shipping Condition Type"" is required",Biospecimen -Slide Charge Type,Slide Charge Type,SlideChargeType,A description of the charge on the glass slide.,False,True,"['Not applicable', 'Uncharged', 'Charged', 'Other', 'Coverslip', '']"," If Biospecimen is ""Analyte"" then ""Slide Charge Type"" is required",Biospecimen -Fixation Duration,Fixation Duration,FixationDuration,"The length of time, from beginning to end, required to process or preserve biospecimens in fixative (measured in minutes)",False,True,," If Biospecimen is ""Analyte"" then ""Fixation Duration"" is required",Biospecimen -Section Thickness Value,Section Thickness Value,SectionThicknessValue,"Numeric value to describe the thickness of a slice to tissue taken from a biospecimen, measured in microns (um).",False,True,," If Biospecimen is ""Analyte"" then ""Section Thickness Value"" is required",Biospecimen -Sectioning Days from Index,Sectioning Days from Index,SectioningDaysfromIndex,Number of days from the research participant's index date that the biospecimen was sectioned after collection,False,True,," If Biospecimen is ""Analyte"" then ""Sectioning Days from Index"" is required",Biospecimen -Analyte Type,Analyte Type,AnalyteType,The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen,False,True,"['cfDNA Analyte', 'RNA Analyte', 'PBMCs or Plasma or Serum Analyte', 'PBMCs', 'Plasma', 'DNA Analyte', 'cDNA Libraries Analyte', 'Total RNA Analyte', 'Serum Analyte', 'Tissue Section Analyte', 'Tissue Block Analyte', '']"," If Biospecimen is ""Analyte"" then ""Analyte Type"" is required",Biospecimen -Acquisition Method Other Specify,Acquisition Method Other Specify,AcquisitionMethodOtherSpecify,A custom acquisition method [Text - max length 100 characters],False,True,," If Acquisition is ""Other Acquisition Method"" then ""Acquisition Method Other Specify"" is required",Biospecimen -Dimensions Unit,Dimensions Unit,DimensionsUnit,"Unit of measurement used for dimension CDEs in metric system (i.e. cm, mm, etc)",False,,"['cm', 'mm', '']",,Biospecimen -Total Volume Unit,Total Volume Unit,TotalVolumeUnit,Unit of measurement used for the total amount of sample or specimen,False,,"['mL', 'cubic millimeter', 'square centimeter', '']",,Biospecimen -Precancerous Condition Type,Precancerous Condition Type,PrecancerousConditionType,The classification of pre-cancerous cells found in a specific collection of data being studied by the Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions (MCL).,False,,"['Benign tumor NOS', 'No diagnosis possible', 'Pancreatic Intraductal Papillary-Mucinous Neoplasm', 'Normal WDA', 'Persistent melanoma in situ', 'Atypical adenomatous hyperplasia', 'Invasive melanoma - nevoid', 'Invasive melanoma - nodular type', 'Severe dysplasia', 'Reserve cell hyperplasia', 'Melanocytic hyperplasia', 'Squamous metaplasia - immature', 'Atypical melanocytic proliferation', 'Carcinoma NOS', 'Mild dysplasia', 'Superficial spreading', 'Ductal Carcinoma In Situ', 'Squamous metaplasia - mature', 'Moderate dysplasia', 'Invasive melanoma - acral lentiginous', 'Adenocarcinoma in situ - mucinous', 'Pancreatic Intraepithelial Neoplasia', 'Acral-lentiginous', 'Invasive melanoma - desmoplastic', 'Hamartoma', 'Atypical Adenomatous Lung Hyperplasia', 'Scar - no residual melanoma', 'Invasive melanoma - superficial spreading', 'Melanoma in situ not otherwise classified', 'Lentigo maligna type', 'Invasive melanoma', 'Melanoma in situ arising in a giant congenital nevus', 'Other', 'Adenocarcinoma in situ - non mucinous', 'Invasive melanoma - lentigo maligna', 'Melanoma in situ', 'Prostatic Intraepithelial Neoplasia', '']",,ClinicalDataTier2 -Mutational Signatures,Mutational Signatures,MutationalSignatures,"Mutational signatures identified in the patient, includes signatures linked to selected exogenous carcinogens, endogenous and enzymatic modification of DNA or defective DNA repair. Note: Include only outputs of tests that were completed clinically for the participant and only include data from a diagnostic array that was completed prior to research sequencing was done. ",False,,"['transcriptional strand bias', 'Signature 2', 'Not Applicable', 'methylated CpG sequences mutagenesis(deamination of 5-methyl-cytosine)', 'Signature 1A', 'Alkylating Agents (Temozolomide) induced mutations', 'Signature 15', 'Signature 11', 'Data not available', 'Signature 17', 'Signature 10', 'Signature 16', 'Signature 21', 'microsatellite instability (additions and deletions)', 'Signature 3', 'Signature 18', 'Signature 19', 'Unknown', 'Activation Induced Deaminases (AID) associated mutations', 'Signature 4', 'localized substitution hypermutation (kataegis)', 'Ig gene hypermutation', 'altered activity of the error-prone polymerase POLε (POLE)', 'Signature 1B', 'Signature 5', 'Signature 20', 'UV light induced mutations', 'Not Reported', 'Signature 12', 'APOBEC enzymes associated mutations', 'Signature 6', 'Signature 9', 'Signature 14', 'Signature 13', 'Other', 'Signature 7', 'Tobacco use associated mutations', 'age of cancer diagnosis', 'DNA MMR Deficiency', 'Signature 8', '']",,ClinicalDataTier2 -COVID19 Occurrence Indicator,COVID19 Occurrence Indicator,COVID19OccurrenceIndicator,The indicator that describes whether or not a COVID-19 infectious disorder occurred.,False,,"['Yes', 'No', 'Not Applicable', 'Unknown', 'Not Done', '']",,ClinicalDataTier2 -Ecig vape use,Ecig vape use,Ecigvapeuse,"Use of non-traditional cigarette nicotine delivery device (electronic cigarette, ENDS - electronic nicotine delivery system)",False,,"['Unknown', 'Current', 'Former', 'Never', '']",,ClinicalDataTier2 -Extent of Tumor Resection,Extent of Tumor Resection,ExtentofTumorResection,"The degree to which the lesion has been cut out, or resected.",False,,"['Partial debulking', 'Not Reported', 'Not Applicable', 'Open Biopsy', 'Other', 'Optimal debulking', 'Subtotal Resection', 'Segmental', 'Suboptimal', 'Unknown', 'Minor', 'Extensive Subtotal', 'Gross Total Resection', 'NTR', 'Suboptimal debulking', '']",,ClinicalDataTier2 -Chewing tobacco daily use count,Chewing tobacco daily use count,Chewingtobaccodailyusecount,"The quantity of daily use of tobacco, in the form of a plug, usually flavored, for chewing rather than smoking.",False,,,,ClinicalDataTier2 -Education Level,Education Level,EducationLevel,Highest level of education that the patient completed (direct patient-derived information),False,,"['Data not available', 'Grade school', ""Bachelor's degree"", 'High school graduate (including equivalency)', ""Master's degree"", 'Doctoral degree or professional degree', 'Graduate or professional degree', 'Some college or associate degree', 'No formal education', 'Not high school graduate', '']",,ClinicalDataTier2 -Hereditary Cancer Predisposition Syndrome,Hereditary Cancer Predisposition Syndrome,HereditaryCancerPredispositionSyndrome,History of presence of inherited genetic predisposition syndrome that confers heightened susceptibility to cancer in the patient.,False,,"['Tyrosinemia', 'von Hippel-Lindau Syndrome', 'Carney complex', 'Not Applicable', 'Gorlin syndrome', 'Familial adenomatous polyposis', 'Familial prostate cancer', 'Hereditary paraganglioma–pheochromocytoma syndrome', 'Rhabdoid tumor predisposition syndrome type II', 'Familial gastrointestinal stromal tumor', 'Multiple endocrine neoplasia type I', 'Glycogen Storage Disease', 'Tuberous sclerosis complex', 'Li-Fraumeni syndrome', 'Hereditary diffuse gastric cancer', 'Multiple endocrine neoplasia type II', 'Rhabdoid tumor predisposition syndrome type I', 'Beckwith-Wiedemann', 'Hereditary breast–ovarian cancer syndrome', 'Hereditary renal oncocytoma', 'Rubinstein-Taybi syndrome', 'Unknown', 'Hereditary mixed polyposis syndrome', 'Hereditary retinoblastoma', 'Peutz–Jeghers syndrome', 'Melanoma–astrocytoma syndrome', 'Cirrhosis unknown etiology', 'Alpha-1 antitrypsin', 'Familial pancreatic cancer', 'Lynch syndrome', 'Turcot syndrome', 'Serrated polyposis syndrome', 'Not Reported', 'Birt-Hogg-Dube syndrome', 'Biliary disorder', 'Hereditary papillary renal cell carcinoma', 'Juvenile polyposis syndrome', 'SDH associated renal cancer', 'Hereditary papillary RCC', 'Cowden syndrome', 'Constitutional mismatch repair deficiency', 'BAP1 mutant disease', 'Attenuated familial adenomatous polyposis', 'MUTYH-associated polyposis', 'Hereditary melanoma', 'Hereditary leiomyoma-renal cell carcinoma', 'Fanconi anemia', 'Familial renal cancer', 'Nevoid basal cell carcinoma syndrome', '']",,ClinicalDataTier2 -Cancer Incidence,Cancer Incidence,CancerIncidence,"Incidence of specific cancer type in a defined area (a number between 0 and 100). The rate of incident cases per population of 100,000 persons of a specific type of cancer as designated in the ""primary_diagnosis"" data element in the county where the patient resides, using the most recent 2013-2017 NCI Cancer Atlas derived data. Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the asociated county on the right side of the result field. On the https://gis.cancer.gov/canceratlas/tableview/ website, choose ""Incidence"" from the Topic dropdown menu, state of interest from the Area menu, ""All Races"" from the Race menu, and the cancer type (""Both Sexes"" when possible) from the Statistic menu. Find the county of interest and enter the numeric Age-Adjusted Rate per 100,000 as the value.",False,,,,ClinicalDataTier2 -Sentinel Node Positive Assessment Count,Sentinel Node Positive Assessment Count,SentinelNodePositiveAssessmentCount,The number or amount of metastatic neoplasms related to the confirmed presence of disease or specific microorganisms during examination of the first rounded mass of lymphatic tissue to which cancer is likely to spread from the primary tumor.,False,,,,ClinicalDataTier2 -Rural vs Urban,Rural vs Urban,RuralvsUrban,"Density of population in the county of residence, based on census data (updated last on 4/28/20). Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the associated county on the right side of the result field. Go to https://www2.census.gov/programs-surveys/acs/data/covid_19/Data_Profiles_for_HHS/050-County_By_State/. Select the dp02_XX.csv file where XX = the two letter abbreviation for the appropriate state. On row 166 find the total population for the appropriate county. If the total population is <2,500 enter a value of ""Rural Population""; if 2,500 - 50,000 enter a value of ""Urban Cluster""; or if >50,000 enter ""Urban Population""",False,,"['Rural Population (population <2500)', 'Urban Cluster (population 2500 - 50000)', 'Urban Population (population >50000)', '']",,ClinicalDataTier2 -Type of smoke exposure cumulative years,Type of smoke exposure cumulative years,Typeofsmokeexposurecumulativeyears,The number of cumulative years of the patient's specific type of smoke exposure,False,,,,ClinicalDataTier2 -Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,ClinicalDataTier2 -COVID19 Current Status,COVID19 Current Status,COVID19CurrentStatus,The patient's current COVID-19 status of sign or symptom events or interventions,False,,"['Patient currently has symptoms', 'Status unknown due to other reasons', 'Patient never had any symptoms of COVID-19', 'Patient had symptoms but now is fully recovered', 'Status unknown due to lack of disease/tumor assessment due to COVID-19 diagnosis', 'Status unknown due to general COVID-19 related travel restrictions', '']",,ClinicalDataTier2 -Cancer Incidence Location,Cancer Incidence Location,CancerIncidenceLocation,"The county and state in which the patient lives and to which the cancer_incidence data correlates. Record as ""County, State"" as they appear in the incidence box from which the cancer_incidence data is obtained in the https://gis.cancer.gov/canceratlas/tableview/ website",False,,,,ClinicalDataTier2 -Satellite Metastasis Present Indicator,Satellite Metastasis Present Indicator,SatelliteMetastasisPresentIndicator,A yes/no indicator to ask if intransit metastases or satellite lesions are present.,False,,"['No', 'Unknown', 'Yes', '']",,ClinicalDataTier2 -COVID19 Cancer Treatment Followup,COVID19 Cancer Treatment Followup,COVID19CancerTreatmentFollowup,Indicator that describes if cancer treatment was modified for the patient due to COVID-19 infectious disorder,False,,"['Not Applicable', 'No', 'Unknown', 'Yes', '']",,ClinicalDataTier2 -Second hand smoke exposure years,Second hand smoke exposure years,Secondhandsmokeexposureyears,The number of cumulative years of the patient's exposure to second-hand cigarette smoke,False,,,,ClinicalDataTier2 -Concomitant Medication Received Type,Concomitant Medication Received Type,ConcomitantMedicationReceivedType,An enumerated list of the type of concomitant medication received by the patient.,False,,"['Intravaginal estrogen preparations', 'Prophylactic antiplatelet therapy', 'Not Applicable', 'Antifungal', 'Antidepressants-weak CYP2D2 inhibitors or non-inhibitors', 'Non-steroidal anti-inflammatory agents', 'Diabetes-Insulin', 'Anticonvulsant', 'Diabetes-Metformin containing agents', 'Growth factor', 'Unknown', 'Anticoagulant agents', 'Antidepressants-Strong CYP2D6 inhibitors', 'COX-2 inhibitor', 'Opioids', 'Prescription medications for relief of hot flashes', 'Prescription medications for memory', 'Not Reported', 'Antidepressants-Moderate CYP2D6 inhibitors', 'Anxiolytics or sedatives', 'Tricyclic antidepressants', 'Decadron', 'Aspirin', 'Lipid-lowering drugs', 'Corticosteroid', 'Non-prescription supplements for relief of hot flashes', 'Antiplatelet agents', 'Other', 'Non-prescription supplements for memory', 'Bisphosphonates for treatment/prevention of bone loss', '']",,ClinicalDataTier2 -Ecig vape 30 day use num,Ecig vape 30 day use num,Ecigvape30dayusenum,Number of days e-cigarettes or vaping device was used in the last 30 days,False,,,,ClinicalDataTier2 -Other Biopsy Resection Site,Other Biopsy Resection Site,OtherBiopsyResectionSite,A description of the location on or within the human body where the surgical biopsy/resection procedure was performed (Not covered under HTAN Clinical Data Tier 1),False,,,,ClinicalDataTier2 -COVID19 Antibody Testing,COVID19 Antibody Testing,COVID19AntibodyTesting,Text term that demonstrates the test results of immunoglobulin M (IgM) and immunoglobulin G (IgG) antibodies to the SARS-CoV-2 virus in subject serum samples.,False,,"['SARS-CoV-2 IgG antibody positive', 'SARS-CoV-2 IgM antibody negative', 'SARS-CoV-2 IgG antibody negative', 'Not Applicable', 'SARS-CoV-2 IgM antibody positive', 'Unknown', 'SARS-CoV-2 IgG/IgM antibody positive', 'SARS-CoV-2 IgG/IgM antibody negative', 'Not Done', '']",,ClinicalDataTier2 -Immunosuppression,Immunosuppression,Immunosuppression,The indicator that describes whether or not immunosuppressive therapy was administered.,False,,"['Yes', 'No', 'Not Applicable', 'Unknown', 'Not Done', '']",,ClinicalDataTier2 -Ecig vape times per day,Ecig vape times per day,Ecigvapetimesperday,e-cig frequency of use (times per day—one “time” consists of around 15 puffs or lasts around 10 minutes),False,,,,ClinicalDataTier2 -Stop Days from Index,Stop Days from Index,StopDaysfromIndex,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'",False,,,,ClinicalDataTier2 -Lab Tests for MMR Status,Lab Tests for MMR Status,LabTestsforMMRStatus,Laboratory tests used to evaluate the status of mismatch repair pathways,False,,"['PCR to evaluate microsatellite instability', 'Not Applicable', 'Other', 'Unknown', 'BRAF\xa0sequencing', 'IHC staining for mismatch repair proteins', 'MLH1\xa0promoter methylation analysis', '']",,ClinicalDataTier2 -Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,ClinicalDataTier2 -Cancer Associated Gene Mutations,Cancer Associated Gene Mutations,CancerAssociatedGeneMutations,Type of inherited germline or other gene mutations that confers heightened susceptibility to cancer identified in patient history,False,,"['Not Applicable', 'GREM1 mutation', 'MSH6 mutation', 'NF2 mutation', 'CHK mutation', 'SMARCB1 mutation', 'PolD mutation', 'PRKAR1A mutation', 'HOXB13 mutation', 'NF1 mutation', 'PolE mutation', 'RB1 mutation', 'KIT mutation', 'PAX5 mutation', 'STK11 mutation', 'MLH1 mutation', 'p14ARF mutation', 'EGFR mutation', 'MEN1 mutation', 'SMARCA4 mutation', 'BRCA2 mutation', 'MAX mutation', 'ALK mutation', 'BRAF mutation', 'Unknown', 'ATRX mutation', 'MUTYH mutation', 'VHL mutation', 'H3K27M mutation', 'BMPR1A mutation', 'FLCN mutation', 'ETV6 mutation', 'PHOX2B mutation', 'BRCA1 mutation', 'IKZF1 mutation', 'CDKN2A mutation', 'Not Reported', 'SETD2 mutation', 'PALB2 mutation', 'POT1 mutation', 'KRAS mutation', 'APC mutation', 'SDHB mutation', 'TMEM127 mutation', 'PDGFRA mutation', 'RET mutation', 'ROS1 mutation', 'ACVR1 mutation', 'PMS2 mutation', 'SDHAF2 mutation', 'SMAD4 mutation', 'BAP1 mutation', 'PTEN mutation', 'FH mutation', 'BLM mutation', 'TSC1 mutation', 'BRCA1 and 2 mutation', 'MET mutation', 'CDKN2A and p14ARF mutation', 'TSC2 mutation', 'SDHC mutation', 'TP53 mutation', 'H3G34R/V mutation', 'CDH1 mutation', 'SDHD mutation', 'MSH2 mutation', 'PTCH mutation', 'ARF mutation', 'ATM mutation', '']",,ClinicalDataTier2 -Country of Birth,Country of Birth,CountryofBirth,Country where the patient was born.,False,,"['Belize', 'Monaco', 'Bahrain', 'Iraq', 'South Africa', 'Vietnam', 'Niue', 'Poland', 'Albania', 'Burundi', 'Spain', 'Bhutan', 'Saudi Arabia', 'Madagascar', 'Gambia', 'Switzerland', 'Laos', 'Saint Lucia', 'Myanmar', 'Mayotte', 'Guadeloupe', 'South Korea', 'Tokelau', 'Syria', 'Pakistan', 'Isle of Man', 'Yemen', 'Svalbard & Jan Mayen Islands', 'Jersey', 'Bosnia and Herzegovina', 'Eritrea', 'Guinea', 'Philippines', 'Guinea-Bissau', 'Azerbaijan', 'Somalia', 'Sudan', 'Cambodia', 'Cuba', 'Rwanda', 'Tonga', 'Saint Kitts and Nevis', 'Finland', 'Paraguay', 'Malawi', 'Falkland Islands (Malvinas)', 'Federated States of Micronesia', 'Niger', 'Colombia', 'Democratic Republic of the Congo', 'North Macedonia', 'Haiti', 'Timor-Leste', 'Austria', 'Chad', 'Iceland', 'Dominica', 'Malta', 'Denmark', 'Kosovo', 'Martinique', 'Bangladesh', 'San Marino', 'South Sudan', 'Georgia', 'Nigeria', 'Gibraltar', 'Nauru', 'Tajikistan', 'Montserrat', 'Sweden', 'Antigua and Barbuda', 'Indonesia', 'Sri Lanka', 'Greece', 'Gabon', 'Japan', 'Mauritania', 'Nicaragua', 'China', 'Cape Verde', 'Unknown', 'Grenada', 'French Polynesia', 'Moldova', 'Cayman Islands', 'Dominican Republic', 'Liechtenstein', 'Senegal', 'Holy See', 'Mali', 'Vanuatu', 'India', 'Bermuda', 'Netherlands', 'Ireland', 'Zambia', 'North Korea', 'Macau', 'Romania', 'Solomon Islands', 'Suriname', 'Nepal', 'Croatia', 'Reunion', 'Ghana', 'Saint Helena Ascension and Tristan da Cunha', 'Israel', 'Faroe Islands', 'Greenland', 'State of Palestine', 'Wallis and Futuna', 'Ecuador', 'French Guiana', 'Angola', 'Aruba', 'Guyana', 'Kuwait', 'Taiwan', 'Singapore', 'Togo', 'Andorra', 'Lebanon', 'Northern Mariana Islands', 'Armenia', 'Iran', 'New Zealand', 'Bolivia', 'Cameroon', 'Norway', 'Panama', 'Papua New Guinea', 'Qatar', 'Tanzania', 'Portugal', 'Slovakia', 'Equatorial Guinea', 'Estonia', 'Mongolia', 'Chile', 'Burkina Faso', 'Ethiopia', 'Hungary', 'Djibouti', 'Kenya', 'Kiribati', 'Botswana', 'Australia', 'Guam', 'Congo', 'Belarus', 'Uruguay', 'Czech Republic (Czechia)', 'Lesotho', 'United Kingdom', 'Lithuania', 'Russia', 'Thailand', 'Oman', 'Benin', 'Tunisia', 'Uganda', 'Namibia', 'Honduras', 'Algeria', 'Turkey', 'Morocco', 'Barbados', 'Sierra Leone', 'Venezuela', 'Saint Pierre and Miquelon', 'Kyrgyzstan', 'Trinidad and Tobago', 'Serbia', 'Peru', 'Comoros', 'Canada', 'Hong Kong', 'Liberia', 'Malaysia', 'Puerto Rico', 'Brazil', 'Virgin Islands British', 'Zimbabwe', 'Latvia', 'Eswatini', ""Cote d'Ivoire"", 'United Arab Emirates', 'Bahamas', 'Curacao', 'Slovenia', 'Central African Republic', 'Guatemala', 'Jordan', 'Egypt', 'Germany', 'Mozambique', 'Fiji', 'Turkmenistan', 'Mexico', 'Brunei', 'France', 'Kazakhstan', 'Argentina', 'Uzbekistan', 'Samoa', 'Bulgaria', 'Virgin Islands U.S.', 'Maldives', 'Cyprus', 'Costa Rica', 'Italy', 'Libya', 'Jamaica', 'Tuvalu', 'United States', 'Saint Vincent and the Grenadines', 'Palau', 'Western Sahara', 'Guernsey', 'Mauritius', 'El Salvador', 'Afghanistan', 'Belgium', 'Luxembourg', 'Ukraine', 'Marshall Islands', 'Montenegro', 'Cook Islands', 'Seychelles', 'Sao Tome and Principe', 'New Caledonia', 'Anguilla', '']",,ClinicalDataTier2 -Family Member Vital Status Indicator,Family Member Vital Status Indicator,FamilyMemberVitalStatusIndicator,The response indicates whether the family member of the patient with a history of cancer is alive. (Extension to GDC attributes in Family History Tier 1),False,,"['Unknown', 'Not Reported', 'Vital Status Dead', 'Vital Status Alive', '']",,ClinicalDataTier2 -Known Genetic Predisposition Mutation,Known Genetic Predisposition Mutation,KnownGeneticPredispositionMutation,A yes/no/unknown indicator to identify whether there is a known genetic predisposition mutation present in the patient.,False,,"['No', 'Unknown', 'Yes', '']",,ClinicalDataTier2 -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,ClinicalDataTier2 -COVID19 Complications Severity,COVID19 Complications Severity,COVID19ComplicationsSeverity,Text term that retrospectively indicates the worst complications during COVID-19 infectious disorder in the patient.,False,,"['Pulmonary complications', 'Not Applicable', 'Other', 'Unknown', 'Systemic complications', 'Cardiac complications', '']",,ClinicalDataTier2 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ClinicalDataTier2 -Tumor Extranodal Extension Indicator,Tumor Extranodal Extension Indicator,TumorExtranodalExtensionIndicator,The indicator to determine extranodal involvement or extent of the disease.,False,,"['Not applicable', 'Present - minimal', 'Absent', 'No source documentation', 'NO', 'YES', 'unspecified', 'UNKNOWN', 'Indeterminate', 'Present - extensive', 'Not sampled or dissected', 'Present', '']",,ClinicalDataTier2 -COVID19 Positive Lab Test Indicator,COVID19 Positive Lab Test Indicator,COVID19PositiveLabTestIndicator,The indicator that describes whether or not there was a COVID-19 positive test result.,False,,"['Yes', 'No', 'Not Applicable', 'Unknown', 'Not Done', '']",,ClinicalDataTier2 -Mode of Cancer Detection,Mode of Cancer Detection,ModeofCancerDetection,"Text term used to describe the mode of cancer detection, like standard of care screening or random detection",False,,"['Incidentaloma', 'Interval Cancer', 'Data not available', 'Clinical Examination of unrelated cancer symptoms', 'Standard of Care Screening', '']",,ClinicalDataTier2 -Prior Sites of Radiation,Prior Sites of Radiation,PriorSitesofRadiation,The anatomic location to which radiation treatment was administered to a patient prior to enrollment on a protocol.,False,,"['Conjunctiva', 'Lymph Node(s) Parotid', 'Lung', 'Patella', 'Nasopharynx', 'Descending Colon', 'Lymph Node(s) Axilla', 'Dermal', 'Lymph Node(s) Subclavicular', 'Ureter', 'Chest Wall', 'Pericardium', 'Esophagus Mucosa Only', 'Frontal Cortex', 'Epidural Space', 'Lymph Node(s) Inguinal', 'Periorbital Soft Tissue', 'Skin upper extremity local', 'Arm', 'Joint', 'Genitourinary NOS', 'Ligament', 'Foreskin', 'Bone', 'Lymph Node(s) Iliac-Common', 'Central Nervous System', 'Lymph Node(s) Occipital', 'Retro-Orbital Region', 'Pancreas', 'Buttock', 'Ankle', 'Esophagogastric Junction', 'Cecum', 'Distant Site', 'Not Reported', 'Ileocecal Valve', 'Venous', 'Alveolar Ridge', 'Bile Duct', 'Colon Mucosa Only', 'Hilar', 'Lymph Node(s) Paraaortic', 'Prostate', 'Axilla', 'Frontal Lobe', 'Large Bowel', 'Carina', 'Chin', 'Pylorus', 'Sigmoid Colon', 'Elbow', 'Ischium', 'Nasal Cavity', 'Anorectum', 'Gastrointestinal Tract', 'Spinal Column', 'Adipose', 'Head and Neck', 'Scapula', 'Acetabulum', 'Mediastinal Soft Tissue', 'Other', 'Ganglia', 'Lymph Node(s) Hilar', 'Testis', 'Lymph Node(s) Submandibular', 'Leg', 'Jejunum', 'Ampulla of Vater', 'Small Bowel Mucosa Only', 'Appendix', 'Abdominal Wall', 'Primary tumor site', 'Soft Tissue', 'Lymph Node(s) Scalene', 'Pleura', 'Aortic Body', 'Blood', 'Hepatic Vein', 'Sinus', 'Mesentery', 'Brain', 'Fallopian Tube', 'Hippocampus', 'Bladder', 'Ascending Colon Hepatic Flexure', 'Brow', 'Transverse Colon', 'Adrenal', 'Laryngopharynx', 'Thymus', 'Artery', 'Skin total', 'Antrum', 'Pharynx', 'Islet Cells', 'Unknown', 'Urinary Tract', 'Autonomic Nervous System', 'Clavicle', 'Cerebrum', 'Abdomen total', 'Uterus', 'Vein', 'Ovary', 'Cell-Line', 'Small Finger', 'Thorax', 'Eye', 'Bowel', 'Lymph Node(s) Epitrochlear', 'Kidney', 'Fibula', 'Retina', 'Back', 'Lymph Node(s) Internal Mammary', 'Finger', 'Rectosigmoid Junction', 'Tibia', 'Ilium', 'Lumbar Spine', 'Spinal Cord', 'Thumb', 'Bone Marrow', 'Leptomeninges', 'Peritoneum', 'Vertebra', 'Bone non-spine', 'Lymph Node(s) Splenic', 'Ring Finger', 'Round Ligament', 'Spleen', 'Paraspinal Ganglion', 'Uvula', 'Lymph Node(s) Femoral', 'Lymph Node(s) Pelvic', 'Gastroesophageal Junction', 'Skull', 'Rib', 'Pituitary Gland', 'Anus', 'Anal Sphincter', 'Shoulder', 'Retroperitoneum', 'Parametrium', 'Hypopharynx', 'Cerebral Cortex', 'Ocular Orbits', 'Omentum', 'Hepatic Duct', 'Parathyroid', 'Aqueous Fluid', 'Endocrine Gland', 'Wrist', 'Carotid Artery', 'Mantle', 'Cervical Spine', 'Occipital Cortex', 'Ear Pinna (External)', 'Duodenum', 'Ascending Colon', 'Tonsil', 'Prostate Seminal Vesicles and Lymph Nodes', 'Throat', 'Epitrochlear', 'Buccal Mucosa', 'Lymph Node(s) Retroperitoneal', 'Placenta', 'Groin', 'Penis', 'Subcutaneous Tissue', 'Cardia', 'Peritoneal Cavity', 'Bronchiole', 'Small Bowel', 'Lymph Node(s) Distant', 'Spine', 'Hand', 'Vagina', 'Lymph Node(s) Regional', 'Umbilical Cord', 'Blood Vessel', 'Lymph Node(s) Cervical', 'Popliteal Fossa', 'Rectum', 'Index Finger', 'Regional Site', 'Oropharynx', 'Synovium', 'Mandible', 'Cerebellum', 'Nerve(s) Cranial', 'Breast', 'Colon', 'Mediastinum', 'Nails', 'Pelvis', 'Salivary Gland', 'Ascites', 'Skin', 'Palate', 'Neck', 'Lymph Node', 'Tonsil (Pharyngeal)', 'Head Face Or Neck Nos', 'Chest', 'Hepatic', 'Lacrimal Gland', 'Capillary', 'Forearm', 'Muscle', 'Fibroblasts', 'Fluid', 'Skin lower extremity local', 'Gallbladder', 'Body total', 'Lymph Node(s) Mediastinal', 'Lymph Node(s) Supraclavicular', 'Scrotum', 'Gastrointestinal Intestine', 'Sternum', 'Cervix', 'Oral Cavity Mucosa Only', 'Humerus', 'Adenoid', 'Carotid Body', 'Calf', 'Esophagus', 'Femoral Vein', 'Aorta', 'Femur', 'Foot', 'Primary Tumor Field', 'Heart', 'Antecubital Fossa', 'Connective Tissue', 'Hip', 'Sacrum', 'Trachea / Major Bronchi', 'Cartilage', 'Larynx', 'Scalp', 'Sciatic Nerve', 'Vulva', 'White Blood Cells', 'Epididymis', 'Liver', 'Nerve', 'Skin trunk local', 'Lymph Node(s) Iliac-External', 'Stomach', 'Clitoris', 'Hard Palate', 'Stomach Mucosa Only', 'Femoral Artery', 'Nasal Soft Tissue', 'Broad Ligament', 'Ear', 'Vas Deferens', 'Auditory Canal', 'Bronchus', 'Tendon', 'Lymph Node(s) Popliteal', 'Mesothelium', 'Oral Cavity', 'Ear Canal', 'Middle Finger', 'Common Duct', 'Thyroid', 'Fundus of Stomach', 'Tongue', 'Amniotic Fluid', 'Ileum', 'Pouch', 'Splenic Flexure', 'Pineal', 'Sinus(es) Maxillary', 'Thoracic Spine', 'Knee', 'Parotid Gland', 'Gum', 'Thigh', 'Urethra', 'Forehead', 'Jaw', 'Buccal Cavity', 'Floor of Mouth', 'Skeletal Muscle', 'Seminal Vesicle', 'Temporal Cortex', 'Diaphragm', 'Lymph Node(s) Mesenteric', 'Lymph Node(s) Mammary', 'Maxilla', 'Pineal Gland', 'Mitochondria', 'Lip', 'Cerebrospinal Fluid', 'Trunk', 'Brain Stem', 'Prostate Bed', '']",,ClinicalDataTier2 -Mismatch Repair System Status,Mismatch Repair System Status,MismatchRepairSystemStatus,The text that best describes the condition or state of MMR (mismatch repair system) in the patient,False,,"['unknown or other', 'Mismatch repair deficiency MMRD', 'Microsatellite stable MSS', 'Microsatellite instability high MSIH', 'Mismatch repair proficiency MMPP', '']",,ClinicalDataTier2 -Sentinel Lymph Node Count,Sentinel Lymph Node Count,SentinelLymphNodeCount,Numeric count of sentinel lymph nodes.,False,,,,ClinicalDataTier2 -Medically Underserved Area,Medically Underserved Area,MedicallyUnderservedArea,"Areas or populations designated by HRSA as having too few primary care providers, high infant mortality, high poverty or a high elderly population: Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/ - enter the zip code in the main text field and use the associated county on the right side of the result field. Go to data.hrsa.gov website and select ""Query Data"". Pick the Medically Underserved Areas/Populations (MUA/P) data source in the step 1 menu and select ""View Data"". Enter the name of the county (_______ county) in the first ""Service Area"" column, adding the state in the 5th column may help direct you to the data. If the designation type in the third column is ""medically underserved area"" enter ""Yes"" as the value. If the county generates a ""No data available in table"" enter ""No"" as the value. A value of ""Unknown"" indicates that sufficient data was not available to look up the value. If value is yes, complete the Medically_underserved_score data element.",False,,"['Medically Underserved Area - Yes', 'Medically Underserved Area - Unknown', 'Medically Underserved Area - No', '']",,ClinicalDataTier2 -Medically Underserved Score,Medically Underserved Score,MedicallyUnderservedScore,"Index of Medical Underservice (IMU) score, a number between 0 and 100, where 0 represents completely underserved and 100 represents best served or least underserved. Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the asociated county on the right side of the result field. Go to data.hrsa.gov website and select Query Data. Pick the Medically Underserved Areas/Populations (MUA/P) data source in the step 1 menu and select View Data. Enter the name of the county (______ county) in the first ""Service Area"" column, adding the state in the 5th column may help direct you to the data. Enter the Index of Medical Underservice Score in the fourth column to one decimal place as the value.",False,True,," If Medically Underserved Area is ""Medically Underserved Area - Yes"" then ""Medically Underserved Score"" is required",ClinicalDataTier2 -Days to Recurrence,Days to Recurrence,DaystoRecurrence,Number of days between the date used for index and the date the patient's disease recurred.,True,,,,SRRSClinicalDataTier2 -Days to Last Known Disease Status,Days to Last Known Disease Status,DaystoLastKnownDiseaseStatus,"Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days.",True,,,,SRRSClinicalDataTier2 -Vital Status,Vital Status,VitalStatus,The survival state of the person registered on the protocol.,True,,"['Alive', 'Unknown', 'Dead', 'Not Reported']",,SRRSClinicalDataTier2 -NCI Atlas Cancer Site,NCI Atlas Cancer Site,NCIAtlasCancerSite,"The primary tumor site used to calculate the incidence rate using the NCI Cancer Atlas, a digital atlas which provides geographical data related to cancer utilizing the Surveillance, Epidemiology, and End Results (SEER) Program cancer incidence rates for 2013 to 2017",False,,"['Colon And Rectum', 'Bladder', 'Leukemia', 'Thyroid Gland', 'Prostate Gland', 'Stomach', 'Cervix Uteri', 'Lung And Bronchus', 'Uterus', 'Pancreas', 'Ovary', 'In situ Female Breast', 'Oral Cavity And Pharynx', ""Non-Hodgkin's Lymphoma"", 'Malignant Childhood Neoplasm', 'Liver And Bile Duct', 'Cutaneous Melanoma', 'Female Breast', 'Brain And Other Nervous System', 'Less Than Age', 'Kidney And Renal Pelvis', 'Esophagus', '']",,SRRSClinicalDataTier2 -Tissue or Organ of Origin,Tissue or Organ of Origin,TissueorOrganofOrigin,"The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",True,,"['Paraurethral gland', 'Colon NOS', 'Frontal sinus', 'Overlapping lesion of tongue', 'Overlapping lesion of palate', 'Scrotum NOS', 'Bone marrow', 'Axillary tail of breast', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'unknown primary site', 'Broad ligament', 'Lateral floor of mouth', 'Overlapping lesion of vulva', 'Trigone of bladder', 'Lacrimal gland', 'Thorax NOS', 'Ampulla of Vater', 'Myometrium', 'Penis NOS', 'Female genital tract NOS', 'Submandibular gland', 'Anterior 2/3 of tongue NOS', 'Posterior wall of bladder', 'Thymus', 'Endocrine gland NOS', 'Stomach NOS', 'Unknown', 'Cerebrum', 'Splenic flexure of colon', 'Urachus', 'Skin of lip NOS', 'Mucosa of lip NOS', 'Accessory sinus NOS', 'Cortex of adrenal gland', 'Other ill-defined sites', 'Middle lobe lung', 'Pelvis NOS', 'Anus NOS', 'Upper-inner quadrant of breast', 'Posterior mediastinum', 'Esophagus NOS', 'Duodenum', 'Cervical esophagus', 'Optic nerve', 'Long bones of lower limb and associated joints', 'Middle ear', 'Breast NOS', 'Dorsal surface of tongue NOS', 'Lesser curvature of stomach NOS', 'Overlapping lesion of floor of mouth', 'Overlapping lesion of heart mediastinum and pleura', 'Eye NOS', 'Overlapping lesion of esophagus', 'Ciliary body', 'Ureteric orifice', 'Postcricoid region', 'External ear', 'Base of tongue NOS', 'Liver', 'Commissure of lip', 'Cloacogenic zone', 'Lower lobe lung', 'Transverse colon', 'Acoustic nerve', 'Supraglottis', 'Fallopian tube', 'Upper third of esophagus', 'Skin of scalp and neck', 'Choroid', 'Long bones of upper limb scapula and associated joints', 'Overlapping lesion of brain', 'Upper gum', 'Skin NOS', 'Hard palate', 'Ileum', 'Overlapping lesion of colon', 'Ascending colon', 'Lower gum', 'Pelvic bones sacrum coccyx and associated joints', 'Hepatic flexure of colon', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Vestibule of mouth', 'Cervix uteri', 'Bones of skull and face and associated joints', 'Overlapping lesion of lip oral cavity and pharynx', 'Endometrium', 'Sphenoid sinus', 'Overlapping lesion of ill-defined sites', 'Sigmoid colon', 'Peritoneum NOS', 'Specified parts of peritoneum', 'Meckel diverticulum', 'Rectosigmoid junction', 'Kidney NOS', 'Reticuloendothelial system NOS', 'Rectum NOS', 'Pylorus', 'Overlapping lesion of tonsil', 'Pleura NOS', 'Jejunum', 'Vallecula', 'Skin of lower limb and hip', 'Pelvic lymph nodes', 'External lower lip', 'Overlapping lesion of skin', 'Mucosa of upper lip', 'Ovary', 'Cauda equina', 'Lower limb NOS', 'Body of stomach', 'Overlapping lesion of larynx', 'Pancreas NOS', 'Overlapping lesion of lung', 'Overlapping lesion of major salivary glands', 'Uvula', 'Overlapping lesion of hypopharynx', 'Round ligament', 'Corpus uteri', 'Biliary tract NOS', 'Male genital organs NOS', 'Parametrium', 'External lip NOS', 'Overlapping lesion of accessory sinuses', 'Cardia NOS', 'Islets of Langerhans', 'Carotid body', 'Ventral surface of tongue NOS', 'Autonomic nervous system NOS', 'Overlapping lesion of corpus uteri', 'Spinal meninges', 'Posterior wall of nasopharynx', 'Placenta', 'Intrahepatic bile duct', 'Overlapping lesion of digestive system', 'Mediastinum NOS', 'Hematopoietic system NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Major salivary gland NOS', 'Cerebellum NOS', 'Overlapping lesion of stomach', 'Vulva NOS', 'Craniopharyngeal duct', 'Lung NOS', 'Greater curvature of stomach NOS', 'Upper-outer quadrant of breast', 'Gallbladder', 'Thoracic esophagus', 'Lymph nodes of axilla or arm', 'Ventricle NOS', 'Overlapping lesion of biliary tract', 'Hypopharynx NOS', 'Clitoris', 'Exocervix', 'Parietal lobe', 'Waldeyer ring', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Head face or neck NOS', 'Anterior wall of nasopharynx', 'Urethra', 'Overlapping lesion of nasopharynx', 'Maxillary sinus', 'Lymph nodes of inguinal region or leg', 'Ureter', 'Tonsillar pillar', 'Sublingual gland', 'Pituitary gland', 'Gastrointestinal tract NOS', 'Pineal gland', 'Meninges NOS', 'Lingual tonsil', 'Trachea', 'Pyriform sinus', 'Mucosa of lower lip', 'Not Reported', 'Posterior wall of hypopharynx', 'Urinary system NOS', 'Orbit NOS', 'Short bones of lower limb and associated joints', 'Connective subcutaneous and other soft tissues of thorax', 'Upper limb NOS', 'Gastric antrum', 'Lymph node NOS', 'Peripheral nerves and autonomic nervous system of thorax', 'Ill-defined sites within respiratory system', 'Other specified parts of male genital organs', 'Rib sternum clavicle and associated joints', 'Overlapping lesion of bladder', 'Appendix', 'Prostate gland', 'Lymph nodes of multiple regions', 'Lateral wall of nasopharynx', 'Branchial cleft', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Floor of mouth NOS', 'Connective subcutaneous and other soft tissues NOS', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Bladder neck', 'Border of tongue', 'Connective subcutaneous and other soft tissues of abdomen', 'Overlapping lesion of small intestine', 'Lateral wall of bladder', 'Soft palate NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Isthmus uteri', 'Nasal cavity', 'Endocervix', 'Tonsil NOS', 'Glottis', 'Retroperitoneum', 'Peripheral nerves and autonomic nervous system of pelvis', 'Frontal lobe', 'Vagina NOS', 'Undescended testis', 'Laryngeal cartilage', 'Eyelid', 'Hypopharyngeal aspect of aryepiglottic fold', 'Overlapping lesion of other and unspecified parts of mouth', 'Upper lobe lung', 'Lip NOS', 'Lymph nodes of head face and neck', 'Overlapping lesion of brain and central nervous system', 'Overlapping lesion of penis', 'Overlapping lesion of retroperitoneum and peritoneum', 'Parotid gland', 'Dome of bladder', 'Bone of limb NOS', 'Descended testis', 'Vertebral column', 'Fundus uteri', 'Connective subcutaneous and other soft tissues of pelvis', 'Epididymis', 'Intra-abdominal lymph nodes', 'Paraspinal', 'Prepuce', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Pharynx NOS', 'Overlapping lesion of endocrine glands and related structures', 'Gum NOS', 'Spinal cord', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Skin of upper limb and shoulder', 'Nasopharynx NOS', 'Parathyroid gland', 'Bone NOS', 'Mouth NOS', 'Abdomen NOS', 'Conjunctiva', 'Spermatic cord', 'External upper lip', 'Labium minus', 'Renal pelvis', 'Overlapping lesion of lip', 'Short bones of upper limb and associated joints', 'Main bronchus', 'Upper respiratory tract NOS', 'Body of penis', 'Small intestine NOS', 'Central portion of breast', 'Lower-inner quadrant of breast', 'Labium majus', 'Tonsillar fossa', 'Cecum', 'Glans penis', 'Tail of pancreas', 'Lower third of esophagus', 'Body of pancreas', 'Intestinal tract NOS', 'Brain stem', 'Overlapping lesion of rectum anus and anal canal', 'Posterior wall of oropharynx', 'Pancreatic duct', 'Blood', 'Temporal lobe', 'Anterior floor of mouth', 'Nervous system NOS', 'Cornea NOS', 'Palate NOS', 'Occipital lobe', 'Abdominal esophagus', 'Overlapping lesion of pancreas', 'Overlapping lesion of female genital organs', 'Cheek mucosa', 'Retina', 'Overlapping lesion of male genital organs', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Larynx NOS', 'Skin of other and unspecified parts of face', 'Spleen', 'Oropharynx NOS', 'Anal canal', 'Subglottis', 'Cerebral meninges', 'Lateral wall of oropharynx', 'Middle third of esophagus', 'Nipple', 'Medulla of adrenal gland', 'Overlapping lesion of eye and adnexa', 'Olfactory nerve', 'Ethmoid sinus', 'Overlapping lesion of cervix uteri', 'Descending colon', 'Brain NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Anterior wall of bladder', 'Mandible', 'Other specified parts of pancreas', 'Skin of trunk', 'Other specified parts of female genital organs', 'Uterus NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Intrathoracic lymph nodes', 'Heart', 'Adrenal gland NOS', 'Aortic body and other paraganglia', 'Extrahepatic bile duct', 'Overlapping lesion of breast', 'Superior wall of nasopharynx', 'Fundus of stomach', 'Anterior mediastinum', 'Tongue NOS', 'Cranial nerve NOS', 'Head of pancreas', 'Overlapping lesions of oropharynx', 'Overlapping lesion of bones joints and articular cartilage', 'Retromolar area', 'Testis NOS', 'Connective subcutaneous and other soft tissues of head face and neck', 'Bladder NOS', 'Overlapping lesion of urinary organs', 'Lower-outer quadrant of breast', 'Thyroid gland', 'Anterior surface of epiglottis', 'Uterine adnexa']",,SRRSClinicalDataTier2 -Age at Diagnosis,Age at Diagnosis,AgeatDiagnosis,Age at the time of diagnosis expressed in number of days since birth.,True,,,,SRRSClinicalDataTier2 -Education Level,Education Level,EducationLevel,Highest level of education that the patient completed (direct patient-derived information),False,,"['Data not available', 'Grade school', ""Bachelor's degree"", 'High school graduate (including equivalency)', ""Master's degree"", 'Doctoral degree or professional degree', 'Graduate or professional degree', 'Some college or associate degree', 'No formal education', 'Not high school graduate', '']",,SRRSClinicalDataTier2 -Days to Follow Up,Days to Follow Up,DaystoFollowUp,Number of days between the date used for index and the date of the patient's last follow-up appointment or contact.,True,,,,SRRSClinicalDataTier2 -Years Smoked,Years Smoked,YearsSmoked,Numeric value (or unknown) to represent the number of years a person has been smoking.,True,,,,SRRSClinicalDataTier2 -Rural vs Urban,Rural vs Urban,RuralvsUrban,"Density of population in the county of residence, based on census data (updated last on 4/28/20). Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the associated county on the right side of the result field. Go to https://www2.census.gov/programs-surveys/acs/data/covid_19/Data_Profiles_for_HHS/050-County_By_State/. Select the dp02_XX.csv file where XX = the two letter abbreviation for the appropriate state. On row 166 find the total population for the appropriate county. If the total population is <2,500 enter a value of ""Rural Population""; if 2,500 - 50,000 enter a value of ""Urban Cluster""; or if >50,000 enter ""Urban Population""",False,,"['Rural Population (population <2500)', 'Urban Cluster (population 2500 - 50000)', 'Urban Population (population >50000)', '']",,SRRSClinicalDataTier2 -Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,SRRSClinicalDataTier2 -Cancer Incidence Location,Cancer Incidence Location,CancerIncidenceLocation,"The county and state in which the patient lives and to which the cancer_incidence data correlates. Record as ""County, State"" as they appear in the incidence box from which the cancer_incidence data is obtained in the https://gis.cancer.gov/canceratlas/tableview/ website",False,,,,SRRSClinicalDataTier2 -Morphology,Morphology,Morphology,"The third edition of the International Classification of Diseases for Oncology, published in 2000 used principally in tumor and cancer registries for coding the site (topography) and the histology (morphology) of neoplasms. The study of the structure of the cells and their arrangement to constitute tissues and, finally, the association among these to form organs. In pathology, the microscopic process of identifying normal and abnormal morphologic characteristics in tissues, by employing various cytochemical and immunocytochemical stains. A system of numbered categories for representation of data.",True,,,,SRRSClinicalDataTier2 -Race,Race,Race,"An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation withina a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution.",True,,"['white', 'Not Reported', 'american indian or alaska native', 'asian', 'Other', 'Unknown', 'native hawaiian or other pacific islander', 'not allowed to collect', 'black or african american']",,SRRSClinicalDataTier2 -Days to Last Follow up,Days to Last Follow up,DaystoLastFollowup,"Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days.",True,,,,SRRSClinicalDataTier2 -Tumor Grade,Tumor Grade,TumorGrade,"Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.",True,,"['Low Grade', 'Not Reported', 'High Grade', 'Intermediate Grade', 'Not Applicable', 'GX', 'G2', 'Unknown', 'GB', 'G3', 'G4', 'G1']",,SRRSClinicalDataTier2 -Gene Symbol,Gene Symbol,GeneSymbol,"The text term used to describe a gene targeted or included in molecular analysis. For rearrangements, this is should be used to represent the reference gene. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",True,,,,SRRSClinicalDataTier2 -Primary Diagnosis,Primary Diagnosis,PrimaryDiagnosis,"Text term used to describe the patient's histologic diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",True,,"['Adenocarcinoma in tubular adenoma', 'Tumor cells NOS', 'Malignant lymphoma mixed cell type follicular', 'T-cell large granular lymphocytic leukemia', 'Kaposi sarcoma', 'Carcinoma in adenomatous polyp', 'Adenocarcinoma in situ in tubular adenoma', 'Mixed medullary-papillary carcinoma', 'Liposarcoma NOS', 'Carcinoma intestinal type', 'Classical Hodgkin lymphoma nodular sclerosis grade 1', 'Bile duct adenoma', 'Inflammatory carcinoma', 'Carcinoma in situ in a polyp NOS', 'Intravascular B-cell lymphoma', 'Melanotic psammomatous MPNST', 'Acinar cell carcinoma', 'Papillary renal cell carcinoma', 'Papillary serous cystadenoma NOS', 'Papillary adenoma NOS', 'Interstitial cell tumor benign', 'Mixed small cell carcinoma', 'Rhabdoid sarcoma', 'Malignant lymphoma mixed cell type diffuse', 'Chronic leukemia NOS', 'Intraductal papillary carcinoma', 'Intraductal tubular-papillary neoplasm high grade', 'Central neurocytoma', 'Undifferentiated spindle cell sarcoma', 'Bronchiolo-alveolar carcinoma indeterminate type', 'Pancreatic endocrine tumor NOS', 'Tubulocystic renal cell carcinoma', 'Basophil adenocarcinoma', 'Intraductal carcinoma solid type', 'Papillotubular adenoma', 'Undifferentiated epithelioid sarcoma', 'Renal medullary carcinoma', 'Chronic granulocytic leukemia Philadelphia chromosome (Ph1) positive', 'Unclassified tumor benign', 'Bronchial adenoma cylindroid', 'Classical Hodgkin lymphoma mixed cellularity NOS', 'Pigmented adenoma', 'Infiltrating duct and colloid carcinoma', 'Bronchial-associated lymphoid tissue lymphoma', 'Epidermoid carcinoma in situ NOS', 'Unknown', 'Carcinoma NOS', 'Malignancy', 'Undifferentiated leukaemia', 'Unclassified tumor borderline malignancy', 'Hodgkin lymphoma NOS', 'Papillary cystadenoma NOS', 'Medullary carcinoma NOS', 'Myeloma NOS', 'Acute basophilic leukaemia', 'Renal cell carcinoma NOS', 'Neoplasm secondary', 'Primary amyloidosis', 'Acute lymphoblastic leukemia NOS', 'Malignant melanoma in junctional nevus', 'Nevus NOS', 'Tumor malignant NOS', 'Basal cell adenoma', 'Bronchio-alveolar carcinoma mucinous', 'Mucosal-associated lymphoid tissue lymphoma', 'Pleomorphic lobular carcinoma in situ', 'Small cell carcinoma NOS', 'Dermal nevus', 'Liver cell adenoma', 'Malignant lymphoma lymphocytic diffuse NOS', 'Cerebellar liponeurocytoma', 'Acute lymphoblastic leukemia mature B-cell type', 'Adenocarcinoma combined with other types of carcinoma', 'Adenocarcinoma metastatic NOS', 'Carcinoma in a polyp NOS', 'Pleomorphic adenoma', 'Osteosarcoma NOS', 'Carcinosarcoma NOS', 'Lymphoblastic leukemia NOS', 'Unclassified tumor uncertain whether benign or malignant', 'Renal cell carcinoma unclassified', 'Neoplasm NOS', 'Acute lymphoblastic leukemia precursor cell type', 'Cerebellar sarcoma NOS', 'Renal cell carcinoma spindle cell', 'Small cell sarcoma', 'Bronchiolo-alveolar carcinoma goblet cell type', 'Combined small cell-adenocarcinoma', 'Precancerous melanosis NOS', 'Tumor NOS', 'Neoplasm malignant', 'Melanoma in situ', 'Melanotic neuroectodermal tumor', 'Intraductal carcinoma NOS', 'Lymphoma NOS', 'Tumor cells malignant', 'Hepatocholangiocarcinoma', 'Preleukemic syndrome', 'Papillomatosis glandular', 'Small congenital nevus', 'c-ALL', 'Hodgkin lymphoma nodular sclerosis NOS', 'Bronchiolo-alveolar adenocarcinoma NOS', 'Pancreatic microadenoma', 'Tubular carcinoid', 'Gastrinoma NOS', 'Papillary urothelial carcinoma', 'Carcinoma in situ in adenomatous polyp', 'Pancreatobiliary-type carcinoma', 'Small cell osteosarcoma', 'Adenocarcinoma of anal glands', 'Gastrointestinal stromal tumor malignant', 'Acute myeloid leukemia minimal differentiation', 'Ductal carcinoma NOS', 'Malignant melanoma in Hutchinson melanotic freckle', 'Malignant lymphoma nodular NOS', 'B-cell lymphocytic leukemia/small lymphocytic lymphoma', 'Malignant lymphoma NOS', 'Combined hepatocellular carcinoma and cholangiocarcinoma', 'Combined small cell-large carcinoma', 'Epithelial tumor malignant', 'Intraepidermal carcinoma NOS', 'Endometrioid carcinoma NOS', 'Acute leukemia Burkitt type', 'Pituitary adenoma NOS', 'Adenocarcinoma NOS', 'Papillary epidermoid carcinoma', 'Teratoma NOS', 'Combined small cell-squamous cell carcinoma', 'Lobular carcinoma NOS', 'Basophil carcinoma', 'Serous cystadenocarcinoma NOS', 'Glioma malignant', 'Diffuse astrocytoma IDH-wildtype', 'Renal cell carcinoma sarcomatoid', 'Hepatoid adenocarcinoma', 'Intraductal and lobular carcinoma', 'Malignant melanoma NOS', 'Peripheral T-cell lymphoma large cell', 'Chronic myelomonocytic leukemia Type 1', 'Combined/mixed carcinoid and adenocarcinoma', 'Intraductal carcinoma and lobular carcinoma in situ', 'Pancreatic endocrine tumor nonfunctioning', 'Tubulovillous adenoma NOS', 'Intraductal carcinoma noninfiltrating NOS', 'Tumorlet benign', 'Basal cell epithelioma', 'Endometrioid adenocarcinoma NOS', 'Large cell carcinoma NOS', 'Burkitt tumor', 'Papillary microcarcinoma', 'Melanotic neurofibroma', 'Paget disease and intraductal carcinoma of breast', 'Precursor B-cell lymphoblastic lymphoma', 'Pleomorphic carcinoma', 'Dysplastic nevus', 'Undifferentiated high-grade pleomorphic sarcoma', 'Acute myeloid leukemia NOS', 'Esophageal glandular dysplasia (intraepithelial neoplasia) low grade', 'Unclassified tumor malignant uncertain whether primary or metastatic', 'Mixed pineal tumor', 'Bile duct adenocarcinoma', 'Adenocarcinoma in adenomatous polyp', 'Lymphatic leukemic NOS', 'Papillotubular adenocarcinoma', 'Lobular adenocarcinoma', 'Melanocytoma eyeball', 'Melanoma malignant of soft parts', 'Therapy related myeloid neoplasm', 'Oat cell carcinoma', 'Duct carcinoma desmoplastic type', 'Melanotic MPNST', 'Neurofibromatosis NOS', 'Melanotic medulloblastoma', 'Skin appendage carcinoma', 'Hodgkin disease NOS', 'Diffuse melanocytosis', 'Preleukemia', 'Tumor cells benign', 'Chronic myelomonocytic leukemia Type II', 'Cervical intraepithelial neoplasia low grade', 'Tubulo-papillary adenoma', 'Adenocarcinoma of anal ducts', 'Papillary carcinoma in situ', 'Acute lymphocytic leukemia', 'Myeloid leukemia NOS', 'T-cell large granular lymphocytosis', 'Bronchial adenoma NOS', 'Pulmonary blastoma', 'Intraductal carcinoma clinging', 'Adult T-cell lymphoma/leukemia', 'Intraductal adenocarcinoma noninfiltrating NOS', 'Acute lymphatic leukemia', 'Infiltrating duct and cribriform carcinoma', 'Neoplasm metastatic', 'Basal cell tumor', 'Papilloma of bladder', 'Teratoma malignant NOS', 'Pancreatoblastoma', 'Infiltrating duct carcinoma NOS', 'Precursor T-cell lymphoblastic lymphoma', 'Basal cell carcinoma NOS', 'Malignant melanoma in precancerous melanosis', 'Inflammatory adenocarcinoma', 'Splenic B-cell lymphoma/leukemia unclassifiable', 'Squamous cell carcinoma adenoid', 'T-cell lymphoma NOS', 'Tubular adenoma NOS', 'Papillary adenocarcinoma NOS', 'Esophageal intraepithelial neoplasia high grade', 'Papillary squamous cell carcinoma', 'Pulmonary adenomatosis', 'Bile duct cystadenoma', 'Combined large cell neuroendocrine carcinoma', 'Neoplasm uncertain whether benign or malignant', 'Mammary carcinoma in situ', 'Melanoma NOS', 'Spindle cell melanoma NOS', 'Esophageal glandular dysplasia (intraepithelial neoplasia) high grade', 'Neuroendocrine carcinoma NOS', 'Meningeal melanoma', 'Burkitt-like lymphoma', 'Precursor cell lymphoblastic leukemia NOS', 'Acute lymphoid leukemia', 'Chondrosarcoma grade 2/3', 'Tubulopapillary adenocarcinoma', 'B lymphoblastic leukemia/lymphoma NOS', 'Non-lymphocytic leukemia NOS', 'Pleomorphic liposarcoma', 'Mixed medullary-follicular carcinoma', 'Bronchiolo-alveolar carcinoma NOS', 'Myelocytic leukemia NOS', 'Splenic lymphoma with villous lymphocytes', 'Transitional carcinoma', 'Melanocytic nevus', 'Liposarcoma well differentiated', 'Eosinophilic leukemia', 'Chronic myeloproliferative disease NOS', 'Adenocarcinoma in situ in a polyp NOS', 'Hodgkin lymphoma mixed cellularity NOS', 'Classical Hodgkin lymphoma nodular sclerosis grade 2', 'Eosinophilic granuloma', 'Tumor embolus', 'Mixed tumor NOS', 'Carcinoma diffuse type', 'Precursor T-cell lymphoblastic leukemia', 'Neurofibrosarcoma', 'Melanocytoma NOS', 'B-ALL', 'Bronchio-alveolar carcinoma mixed mucinous and non-mucinous', 'Acute myeloid leukemia MLL', 'Adenocarcinoma in situ non-mucinous', 'Malignant lymphoma lymphoblastic NOS', 'Papillary adenocarcinoma follicular variant', 'Tumor cells uncertain whether benign or malignant', 'Pleomorphic lipoma', 'Lymphocytic leukemia NOS', 'Astrocytoma anaplastic', 'Non-Hodgkin lymphoma NOS', 'Papillary serous adenocarcinoma', 'Meningioma malignant', 'Chronic lymphoid leukemia', 'Ductal carcinoma in situ NOS', 'Neuroepithelioma NOS', 'Melanotic progonoma', 'Melanotic schwannoma', 'Diffuse astrocytoma IDH-mutant', 'Small cell neuroendocrine carcinoma', 'Esophageal squamous intraepithelial neoplasia (dysplasia) high grade', 'Paget disease extramammary', 'Prostatic intraepithelial neoplasia grade III', 'Ewing sarcoma', 'Micropapillary carcinoma NOS', 'Epithelial tumor benign', 'Hepatocellular adenoma', 'Cementoma NOS', 'Malignant lymphoma mixed cell type nodular', 'Acute leukemia NOS', 'Bile duct carcinoma', 'Nephroblastoma NOS', 'Pagetoid reticulosis', 'Hepatocarcinoma', 'Not Reported', 'Neoplasm malignant uncertain whether primary or metastatic', 'Malignant melanoma regressing', 'Bronchiolo-alveolar carcinoma Clara cell and goblet cell type', 'Dermatofibroma NOS', 'Interstitial cell tumor malignant', 'Adenocarcinoma in situ NOS', 'Adenocarcinoma endocervical type', 'Meningioma anaplastic', 'B lymphoblastic leukemia/lymphoma with hypodiploidy (Hypodiploid ALL)', 'Intraductal tubulopapillary neoplasm', 'Tumor secondary', 'Chronic myelogenous leukemia Philadelphia chromosome (Ph 1) positive', 'Sclerosing hemangioma', 'Papillary transitional cell carcinoma', 'Tubular androblastoma NOS', 'Ependymoma NOS', 'Papillary tumor of the pineal region', 'Chronic myelocytic leukemia NOS', 'Papillary serous cystadenocarcinoma', 'Haemangiosarcoma', 'Papillary and follicular carcinoma', 'Chronic myelomonocytic leukemia in transformation', 'Carcinoma anaplastic NOS', 'Paget disease mammary', 'Liver cell carcinoma', 'Eosinophil adenocarcinoma', 'Sclerosing hepatic carcinoma', 'Tumor metastatic', 'Endometrial sarcoma NOS', 'Gastrin cell tumor', 'Chronic myeloproliferative disorder', 'Acute promyelocytic leukemia NOS', 'Malignant lymphoma Hodgkin', 'Classical Hodgkin lymphoma lymphocyte depletion NOS', 'Lobular carcinoma noninfiltrating', 'Mixed pancreatic endocrine and exocrine tumor malignant', 'Unclassified tumor malignant', 'Chondroma NOS', 'Basophil adenoma', 'Transitional cell carcinoma', 'Carcinoma metastatic NOS', 'Medullary adenocarcinoma', 'Adenocarcinoma in villous adenoma', 'Ganglioglioma NOS', 'Intradermal nevus', 'Osteoblastoma malignant', 'Papillary squamous cell carcinoma in situ', 'Undifferentiated pleomorphic sarcoma', 'Bronchiolar carcinoma', 'Pancreatic endocrine tumor benign', 'Malignant melanoma in congenital melanocytic nevus', 'Malignant lymphoma diffuse NOS', 'Composite Hodgkin and non-Hodgkin lymphoma', 'Monocytic leukemia NOS', 'Paraganglioma malignant', 'Splenic diffuse red pulp small B-cell lymphoma', 'B lymphoblastic leukemia/lymphoma with hyperdiploidy', 'Rodent ulcer', 'Hodgkin sarcoma', 'Familial adenomatous polyposis', 'Duct cell carcinoma', 'Rhabdomyosarcoma NOS', 'Eosinophil carcinoma', 'Pulmonary artery intimal sarcoma', 'Capillary hemangioma', 'Adult rhabdomyoma', 'Tubular carcinoma', 'Burkitt cell leukemia', 'Bronchiolo-alveolar carcinoma Clara cell', 'Papillary glioneuronal tumor', 'T lymphoblastic leukemia/lymphoma', 'Neuroblastoma NOS', 'Meningioma NOS', 'Adenocarcinoid tumor', 'Malignant lymphoma large cell NOS', 'Combined small cell carcinoma', 'Mucous adenocarcinoma', 'Peripheral T-cell lymphoma NOS', 'Renal carcinoma collecting duct type', 'Bile duct cystadenocarcinoma', 'Chronic myelogenous leukemia BCR-ABL positive', 'Intraductal tubular-papillary neoplasm low grade', 'Tumor benign', 'Adenocarcinoma intestinal type', 'Pro-B ALL', 'Malignant lymphoma large B-cell diffuse NOS', 'Secondary carcinoma', 'Gastrinoma malignant', 'Intracystic papilloma', 'Cancer', 'Intraductal papillary adenocarcinoma with invasion', 'Mixed squamous cell and glandular papilloma', 'Sarcoma NOS', 'Non-invasive low grade serous carcinoma', 'Serous surface papillary carcinoma', 'Pro-T ALL', 'Neurofibroma NOS', 'Pancreatobiliary neoplasm non-invasive', 'Bronchial adenoma carcinoid', 'Precursor B-cell lymphoblastic leukemia', 'Melanoameloblastoma', 'Mixed adenocarcinoma and epidermoid carcinoma', 'Splenic marginal zone lymphoma NOS', 'Intraepidermal squamous cell carcinoma Bowen type', 'Carcinoma undifferentiated NOS', 'Capillary lymphangioma', 'Chronic myelomonocytic leukemia NOS', 'Adenocarcinoma in a polyp NOS', 'Astrocytoma NOS', 'Glioblastoma', 'Adult T-cell lymphoma', 'Transitional cell carcinoma in situ', 'Carcinoma in pleomorphic adenoma', 'Renal cell adenocarcinoma', 'Medulloblastoma NOS', 'Papillomatosis NOS', 'Acute myelomonocytic leukemia', 'Malignant lymphoma immunoblastic NOS', 'Chronic lymphocytic leukemia B-cell type (includes all variants of BCLL)', 'Malignant lymphoma lymphocytic NOS', 'Nonpigmented nevus', 'Squamous cell carcinoma clear cell type', 'Mixed adenocarcinoma and squamous cell carcinoma', 'Diffuse large B-cell lymphoma NOS', 'Paraganglioma benign', 'Malignant lymphoma non-Hodgkin NOS', 'Classical Hodgkin lymphoma lymphocyte-rich', 'Intraductal micropapillary carcinoma', 'Secretory carcinoma of breast', 'Gastrin cell tumor malignant', 'Papilloma NOS', 'Infiltrating basal cell carcinoma NOS', 'Adenocarcinoma in polypoid adenoma', 'Chronic neutrophilic leukemia', 'Undifferentiated sarcoma', 'Neurosarcoma', 'Medullary osteosarcoma', 'Papillary carcinoma NOS', 'Chronic lymphocytic leukemia', 'Undifferentiated uterine sarcoma', 'Malignant lymphoma lymphocytic nodular NOS', 'Adenocarcinoma in situ mucinous', 'Multiple myeloma', 'Lobular and ductal carcinoma', 'Undifferentiated round cell sarcoma', 'Chronic lymphatic leukemia', 'Endometrioid adenofibroma NOS', 'Malignant lymphoma large B-cell NOS', 'Pancreatic endocrine tumor malignant', 'Cervical intraepithelial neoplasia grade III', 'Glioma NOS', 'Papillary adenofibroma', 'Classical Hodgkin lymphoma nodular sclerosis NOS', 'Non-small cell carcinoma', 'Squamous cell carcinoma NOS', 'Haemangioblastoma', 'Paraganglioma NOS', 'Bronchiolar adenocarcinoma', 'Liposarcoma differentiated', 'Mixed tumor malignant NOS', 'Burkitt lymphoma NOS (Includes all variants)', 'Renal cell carcinoma chromophobe type', 'Malignant melanoma in giant pigmented nevus', 'Chronic monocytic leukemia', 'Carcinoma in situ NOS', 'Lymphoblastoma', 'Tubulolobular carcinoma', 'Rhabdoid tumor NOS', 'Hepatocellular carcinoma NOS', 'Adenocarcinoma in situ in adenomatous polyp', 'Classical Hodgkin lymphoma nodular sclerosis cellular phase', 'Paget disease of breast', 'Squamous cell carcinoma in situ NOS', 'Classical Hodgkin lymphoma lymphocyte depletion diffuse fibrosis', 'Bronchiolo-alveolar carcinoma non-mucinous', 'Rhabdosarcoma', 'Astrocytoma low grade', 'Chronic myeloid leukemia NOS', 'Chronic granulocytic leukemia NOS', 'Endometrioid adenoma NOS', 'Typical carcinoid', 'Rhabdoid meningioma', 'Hodgkin paragranuloma NOS', 'Hodgkin granuloma', 'Duct adenocarcinoma NOS', 'Juvenile myelomonocytic leukemia', 'Adenocarcinoma diffuse type', 'Osteoblastoma NOS', 'Rhabdomyosarcoma with ganglionic differentiation', 'Eosinophil adenoma', 'Interstitial cell tumor NOS', 'Tubular adenocarcinoma', 'Myoepithelioma', 'Pigmented nevus NOS', 'Duct carcinoma NOS', 'Neoplasm benign', 'Rhabdomyoma NOS', 'Spindle cell carcinoma NOS', 'Pleomorphic lobular carcinoma', 'Lobular carcinoma in situ NOS', 'Central neuroblastoma', 'Adenocarcinoma pancreatobiliary type', 'Chronic granulocytic leukemia BCR/ABL', 'Pigmented basal cell carcinoma', 'Paget disease and infiltrating duct carcinoma of breast', 'Acute lymphoblastic leukemia-lymphoma NOS', 'Epidermoid carcinoma NOS', 'Hepatoid carcinoma', 'Papillary meningioma', 'High-grade serous carcinoma', 'Basal cell adenocarcinoma', 'Esophageal squamous intraepithelial neoplasia (dysplasia) low grade', 'Malignant lymphoma small B lymphocytic NOS', 'Pituitary carcinoma NOS', 'Tubular androblastoma with lipid storage', 'Meningeal melanocytoma', 'Duct adenoma NOS', 'Diffuse astrocytoma low grade', 'Intraductal papillary adenocarcinoma NOS', 'Splenic marginal zone B-cell lymphoma', 'Classical Hodgkin lymphoma lymphocyte depletion reticular', 'B cell lymphoma NOS']",,SRRSClinicalDataTier2 -Molecular Analysis Method,Molecular Analysis Method,MolecularAnalysisMethod,The text term used to describe the method used for molecular analysis. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,True,,"['Not Applicable', 'WGS', 'Targeted Sequencing', 'FISH', 'IHC', 'Unknown', 'Microarray', 'Cytogenetics NOS', 'Nuclear Staining', 'Microsatellite Analysis', 'Sequencing NOS', 'Comparative Genomic Hybridization', 'Not Reported', 'Flow Cytometry', 'Southern Blotting', 'ISH', 'RNA Sequencing', 'Other', 'RT-PCR', 'WXS', 'Karyotype']",,SRRSClinicalDataTier2 -Test Result,Test Result,TestResult,The text term used to describe the result of the molecular test. If the test result was a numeric value see test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,True,,"['Equivocal', 'Copy Number Reported', 'Abnormal NOS', 'Not Reported', 'Low', 'Overexpressed', 'Test Value Reported', 'Intermediate', 'Not Applicable', 'Positive', 'Unknown', 'High', 'Normal', 'Negative', 'Loss of Expression']",,SRRSClinicalDataTier2 -Pack Years Smoked,Pack Years Smoked,PackYearsSmoked,Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes smoked per day x number of years smoked divided by 20.,True,,,,SRRSClinicalDataTier2 -Site of Resection or Biopsy,Site of Resection or Biopsy,SiteofResectionorBiopsy,"The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",True,,"['Paraurethral gland', 'Colon NOS', 'Frontal sinus', 'Overlapping lesion of tongue', 'Overlapping lesion of palate', 'Scrotum NOS', 'Bone marrow', 'Axillary tail of breast', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'unknown primary site', 'Broad ligament', 'Lateral floor of mouth', 'Overlapping lesion of vulva', 'Trigone of bladder', 'Lacrimal gland', 'Thorax NOS', 'Ampulla of Vater', 'Myometrium', 'Penis NOS', 'Female genital tract NOS', 'Submandibular gland', 'Anterior 2/3 of tongue NOS', 'Posterior wall of bladder', 'Thymus', 'Endocrine gland NOS', 'Stomach NOS', 'Unknown', 'Cerebrum', 'Splenic flexure of colon', 'Urachus', 'Skin of lip NOS', 'Mucosa of lip NOS', 'Accessory sinus NOS', 'Cortex of adrenal gland', 'Other ill-defined sites', 'Middle lobe lung', 'Pelvis NOS', 'Anus NOS', 'Upper-inner quadrant of breast', 'Posterior mediastinum', 'Esophagus NOS', 'Duodenum', 'Cervical esophagus', 'Optic nerve', 'Long bones of lower limb and associated joints', 'Middle ear', 'Breast NOS', 'Dorsal surface of tongue NOS', 'Lesser curvature of stomach NOS', 'Overlapping lesion of floor of mouth', 'Overlapping lesion of heart mediastinum and pleura', 'Eye NOS', 'Overlapping lesion of esophagus', 'Ciliary body', 'Ureteric orifice', 'Postcricoid region', 'External ear', 'Base of tongue NOS', 'Liver', 'Commissure of lip', 'Cloacogenic zone', 'Lower lobe lung', 'Transverse colon', 'Acoustic nerve', 'Supraglottis', 'Fallopian tube', 'Upper third of esophagus', 'Skin of scalp and neck', 'Choroid', 'Long bones of upper limb scapula and associated joints', 'Overlapping lesion of brain', 'Upper gum', 'Skin NOS', 'Hard palate', 'Ileum', 'Overlapping lesion of colon', 'Ascending colon', 'Lower gum', 'Pelvic bones sacrum coccyx and associated joints', 'Hepatic flexure of colon', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Vestibule of mouth', 'Cervix uteri', 'Bones of skull and face and associated joints', 'Overlapping lesion of lip oral cavity and pharynx', 'Endometrium', 'Sphenoid sinus', 'Overlapping lesion of ill-defined sites', 'Sigmoid colon', 'Peritoneum NOS', 'Specified parts of peritoneum', 'Meckel diverticulum', 'Rectosigmoid junction', 'Kidney NOS', 'Reticuloendothelial system NOS', 'Rectum NOS', 'Pylorus', 'Overlapping lesion of tonsil', 'Pleura NOS', 'Jejunum', 'Vallecula', 'Skin of lower limb and hip', 'Pelvic lymph nodes', 'External lower lip', 'Overlapping lesion of skin', 'Mucosa of upper lip', 'Ovary', 'Cauda equina', 'Lower limb NOS', 'Body of stomach', 'Overlapping lesion of larynx', 'Pancreas NOS', 'Overlapping lesion of lung', 'Overlapping lesion of major salivary glands', 'Uvula', 'Overlapping lesion of hypopharynx', 'Round ligament', 'Corpus uteri', 'Biliary tract NOS', 'Male genital organs NOS', 'Parametrium', 'External lip NOS', 'Overlapping lesion of accessory sinuses', 'Cardia NOS', 'Islets of Langerhans', 'Carotid body', 'Ventral surface of tongue NOS', 'Autonomic nervous system NOS', 'Overlapping lesion of corpus uteri', 'Spinal meninges', 'Posterior wall of nasopharynx', 'Placenta', 'Intrahepatic bile duct', 'Overlapping lesion of digestive system', 'Mediastinum NOS', 'Hematopoietic system NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Major salivary gland NOS', 'Cerebellum NOS', 'Overlapping lesion of stomach', 'Vulva NOS', 'Craniopharyngeal duct', 'Lung NOS', 'Greater curvature of stomach NOS', 'Upper-outer quadrant of breast', 'Gallbladder', 'Thoracic esophagus', 'Lymph nodes of axilla or arm', 'Ventricle NOS', 'Overlapping lesion of biliary tract', 'Hypopharynx NOS', 'Clitoris', 'Exocervix', 'Parietal lobe', 'Waldeyer ring', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Head face or neck NOS', 'Anterior wall of nasopharynx', 'Urethra', 'Overlapping lesion of nasopharynx', 'Maxillary sinus', 'Lymph nodes of inguinal region or leg', 'Ureter', 'Tonsillar pillar', 'Sublingual gland', 'Pituitary gland', 'Gastrointestinal tract NOS', 'Pineal gland', 'Meninges NOS', 'Lingual tonsil', 'Trachea', 'Pyriform sinus', 'Mucosa of lower lip', 'Not Reported', 'Posterior wall of hypopharynx', 'Urinary system NOS', 'Orbit NOS', 'Short bones of lower limb and associated joints', 'Connective subcutaneous and other soft tissues of thorax', 'Upper limb NOS', 'Gastric antrum', 'Lymph node NOS', 'Peripheral nerves and autonomic nervous system of thorax', 'Ill-defined sites within respiratory system', 'Other specified parts of male genital organs', 'Rib sternum clavicle and associated joints', 'Overlapping lesion of bladder', 'Appendix', 'Prostate gland', 'Lymph nodes of multiple regions', 'Lateral wall of nasopharynx', 'Branchial cleft', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Floor of mouth NOS', 'Connective subcutaneous and other soft tissues NOS', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Bladder neck', 'Border of tongue', 'Connective subcutaneous and other soft tissues of abdomen', 'Overlapping lesion of small intestine', 'Lateral wall of bladder', 'Soft palate NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Isthmus uteri', 'Nasal cavity', 'Endocervix', 'Tonsil NOS', 'Glottis', 'Retroperitoneum', 'Peripheral nerves and autonomic nervous system of pelvis', 'Frontal lobe', 'Vagina NOS', 'Undescended testis', 'Laryngeal cartilage', 'Eyelid', 'Hypopharyngeal aspect of aryepiglottic fold', 'Overlapping lesion of other and unspecified parts of mouth', 'Upper lobe lung', 'Lip NOS', 'Lymph nodes of head face and neck', 'Overlapping lesion of brain and central nervous system', 'Overlapping lesion of penis', 'Overlapping lesion of retroperitoneum and peritoneum', 'Parotid gland', 'Dome of bladder', 'Bone of limb NOS', 'Descended testis', 'Vertebral column', 'Fundus uteri', 'Connective subcutaneous and other soft tissues of pelvis', 'Epididymis', 'Intra-abdominal lymph nodes', 'Paraspinal', 'Prepuce', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Pharynx NOS', 'Overlapping lesion of endocrine glands and related structures', 'Gum NOS', 'Spinal cord', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Skin of upper limb and shoulder', 'Nasopharynx NOS', 'Parathyroid gland', 'Bone NOS', 'Mouth NOS', 'Abdomen NOS', 'Conjunctiva', 'Spermatic cord', 'External upper lip', 'Labium minus', 'Renal pelvis', 'Overlapping lesion of lip', 'Short bones of upper limb and associated joints', 'Main bronchus', 'Upper respiratory tract NOS', 'Body of penis', 'Small intestine NOS', 'Central portion of breast', 'Lower-inner quadrant of breast', 'Labium majus', 'Tonsillar fossa', 'Cecum', 'Glans penis', 'Tail of pancreas', 'Lower third of esophagus', 'Body of pancreas', 'Intestinal tract NOS', 'Brain stem', 'Overlapping lesion of rectum anus and anal canal', 'Posterior wall of oropharynx', 'Pancreatic duct', 'Blood', 'Temporal lobe', 'Anterior floor of mouth', 'Nervous system NOS', 'Cornea NOS', 'Palate NOS', 'Occipital lobe', 'Abdominal esophagus', 'Overlapping lesion of pancreas', 'Overlapping lesion of female genital organs', 'Cheek mucosa', 'Retina', 'Overlapping lesion of male genital organs', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Larynx NOS', 'Skin of other and unspecified parts of face', 'Spleen', 'Oropharynx NOS', 'Anal canal', 'Subglottis', 'Cerebral meninges', 'Lateral wall of oropharynx', 'Middle third of esophagus', 'Nipple', 'Medulla of adrenal gland', 'Overlapping lesion of eye and adnexa', 'Olfactory nerve', 'Ethmoid sinus', 'Overlapping lesion of cervix uteri', 'Descending colon', 'Brain NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Anterior wall of bladder', 'Mandible', 'Other specified parts of pancreas', 'Skin of trunk', 'Other specified parts of female genital organs', 'Uterus NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Intrathoracic lymph nodes', 'Heart', 'Adrenal gland NOS', 'Aortic body and other paraganglia', 'Extrahepatic bile duct', 'Overlapping lesion of breast', 'Superior wall of nasopharynx', 'Fundus of stomach', 'Anterior mediastinum', 'Tongue NOS', 'Cranial nerve NOS', 'Head of pancreas', 'Overlapping lesions of oropharynx', 'Overlapping lesion of bones joints and articular cartilage', 'Retromolar area', 'Testis NOS', 'Connective subcutaneous and other soft tissues of head face and neck', 'Bladder NOS', 'Overlapping lesion of urinary organs', 'Lower-outer quadrant of breast', 'Thyroid gland', 'Anterior surface of epiglottis', 'Uterine adnexa']",,SRRSClinicalDataTier2 -Stop Days from Index,Stop Days from Index,StopDaysfromIndex,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'",False,,,,SRRSClinicalDataTier2 -Treatment Type,Treatment Type,TreatmentType,Text term that describes the kind of treatment administered.,False,,,,SRRSClinicalDataTier2 -Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,SRRSClinicalDataTier2 -Country of Birth,Country of Birth,CountryofBirth,Country where the patient was born.,False,,"['Belize', 'Monaco', 'Bahrain', 'Iraq', 'South Africa', 'Vietnam', 'Niue', 'Poland', 'Albania', 'Burundi', 'Spain', 'Bhutan', 'Saudi Arabia', 'Madagascar', 'Gambia', 'Switzerland', 'Laos', 'Saint Lucia', 'Myanmar', 'Mayotte', 'Guadeloupe', 'South Korea', 'Tokelau', 'Syria', 'Pakistan', 'Isle of Man', 'Yemen', 'Svalbard & Jan Mayen Islands', 'Jersey', 'Bosnia and Herzegovina', 'Eritrea', 'Guinea', 'Philippines', 'Guinea-Bissau', 'Azerbaijan', 'Somalia', 'Sudan', 'Cambodia', 'Cuba', 'Rwanda', 'Tonga', 'Saint Kitts and Nevis', 'Finland', 'Paraguay', 'Malawi', 'Falkland Islands (Malvinas)', 'Federated States of Micronesia', 'Niger', 'Colombia', 'Democratic Republic of the Congo', 'North Macedonia', 'Haiti', 'Timor-Leste', 'Austria', 'Chad', 'Iceland', 'Dominica', 'Malta', 'Denmark', 'Kosovo', 'Martinique', 'Bangladesh', 'San Marino', 'South Sudan', 'Georgia', 'Nigeria', 'Gibraltar', 'Nauru', 'Tajikistan', 'Montserrat', 'Sweden', 'Antigua and Barbuda', 'Indonesia', 'Sri Lanka', 'Greece', 'Gabon', 'Japan', 'Mauritania', 'Nicaragua', 'China', 'Cape Verde', 'Unknown', 'Grenada', 'French Polynesia', 'Moldova', 'Cayman Islands', 'Dominican Republic', 'Liechtenstein', 'Senegal', 'Holy See', 'Mali', 'Vanuatu', 'India', 'Bermuda', 'Netherlands', 'Ireland', 'Zambia', 'North Korea', 'Macau', 'Romania', 'Solomon Islands', 'Suriname', 'Nepal', 'Croatia', 'Reunion', 'Ghana', 'Saint Helena Ascension and Tristan da Cunha', 'Israel', 'Faroe Islands', 'Greenland', 'State of Palestine', 'Wallis and Futuna', 'Ecuador', 'French Guiana', 'Angola', 'Aruba', 'Guyana', 'Kuwait', 'Taiwan', 'Singapore', 'Togo', 'Andorra', 'Lebanon', 'Northern Mariana Islands', 'Armenia', 'Iran', 'New Zealand', 'Bolivia', 'Cameroon', 'Norway', 'Panama', 'Papua New Guinea', 'Qatar', 'Tanzania', 'Portugal', 'Slovakia', 'Equatorial Guinea', 'Estonia', 'Mongolia', 'Chile', 'Burkina Faso', 'Ethiopia', 'Hungary', 'Djibouti', 'Kenya', 'Kiribati', 'Botswana', 'Australia', 'Guam', 'Congo', 'Belarus', 'Uruguay', 'Czech Republic (Czechia)', 'Lesotho', 'United Kingdom', 'Lithuania', 'Russia', 'Thailand', 'Oman', 'Benin', 'Tunisia', 'Uganda', 'Namibia', 'Honduras', 'Algeria', 'Turkey', 'Morocco', 'Barbados', 'Sierra Leone', 'Venezuela', 'Saint Pierre and Miquelon', 'Kyrgyzstan', 'Trinidad and Tobago', 'Serbia', 'Peru', 'Comoros', 'Canada', 'Hong Kong', 'Liberia', 'Malaysia', 'Puerto Rico', 'Brazil', 'Virgin Islands British', 'Zimbabwe', 'Latvia', 'Eswatini', ""Cote d'Ivoire"", 'United Arab Emirates', 'Bahamas', 'Curacao', 'Slovenia', 'Central African Republic', 'Guatemala', 'Jordan', 'Egypt', 'Germany', 'Mozambique', 'Fiji', 'Turkmenistan', 'Mexico', 'Brunei', 'France', 'Kazakhstan', 'Argentina', 'Uzbekistan', 'Samoa', 'Bulgaria', 'Virgin Islands U.S.', 'Maldives', 'Cyprus', 'Costa Rica', 'Italy', 'Libya', 'Jamaica', 'Tuvalu', 'United States', 'Saint Vincent and the Grenadines', 'Palau', 'Western Sahara', 'Guernsey', 'Mauritius', 'El Salvador', 'Afghanistan', 'Belgium', 'Luxembourg', 'Ukraine', 'Marshall Islands', 'Montenegro', 'Cook Islands', 'Seychelles', 'Sao Tome and Principe', 'New Caledonia', 'Anguilla', '']",,SRRSClinicalDataTier2 -Gender,Gender,Gender,"Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.]",True,,"['Not Reported', 'unspecified', 'Unknown', 'female', 'male']",,SRRSClinicalDataTier2 -Progression or Recurrence,Progression or Recurrence,ProgressionorRecurrence,Yes/No/unknown indicator to identify whether a patient has had a new tumor event after initial treatment.,True,,"['No', 'Yes - Progression or Recurrence', 'Unknown', 'Not Reported']",,SRRSClinicalDataTier2 -Tumor Largest Dimension Diameter,Tumor Largest Dimension Diameter,TumorLargestDimensionDiameter,"Numeric value used to describe the maximum diameter or dimension of the primary tumor, measured in centimeters.",False,,,,SRRSClinicalDataTier2 -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,SRRSClinicalDataTier2 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,SRRSClinicalDataTier2 -Last Known Disease Status,Last Known Disease Status,LastKnownDiseaseStatus,Text term that describes the last known state or condition of an individual's neoplasm.,True,,"['With tumor', 'Not Reported', 'Not Applicable', 'unknown tumor status', 'Distant met recurrence/progression', 'Loco-regional recurrence/progression', 'Tumor free', 'Biochemical evidence of disease without structural correlate', 'Not Allowed To Collect']",,SRRSClinicalDataTier2 -Ethnicity,Ethnicity,Ethnicity,"An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.",True,,"['Not Reported', 'Unknown', 'hispanic or latino', 'not hispanic or latino', 'not allowed to collect']",,SRRSClinicalDataTier2 -Cancer Incidence,Cancer Incidence,CancerIncidence,"Incidence of specific cancer type in a defined area (a number between 0 and 100). The rate of incident cases per population of 100,000 persons of a specific type of cancer as designated in the ""primary_diagnosis"" data element in the county where the patient resides, using the most recent 2013-2017 NCI Cancer Atlas derived data. Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the asociated county on the right side of the result field. On the https://gis.cancer.gov/canceratlas/tableview/ website, choose ""Incidence"" from the Topic dropdown menu, state of interest from the Area menu, ""All Races"" from the Race menu, and the cancer type (""Both Sexes"" when possible) from the Statistic menu. Find the county of interest and enter the numeric Age-Adjusted Rate per 100,000 as the value.",False,,,,SRRSClinicalDataTier2 -Medically Underserved Area,Medically Underserved Area,MedicallyUnderservedArea,"Areas or populations designated by HRSA as having too few primary care providers, high infant mortality, high poverty or a high elderly population: Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/ - enter the zip code in the main text field and use the associated county on the right side of the result field. Go to data.hrsa.gov website and select ""Query Data"". Pick the Medically Underserved Areas/Populations (MUA/P) data source in the step 1 menu and select ""View Data"". Enter the name of the county (_______ county) in the first ""Service Area"" column, adding the state in the 5th column may help direct you to the data. If the designation type in the third column is ""medically underserved area"" enter ""Yes"" as the value. If the county generates a ""No data available in table"" enter ""No"" as the value. A value of ""Unknown"" indicates that sufficient data was not available to look up the value. If value is yes, complete the Medically_underserved_score data element.",False,,"['Medically Underserved Area - Yes', 'Medically Underserved Area - Unknown', 'Medically Underserved Area - No', '']",,SRRSClinicalDataTier2 -Year of Death,Year of Death,YearofDeath,Numeric value to represent the year of the death of an individual.,False,True,," If Vital Status is ""Dead"" then ""Year of Death"" is required",SRRSClinicalDataTier2 -Cause of Death Source,Cause of Death Source,CauseofDeathSource,The text term used to describe the source used to determine the patient's cause of death.,False,True,"['Medical Record', 'Not Reported', 'Unknown', 'Death Certificate', 'Autopsy', 'Social Security Death Index', '']"," If Vital Status is ""Dead"" then ""Cause of Death Source"" is required",SRRSClinicalDataTier2 -Cause of Death,Cause of Death,CauseofDeath,The cause of death,False,True,"['Cancer Related', 'Not Reported', 'Renal Disorder NOS', 'Not Applicable', 'Spinal Muscular Atrophy', 'End-stage Renal Disease', 'Not Cancer Related', 'Unknown', 'Infection', 'Surgical Complications', 'Cardiovascular Disorder NOS', 'Toxicity', '']"," If Vital Status is ""Dead"" then ""Cause of Death"" is required",SRRSClinicalDataTier2 -Days to Death,Days to Death,DaystoDeath,Number of days between the date used for index and the date from a person's date of death represented as a calculated number of days.,False,True,," If Vital Status is ""Dead"" then ""Days to Death"" is required",SRRSClinicalDataTier2 -Days to Progression,Days to Progression,DaystoProgression,Number of days between the date used for index and the date the patient's disease progressed.,False,True,," If Progression or Recurrence is ""Yes - Progression or Recurrence"" then ""Days to Progression"" is required",SRRSClinicalDataTier2 -Progression or Recurrence Type,Progression or Recurrence Type,ProgressionorRecurrenceType,The text term used to describe the type of progressive or recurrent disease or relapsed disease.,False,True,"['Distant', 'Not Reported', 'Unknown', 'Biochemical', 'Regional', 'Local', '']"," If Progression or Recurrence is ""Yes - Progression or Recurrence"" then ""Progression or Recurrence Type"" is required",SRRSClinicalDataTier2 -Progression or Recurrence Anatomic Site,Progression or Recurrence Anatomic Site,ProgressionorRecurrenceAnatomicSite,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,False,True,"['Paraurethral gland', 'Colon NOS', 'Frontal sinus', 'Overlapping lesion of tongue', 'Overlapping lesion of palate', 'Scrotum NOS', 'Bone marrow', 'Axillary tail of breast', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'unknown primary site', 'Broad ligament', 'Lateral floor of mouth', 'Overlapping lesion of vulva', 'Trigone of bladder', 'Lacrimal gland', 'Thorax NOS', 'Ampulla of Vater', 'Myometrium', 'Penis NOS', 'Female genital tract NOS', 'Submandibular gland', 'Anterior 2/3 of tongue NOS', 'Posterior wall of bladder', 'Thymus', 'Endocrine gland NOS', 'Stomach NOS', 'Unknown', 'Cerebrum', 'Splenic flexure of colon', 'Urachus', 'Skin of lip NOS', 'Mucosa of lip NOS', 'Accessory sinus NOS', 'Cortex of adrenal gland', 'Other ill-defined sites', 'Middle lobe lung', 'Pelvis NOS', 'Anus NOS', 'Upper-inner quadrant of breast', 'Posterior mediastinum', 'Esophagus NOS', 'Duodenum', 'Cervical esophagus', 'Optic nerve', 'Long bones of lower limb and associated joints', 'Middle ear', 'Breast NOS', 'Dorsal surface of tongue NOS', 'Lesser curvature of stomach NOS', 'Overlapping lesion of floor of mouth', 'Overlapping lesion of heart mediastinum and pleura', 'Eye NOS', 'Overlapping lesion of esophagus', 'Ciliary body', 'Ureteric orifice', 'Postcricoid region', 'External ear', 'Base of tongue NOS', 'Liver', 'Commissure of lip', 'Cloacogenic zone', 'Lower lobe lung', 'Transverse colon', 'Acoustic nerve', 'Supraglottis', 'Fallopian tube', 'Upper third of esophagus', 'Skin of scalp and neck', 'Choroid', 'Long bones of upper limb scapula and associated joints', 'Overlapping lesion of brain', 'Upper gum', 'Skin NOS', 'Hard palate', 'Ileum', 'Overlapping lesion of colon', 'Ascending colon', 'Lower gum', 'Pelvic bones sacrum coccyx and associated joints', 'Hepatic flexure of colon', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Vestibule of mouth', 'Cervix uteri', 'Bones of skull and face and associated joints', 'Overlapping lesion of lip oral cavity and pharynx', 'Endometrium', 'Sphenoid sinus', 'Overlapping lesion of ill-defined sites', 'Sigmoid colon', 'Peritoneum NOS', 'Specified parts of peritoneum', 'Meckel diverticulum', 'Rectosigmoid junction', 'Kidney NOS', 'Reticuloendothelial system NOS', 'Rectum NOS', 'Pylorus', 'Overlapping lesion of tonsil', 'Pleura NOS', 'Jejunum', 'Vallecula', 'Skin of lower limb and hip', 'Pelvic lymph nodes', 'External lower lip', 'Overlapping lesion of skin', 'Mucosa of upper lip', 'Ovary', 'Cauda equina', 'Lower limb NOS', 'Body of stomach', 'Overlapping lesion of larynx', 'Pancreas NOS', 'Overlapping lesion of lung', 'Overlapping lesion of major salivary glands', 'Uvula', 'Overlapping lesion of hypopharynx', 'Round ligament', 'Corpus uteri', 'Biliary tract NOS', 'Male genital organs NOS', 'Parametrium', 'External lip NOS', 'Overlapping lesion of accessory sinuses', 'Cardia NOS', 'Islets of Langerhans', 'Carotid body', 'Ventral surface of tongue NOS', 'Autonomic nervous system NOS', 'Overlapping lesion of corpus uteri', 'Spinal meninges', 'Posterior wall of nasopharynx', 'Placenta', 'Intrahepatic bile duct', 'Overlapping lesion of digestive system', 'Mediastinum NOS', 'Hematopoietic system NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Major salivary gland NOS', 'Cerebellum NOS', 'Overlapping lesion of stomach', 'Vulva NOS', 'Craniopharyngeal duct', 'Lung NOS', 'Greater curvature of stomach NOS', 'Upper-outer quadrant of breast', 'Gallbladder', 'Thoracic esophagus', 'Lymph nodes of axilla or arm', 'Ventricle NOS', 'Overlapping lesion of biliary tract', 'Hypopharynx NOS', 'Clitoris', 'Exocervix', 'Parietal lobe', 'Waldeyer ring', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Head face or neck NOS', 'Anterior wall of nasopharynx', 'Urethra', 'Overlapping lesion of nasopharynx', 'Maxillary sinus', 'Lymph nodes of inguinal region or leg', 'Ureter', 'Tonsillar pillar', 'Sublingual gland', 'Pituitary gland', 'Gastrointestinal tract NOS', 'Pineal gland', 'Meninges NOS', 'Lingual tonsil', 'Trachea', 'Pyriform sinus', 'Mucosa of lower lip', 'Not Reported', 'Posterior wall of hypopharynx', 'Urinary system NOS', 'Orbit NOS', 'Short bones of lower limb and associated joints', 'Connective subcutaneous and other soft tissues of thorax', 'Upper limb NOS', 'Gastric antrum', 'Lymph node NOS', 'Peripheral nerves and autonomic nervous system of thorax', 'Ill-defined sites within respiratory system', 'Other specified parts of male genital organs', 'Rib sternum clavicle and associated joints', 'Overlapping lesion of bladder', 'Appendix', 'Prostate gland', 'Lymph nodes of multiple regions', 'Lateral wall of nasopharynx', 'Branchial cleft', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Floor of mouth NOS', 'Connective subcutaneous and other soft tissues NOS', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Bladder neck', 'Border of tongue', 'Connective subcutaneous and other soft tissues of abdomen', 'Overlapping lesion of small intestine', 'Lateral wall of bladder', 'Soft palate NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Isthmus uteri', 'Nasal cavity', 'Endocervix', 'Tonsil NOS', 'Glottis', 'Retroperitoneum', 'Peripheral nerves and autonomic nervous system of pelvis', 'Frontal lobe', 'Vagina NOS', 'Undescended testis', 'Laryngeal cartilage', 'Eyelid', 'Hypopharyngeal aspect of aryepiglottic fold', 'Overlapping lesion of other and unspecified parts of mouth', 'Upper lobe lung', 'Lip NOS', 'Lymph nodes of head face and neck', 'Overlapping lesion of brain and central nervous system', 'Overlapping lesion of penis', 'Overlapping lesion of retroperitoneum and peritoneum', 'Parotid gland', 'Dome of bladder', 'Bone of limb NOS', 'Descended testis', 'Vertebral column', 'Fundus uteri', 'Connective subcutaneous and other soft tissues of pelvis', 'Epididymis', 'Intra-abdominal lymph nodes', 'Prepuce', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Pharynx NOS', 'Overlapping lesion of endocrine glands and related structures', 'Gum NOS', 'Spinal cord', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Skin of upper limb and shoulder', 'Nasopharynx NOS', 'Parathyroid gland', 'Bone NOS', 'Mouth NOS', 'Abdomen NOS', 'Conjunctiva', 'Spermatic cord', 'External upper lip', 'Labium minus', 'Renal pelvis', 'Overlapping lesion of lip', 'Short bones of upper limb and associated joints', 'Main bronchus', 'Upper respiratory tract NOS', 'Body of penis', 'Small intestine NOS', 'Central portion of breast', 'Lower-inner quadrant of breast', 'Labium majus', 'Tonsillar fossa', 'Cecum', 'Glans penis', 'Tail of pancreas', 'Lower third of esophagus', 'Body of pancreas', 'Intestinal tract NOS', 'Brain stem', 'Overlapping lesion of rectum anus and anal canal', 'Posterior wall of oropharynx', 'Pancreatic duct', 'Blood', 'Temporal lobe', 'Anterior floor of mouth', 'Nervous system NOS', 'Cornea NOS', 'Palate NOS', 'Occipital lobe', 'Abdominal esophagus', 'Overlapping lesion of pancreas', 'Overlapping lesion of female genital organs', 'Cheek mucosa', 'Retina', 'Overlapping lesion of male genital organs', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Larynx NOS', 'Skin of other and unspecified parts of face', 'Spleen', 'Oropharynx NOS', 'Anal canal', 'Subglottis', 'Cerebral meninges', 'Lateral wall of oropharynx', 'Middle third of esophagus', 'Nipple', 'Medulla of adrenal gland', 'Overlapping lesion of eye and adnexa', 'Olfactory nerve', 'Ethmoid sinus', 'Overlapping lesion of cervix uteri', 'Descending colon', 'Brain NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Anterior wall of bladder', 'Mandible', 'Other specified parts of pancreas', 'Skin of trunk', 'Other specified parts of female genital organs', 'Uterus NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Intrathoracic lymph nodes', 'Heart', 'Adrenal gland NOS', 'Aortic body and other paraganglia', 'Extrahepatic bile duct', 'Overlapping lesion of breast', 'Superior wall of nasopharynx', 'Fundus of stomach', 'Anterior mediastinum', 'Tongue NOS', 'Cranial nerve NOS', 'Head of pancreas', 'Overlapping lesions of oropharynx', 'Overlapping lesion of bones joints and articular cartilage', 'Retromolar area', 'Testis NOS', 'Connective subcutaneous and other soft tissues of head face and neck', 'Bladder NOS', 'Overlapping lesion of urinary organs', 'Lower-outer quadrant of breast', 'Thyroid gland', 'Anterior surface of epiglottis', 'Uterine adnexa', '']"," If Progression or Recurrence is ""Yes - Progression or Recurrence"" then ""Progression or Recurrence Anatomic Site"" is required",SRRSClinicalDataTier2 -Days to Progression Free,Days to Progression Free,DaystoProgressionFree,Number of days between the date used for index and the date the patient's disease was formally confirmed as progression-free.,False,True,," If Progression or Recurrence is ""Yes - Progression or Recurrence"" then ""Days to Progression Free"" is required",SRRSClinicalDataTier2 -Medically Underserved Score,Medically Underserved Score,MedicallyUnderservedScore,"Index of Medical Underservice (IMU) score, a number between 0 and 100, where 0 represents completely underserved and 100 represents best served or least underserved. Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the asociated county on the right side of the result field. Go to data.hrsa.gov website and select Query Data. Pick the Medically Underserved Areas/Populations (MUA/P) data source in the step 1 menu and select View Data. Enter the name of the county (______ county) in the first ""Service Area"" column, adding the state in the 5th column may help direct you to the data. Enter the Index of Medical Underservice Score in the fourth column to one decimal place as the value.",False,True,," If Medically Underserved Area is ""Medically Underserved Area - Yes"" then ""Medically Underserved Score"" is required",SRRSClinicalDataTier2 -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,LungCancerTier3 -Lung Tumor Location Anatomic Site,Lung Tumor Location Anatomic Site,LungTumorLocationAnatomicSite,Anatomic location of the tumor inside the lung,False,,"['Not Reported', 'Main carina', 'Unknown', 'Left', 'Right', '']",,LungCancerTier3 -Lung Cancer Harboring Genomic Aberrations,Lung Cancer Harboring Genomic Aberrations,LungCancerHarboringGenomicAberrations,Genomic aberrations in participants with lung cancer (specific lung cancer associated gene mutations not covered in Tiers 1 and 2),False,,"['D963 splice MET mutation', 'A146T KRAS mutation', 'G12A KRAS mutation', 'G12D KRAS mutation', 'EML4-ALK translocation-variant 5', 'L858R EGFR mutation', 'G13C KRAS mutation', 'Intron 13 mutation', 'G13V KRAS mutation', 'EML4-ALK translocation-variant 2', 'Exon 20 insertion', 'EML4-ALK translocation-variant 1', 'D1010 splice MET mutation', 'Unknown', 'G12C KRAS mutation', 'G12V KRAS mutation', 'Q61H KRAS mutation', 'G719X EGFR mutation', 'C797S EGFR mutation', 'G13R KRAS mutation', 'G13D KRAS mutation', 'G13A KRAS mutation', 'G12S KRAS mutation', 'Exon 14 deletion', 'Not Reported', 'T790M EGFR mutation', 'L861Q EGFR mutation', 'V600K BRAF mutation', 'Q61L KRAS mutation', 'V600E BRAF mutation', 'Exon 19 deletion', 'K601E BRAF mutation', 'EML4-ALK translocation-variant 3', 'Intron 14 mutation', 'V600R BRAF mutation', 'G12R KRAS mutation', 'Other', 'Exon 14 mutation', 'EML4-ALK translocation-variant 4', 'D1010N MET mutation', 'V600D BRAF mutation', '']",,LungCancerTier3 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,LungCancerTier3 -Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,LungCancerTier3 -Stop Days from Index,Stop Days from Index,StopDaysfromIndex,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'",False,,,,LungCancerTier3 -Lung Adjacent Histology Type,Lung Adjacent Histology Type,LungAdjacentHistologyType,The type of morphologic characteristics observed by microscope in the tissue next to a benign or malignant tissue growth,False,,"['Sarcomatoid carcinoma', 'Squamous cell lung carcinoma', 'Thoracic NUT carcinoma', 'Large cell lung carcinoma', 'Not Reported', 'Carcinoid tumor and lung atypical carcinoid tumor', 'Bronchioalveolar carcinoma', 'Other', 'Lung adenocarcinoma', 'Small cell lung carcinoma', 'Unknown', 'Adenosquamous carcinoma', 'Lung squamous cell carcinoma in situ', 'Large cell neuroendocrine carcinoma', 'Lung lymphoepithelioma-like carcinoma', 'Lung adenocarcinoma in situ', '']",,LungCancerTier3 -Lung Tumor Lobe Bronchial Location,Lung Tumor Lobe Bronchial Location,LungTumorLobeBronchialLocation,Anatomic lobe and bronchial location of the tumor inside the lung,False,,"['Not Reported', 'Stump', 'Lower lobe', 'Bronchus', 'Upper lobe', 'Unknown', 'Middle lobe', '']",,LungCancerTier3 -Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,LungCancerTier3 -Current Lung Cancer Symptoms,Current Lung Cancer Symptoms,CurrentLungCancerSymptoms,Reported lung cancer related symptoms person is currently experiencing,False,,"['no evidence of lung cancer recurrence', 'asbestosis', 'Dysphagia', 'dullness to percussion', 'non-productive cough', 'unlabored/normal breathing', 'abnormal breath sounds', 'unexplained weight loss', 'fair/poor aeration', 'Pneumonia', 'breath sounds coarse/diminished', 'prolonged expiration-long/forced expiratory phase', 'clear lungs to auscultation or percussion', 'Wheezing', 'unexplained loss of energy/fatigue', 'Unknown', 'crackles', 'air entry decreased/fair/poor/diminished', 'chest pain or discomfort', 'finger clubbing', 'Not Reported', 'patient is NED', 'hoarseness/laryngitis/vocal cord inflammation', 'shallow inspiration', 'cold symptoms/flu/sinus/nasal congestion', 'rhonci', 'Dyspnea', 'sinus pain/infection', 'Other', 'oxygen supplemental-portable O2 at night or continuous', 'productive cough', 'hemoptysis', '']",,LungCancerTier3 -Lung Topography,Lung Topography,LungTopography,Lung PCA specific topography (not covered in previous tiers),False,,"['LL NOS (Left lung not otherwise specified)', 'LB10A/B Carina between the apical and lateral subsegments of the posterior segment of the LLL', 'RB5A/B - Carina between the medial and lateral subsegments of the medial segment of the right middle lobe', 'RB10B/C - Carina between medial and lateral subsegments posterior segment RLL', 'RB7 Medial basal segment right lower lobe (Carina at RB7 orifice takeoff from RLL orifice)', 'LB4/5 Carina between superior and inferior segment lingula (Carina between LB4 orifice and LB5 orifice)', 'RB6 - Carina of superior segment RLL (Carina between RB6 orifice and lower portion of RLL orifice)', 'LB5A/B Carina between the medial and lateral subsegments inferior segment lingula', 'LB9 orifice Lateral segment left lower lobe(airway wall between LB9 and LB9A/B carinae)', 'LB1/2 Carina between apical and posterior segment left upper lobe (Carina between LB1 orifice and LB2 orifice)', 'RB6A/B - Carina between apical and lateral subsegments superior segment RLL', 'LB2A/C Carina between the apical and medial subsegments of the posterior segment of the left upper lobe', 'RB7 orifice Airway wall between RB7 and RB7A/B carinae', 'LB10A/C Carina between the apical and medial segments of the posterior segment of the LLL', 'RML orifice Airway wall between RML and RB4/5', 'Not Reported', 'LUL orifice Airway wall between LUL and LUDB', 'RB7A/B - Carina between medial and lateral subsegments medial basal segment RLL', 'TR -Trachea (airway wall between tracheo-esophageal bifurcation and main carina)', 'RB4 orifice Lateral segment right middle lobe (airway wall between RB4 and RB4A/B carinae)', 'RB10A/C - Carina between medial and apical subsegments posterior segment RLL', 'Other', 'LUL Carina between the LUL orifice and LLL orifice (airways)', 'RB5 orifice Medial segment right middle lobe (airway wall between RB5 and RB5A/B carinae)', 'RB4/5 - Carina between the lateral and medial segments right middle lobe (Carina between RB4 orifice and RB5 orifice)', 'LB10 orifice Posterior segment left lower lobe(airway wall between LB10 and LB10A/B carinae)', 'LB3A/B Carina between the apical and lateral subsegments of the anterior segment of the left upper lobe', 'RB10A/B - Carina between medial and lateral subsegments posterior segment RLL', 'LB8A/B Carina between the medial and lateral subsegments of the anterior segment LLL', 'RLL orifice Airway wall between RML and RB6-10 carinae', 'RB10 Posterior segment right lower lobe (Carina at RB10 orifice takeoff from RLL orifice)', 'LB6 The superior segment of the left lower lobe (Carina between LB6 orifice and lower portion of LLL orifice)', 'MC-Carina between right and left lungs (main carina)', 'Unknown', 'RB6 orifice Airway wall between RB6 and RB6A/B/C carinae', 'LB6 orifice Airway wall between LB6 and LB6A/B carinae', 'LB9A/B Carina between the medial and lateral subsegments of the lateral segment LLL', 'LB6B/C Carina between the medial and lateral subsegments of the superior segment LLL', 'RB1/3 - Carina between apical and anterior segments RUL (Carina between RB1 orifice and RB3 orifice)', 'RB4A/B - Carina between the medial and lateral subsegments of the lateral segment of the right middle lobe', 'LB4 orifice Superior segment lingula(airway wall between LB4 and LB4A/B carinae)', 'RB1A/B - Carina between medial and lateral subsegments apical segment RUL', 'RB8A/B - Carina between medial and lateral subsegments anterior segment RLL', 'LLL orifice Airway wall between LUL carina and LB6-10 carinae', 'RB1/2 - Carina between apical and posterior segments right upper lobe (Carina between RB1 orifice and RB2 orifice)', 'RB3A/B - Carina between the medial and lateral subsegments of the anterior segment RUL', 'RB10 orifice Airway wall between RB10 and RB10A/B carinae', 'LUDB-Carina between the lingula and upper division left upper lobe', 'RB1 orifice Apical segment - right upper lobe(airway wall between RB1 and RB1A/B carinae)', 'LB5 orifice Inferior segment lingula(airway wall between LB5 and LB5A/B carinae)', 'LB6A/B Carina between the superior and lateral subsegments superior segment LLL', 'RB2 orifice Posterior segment - right upper lobe(airway wall between RB2 and RB2A/B carinae)', 'RUL Carinae between RUL orifice and bronchus intermedius', 'LB2A/B Carina between the apical and lateral subsegments of the posterior segment of the left upper lobe', 'RB9A/B - Carina between medial and lateral subsegments lateral segment RLL', 'RB8/9 - Carina between anterior and lateral segments RLL (Carina between RB8 orifice and RB9 orifice)', 'RB9 orifice Lateral segment right lower lobe(airway wall between RB9 and RB9A/B carinae)', 'Bronchus Intermedius Bronchus (airway wall) between right upper and right middle lobes', 'RB3 orifice Anterior segment - right upper lobe(airway wall between RB3 and RB3A/B carinae)', 'LB1A/B Carina between the lateral and medial subsegments of the apical segment of the LUL', 'LB4A/B Carina between medial and lateral subsegments superior segment lingula', 'Carina NOS (Carina not otherwise specified)', 'LB8 orifice Anterior segment left lower lobe(airway wall between LB8 and LB8A/B carinae)', 'LUDB-orifice airway wall between LUDB and LB3(LB1+2 carinae)', 'Carina between LUDB orifice and lingula orifice', 'LB1+2/3 Carina between the apico-posterior and anterior segments of the left upper lobe (Carina between LB1+2 orifice and LB3 orifice)', 'LMB-Left mainstem bronchus(airway wall between MC & LUL carina)', 'RB9/10 - Carina between lateral and posterior segments RLL', 'RB6A/C - Carina between apical and medial subsegments superior segment RLL', 'RB2/3 - Carina between anterior and posterior segments RUL (Carina between RB2 orifice and RB3 orifice)', 'LB1A/C Carina between the apical and lateral subsegments of the apical segment left upper lobe', 'LB1B/C Carina between the medial and lateral subsegments of the apical segment of the left upper lobe', 'RMB-Right mainstem bronchus(airway wall between MC & RUL carina)', 'RB2A/B - Carina between the medial and lateral subsegments of the posterior segment (RUL)', 'LB8/9 Carina between the anterior and lateral segments LLL (Carina between LB8 orifice and LB9 orifice)', 'LB6A/C Carina between the superior and medial subsegments of superior segment LLL', 'LB10B/C Carina between the medial and lateral subsegments of the posterior segment of the LLL', 'RUL orifice Airway wall between RUL and RB1/RB2/RB3', 'LB9/10 Carina between the lateral and posterior segments LLL (Carina between LB9 orifice and LB10 orifice)', 'LB2B/C Carina between the medial and lateral subsegments of the posterior segment left upper lobe', 'LB3 orifice Anterior segment left upper lobe(airway wall between LB3 and LB3A/B carinae)', 'LB1+2 orifice The apico-posterior segment of the left upper lobe (airway wall between LB1+2/3 carina and LB1 or LB2)', 'RB8 orifice Anterior segment right lower lobe(airway wall between RB8 and RB8A/B carinae)', 'Lingula orifice airway wall between LUDB and LB4/5 carinae', 'RML - Carina between RML orifice and RLL orifice', 'RB6B/C - Carina between medial and lateral subsegments superior segment RLL', 'RL NOS (Right lung not otherwise specified)', '']",,LungCancerTier3 -Lung Cancer Detection Method Type,Lung Cancer Detection Method Type,LungCancerDetectionMethodType,"The means, manner of procedure, or systematic course of actions performed in order to discover or identify lung cancer",False,,"['Data not available', 'Chest CT', 'Low Dose Computed Tomography (LDCT)', 'Other', 'Unknown', 'Chest X-ray', '']",,LungCancerTier3 -Lung Cancer Participant Procedure History,Lung Cancer Participant Procedure History,LungCancerParticipantProcedureHistory,Text name of a surgical or operative procedure used in a natural history protocol of a lung cancer participant.,False,,"['Lung Wedge Resection Bilateral', 'Lobectomy Right', 'Lung Wedge Resection Left', 'Pneumonectomy Left', 'Lung Wedge Resection Multiple', 'Endobronchial biopsy', 'Mediastinoscopy', 'Not Reported', 'Lobectomy Left', 'Other', 'Unknown', 'Lung Wedge Resection Right', 'VATS Sclerosis', 'Segmentectomy', 'Lobectomy Bilateral', 'Brain resection', 'Pneumonectomy Right', '']",,LungCancerTier3 -Colorectal Polyp Type,Colorectal Polyp Type,ColorectalPolypType,Type of polyp found in the participant,False,,"['Adenoma', 'Hyperplastic', 'Other', 'Unknown', 'Normal', 'Mixed', 'Papillomatous', 'Cancer', '']",,ColorectalCancerTier3 -Colorectal Cancer Detection Method Type,Colorectal Cancer Detection Method Type,ColorectalCancerDetectionMethodType,"The means, manner of procedure, or systematic course of actions performed in order to discover or identify colorectal cancer",False,,"['Data not available', 'DNA stool test', 'Sigmoidoscopy', 'Virtual colonoscopy', 'Other', 'Unknown', 'Fecal occult blood test', 'Colonoscopy', '']",,ColorectalCancerTier3 -Patient Inflammatory Bowel Disease Personal Medica History,Patient Inflammatory Bowel Disease Personal Medica History,PatientInflammatoryBowelDiseasePersonalMedicaHistory,"The indicator for patient's personal medical history of inflammatory bowel disease (chronic, non-specific disorders of unknown etiology, including Crohn disease and ulcerative colitis).",False,,"['Yes - Ulcerative colitis', 'No', 'Not Applicable', ""Yes - Crohn's disease"", 'Unknown', '']",,ColorectalCancerTier3 -History of Prior Colon Polyps,History of Prior Colon Polyps,HistoryofPriorColonPolyps,Yes/No indicator to describe if the subject had a previous history of colon polyps as noted in the history/physical or previous endoscopic report (s).,False,,"['No', 'Not Applicable', 'Unknown', 'Yes', '']",,ColorectalCancerTier3 -Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,ColorectalCancerTier3 -Colorectal Polyp Shape,Colorectal Polyp Shape,ColorectalPolypShape,Shape of polyp identified in the participant,False,,"['Pedunculated', 'Sessile', 'Not Applicable', 'Not stated', 'Flat', '']",,ColorectalCancerTier3 -Colorectal Cancer KRAS Indicator,Colorectal Cancer KRAS Indicator,ColorectalCancerKRASIndicator,The yes/no/not applicable indicator that describes if patient has diagnosis of colorectal cancer with known KRAS.,False,,"['Not Applicable', 'No', 'Unknown', 'Yes', '']",,ColorectalCancerTier3 -MLH1 Promoter Methylation Status,MLH1 Promoter Methylation Status,MLH1PromoterMethylationStatus,Text term to define the status of promoter methylation for the MLH1 gene. Note: MLH1 gene is commonly associated with hereditary nonpolyposis colorectal cancer. Testing for methylation of the MLH1 promoter can help distinguish sporadic from inherited cancers.,False,,"['Absent', 'Indeterminate', 'Not Assessed', 'Present', '']",,ColorectalCancerTier3 -Colon Polyp Occurence Indicator,Colon Polyp Occurence Indicator,ColonPolypOccurenceIndicator,Yes/No indicator to describe if the subject had a previous history of colon polyps as noted in the history/physical or previous endoscopic report (s).,False,,"['Not Applicable', 'No', 'Unknown', 'Yes', '']",,ColorectalCancerTier3 -Stop Days from Index,Stop Days from Index,StopDaysfromIndex,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'",False,,,,ColorectalCancerTier3 -Family Medical History Colorectal Polyp Diagnosis,Family Medical History Colorectal Polyp Diagnosis,FamilyMedicalHistoryColorectalPolypDiagnosis,A yes/no/unknown/not applicable indicator related to family medical history diagnosis of polypoid lesion that arises from the colon or rectum and protrudes into the lumen.,False,,"['No', 'Not Applicable', 'Unknown', 'Yes', '']",,ColorectalCancerTier3 -Colorectal Polyp Count,Colorectal Polyp Count,ColorectalPolypCount,The total number of polyps detected,False,,,,ColorectalCancerTier3 -Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,ColorectalCancerTier3 -Immediate Family History Ovarian Cancer,Immediate Family History Ovarian Cancer,ImmediateFamilyHistoryOvarianCancer,Text that describes the age at which the family member was diagnosed with ovarian cancer in relationship to their 50th birthday.,False,,"['Not Applicable', 'Unknown', 'Not before age 50', 'Before age 50', '']",,ColorectalCancerTier3 -Colorectal Cancer Tumor Border Configuration,Colorectal Cancer Tumor Border Configuration,ColorectalCancerTumorBorderConfiguration,The description of the border configuration of a colorectal tumor at pathologic assessment.,False,,"['Not Applicable', 'Other', 'Infiltrating', 'Pushing', 'Indeterminate', '']",,ColorectalCancerTier3 -Family Colon Cancer History Indicator,Family Colon Cancer History Indicator,FamilyColonCancerHistoryIndicator,The indicator to designate if any first degree relative has a history of colorectal cancer.,False,,"['No', 'Not Applicable', 'Unknown', 'Yes', '']",,ColorectalCancerTier3 -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,ColorectalCancerTier3 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ColorectalCancerTier3 -Size of Polyp Removed,Size of Polyp Removed,SizeofPolypRemoved,Size of the polyp removed in cm,False,,,,ColorectalCancerTier3 -Colorectal Polyp New Indicator,Colorectal Polyp New Indicator,ColorectalPolypNewIndicator,A yes/no response to a question that asks whether any new polyps greater or equal to two millimeter were identified.,False,,"['Not Applicable', 'No', 'Unknown', 'Yes', '']",,ColorectalCancerTier3 -Colorectal Polyp Adenoma Type,Colorectal Polyp Adenoma Type,ColorectalPolypAdenomaType,Type of adenoma associated with the polyp,False,,"['Serrated not specified', 'Tubulovillous', 'Villous', 'Not Applicable', 'Tubular', 'Sessile serrated', 'Not stated', 'Traditional serrated', '']",,ColorectalCancerTier3 -Immediate Family History Endometrial Cancer,Immediate Family History Endometrial Cancer,ImmediateFamilyHistoryEndometrialCancer,Text that describes the age at which the family member was diagnosed with endometrial or uterine cancer in relationship to their 50th birthday.,False,,"['Not Applicable', 'Unknown', 'Not before age 50', 'Before age 50', '']",,ColorectalCancerTier3 -Family History Colorectal Polyp,Family History Colorectal Polyp,FamilyHistoryColorectalPolyp,A yes/no/unknown/not applicable indicator related to family medical history diagnosis of polypoid lesion that arises from the colon or rectum and protrudes into the lumen.,False,,"['Not Applicable', 'No', 'Unknown', 'Yes', '']",,ColorectalCancerTier3 -Patient Colonoscopy Performed Indicator,Patient Colonoscopy Performed Indicator,PatientColonoscopyPerformedIndicator,The yes/no indicator that records if the subject has undergone a previous colonoscopy.,False,,"['No', 'Not Applicable', 'Unknown', 'Yes', '']",,ColorectalCancerTier3 -Breast Carcinoma Detection Method Type,Breast Carcinoma Detection Method Type,BreastCarcinomaDetectionMethodType,"The means, manner of procedure, or systematic course of actions performed in order to discover or identify breast cancer.",False,,"['Clinical Exam', 'Data not available', 'Screening Mammography', 'Other', 'Unknown', 'Self exam', 'Nipple Discharge', 'Screening MRI', '']",,BreastCancerTier3 -Breast Carcinoma HER2 Centromere17 Copynumber Total,Breast Carcinoma HER2 Centromere17 Copynumber Total,BreastCarcinomaHER2Centromere17CopynumberTotal,Number of Cells Counted for HER2 & Centromere 17 Copy Numbers in a participant with breast cancer,False,,,,BreastCancerTier3 -Breast Carcinoma HER2 Status,Breast Carcinoma HER2 Status,BreastCarcinomaHER2Status,Text term to signify the result of the medical procedure that involves testing a sample of blood or tissue for HER2 in a participant with breast cancer,False,,"['Non-amplified', 'Equivocal', 'Not Performed', 'Positive', 'Unknown', 'Amplified', 'Indeterminate', 'Negative', '']",,BreastCancerTier3 -Prior Invasive Breast Disease,Prior Invasive Breast Disease,PriorInvasiveBreastDisease,Text term to indicate prior invasive breast condition in the participant,False,,"['Data not available', 'Other', 'DCIS', 'Unknown', 'LCIS', 'Invasive breast cancer (unrelated to the current cancer)', '']",,BreastCancerTier3 -Breast Imaging Performed Type,Breast Imaging Performed Type,BreastImagingPerformedType,"The kind of technology or method performed for screening, diagnosis, surgical procedures or therapy that aids in the visualization of the breast(s).",False,,"['Ultrasound', 'Data not available', 'MRI', 'Mammogram', 'Unknown', 'CT', 'Multiple imaging modalities', 'PET/CT', '']",,BreastCancerTier3 -Mammaprint Risk Group,Mammaprint Risk Group,MammaprintRiskGroup,Text term that represents the risk group for breast cancer as determined by assessment of the MammaPrint test.,False,,"['High risk', 'Data not available', 'Unknown', 'Low risk', 'Intermediate risk', '']",,BreastCancerTier3 -Hormone Therapy Breast Cancer Prevention Indicator,Hormone Therapy Breast Cancer Prevention Indicator,HormoneTherapyBreastCancerPreventionIndicator,Did the patient receive hormonal therapy for prevention of breast cancer?,False,,"['Not Applicable', 'No', 'Unknown', 'Yes', '']",,BreastCancerTier3 -Breast Carcinoma ER Status Percentage Value,Breast Carcinoma ER Status Percentage Value,BreastCarcinomaERStatusPercentageValue,A numerical quantity measured or assigned or computed which captures the estrogen receptor level measured in a participant with breast cancer,False,,,,BreastCancerTier3 -Breast Carcinoma Surgical Procedure Name,Breast Carcinoma Surgical Procedure Name,BreastCarcinomaSurgicalProcedureName,Text name of a surgical procedure performed for a person with a diagnosis of breast cancer,False,,"['Modified radical mastectomy', 'Simple mastectomy', 'Surgery not performed', 'Radical mastectomy', 'Other', 'Unknown', 'Partial mastectomy', 'Re-excision', 'Lumpectomy', '']",,BreastCancerTier3 -Multifocal Breast Carcinoma Present Indicator,Multifocal Breast Carcinoma Present Indicator,MultifocalBreastCarcinomaPresentIndicator,A response to indicate if there is breast cancer characterized by the presence of multiple cancerous tumors that originate from the same clone and usually located in the same quadrant of the breast.,False,,"['No', 'Unknown', 'Data not available', 'Yes', '']",,BreastCancerTier3 -Breast Biopsy Procedure Finding Type,Breast Biopsy Procedure Finding Type,BreastBiopsyProcedureFindingType,Text term to describe the result of the examination of the breast tissue specimen or fluid as related to the presence and nature of disease.,False,,"['Atypical hyperplasia', 'No cancer', 'Other', 'DCIS', 'LCIS', 'Cancer', '']",,BreastCancerTier3 -Invasive Ductal Breast Carcinoma Histologic Category,Invasive Ductal Breast Carcinoma Histologic Category,InvasiveDuctalBreastCarcinomaHistologicCategory,The histologic subtype for the most common type of invasive breast carcinoma.,False,,"['Tubulolobular carcinoma', 'Classical type', 'Invasive micropapillary carcinoma', 'Data not available', 'Invasive papillary carcinoma', 'Invasive tubular carcinoma', 'Other', 'Medullary carcinoma', 'Unknown', 'Mucinous carcinoma', 'Invasive carcinoma-type cannot be determined', 'Invasive cribriform carcinoma', '']",,BreastCancerTier3 -Breast Carcinoma Progesteroner Receptor Status,Breast Carcinoma Progesteroner Receptor Status,BreastCarcinomaProgesteronerReceptorStatus,Text term to represent the overall result of Progresterone Receptor (PR) testing in a participant with breast cancer,False,,"['Equivocal', 'Performed but Not Available', 'Not Performed', 'Positive', 'Unknown', 'Indeterminate', 'Negative', 'Borderline', '']",,BreastCancerTier3 -Breast Carcinoma PR Staining Intensity,Breast Carcinoma PR Staining Intensity,BreastCarcinomaPRStainingIntensity,Text term to indicate the PR staining intensity on pathology assessment in a participant with breast cancer,False,,"['Weak-Moderate', 'Weak-Strong', 'Strong', 'Other', 'Unknown', 'Moderate', 'Moderate-Strong', 'Weak', '']",,BreastCancerTier3 -Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,BreastCancerTier3 -Breast Carcinoma Centromere 17 Copy Number,Breast Carcinoma Centromere 17 Copy Number,BreastCarcinomaCentromere17CopyNumber,"Result of Centromere 17 testing in a sample or specimen of metastatic breast carcinoma, expressed as a range of values.",False,,,,BreastCancerTier3 -Breast Carcinoma HER2 Ratio Diagnosis,Breast Carcinoma HER2 Ratio Diagnosis,BreastCarcinomaHER2RatioDiagnosis,HER2 ratio of the participant at diagnosis,False,,,,BreastCancerTier3 -Breast Quadrant Site,Breast Quadrant Site,BreastQuadrantSite,The breast quadrant or structure from which the breast tissue specimen was removed for microscopic examination.,False,,"['Upper inner quadrant', 'Lower outer quadrant', 'Data not available', 'Upper outer quadrant', 'Central', 'Lower inner quadrant', 'Unknown', 'Nipple', '']",,BreastCancerTier3 -Breast Carcinoma HER2 Chromosome17 Ratio,Breast Carcinoma HER2 Chromosome17 Ratio,BreastCarcinomaHER2Chromosome17Ratio,HER2 chromosome 17 ratio in participants with breast cancer,False,,,,BreastCancerTier3 -Breast Cancer Genomic Test Performed,Breast Cancer Genomic Test Performed,BreastCancerGenomicTestPerformed,Text term that represents the name of the genomic test performed for breast cancer.,False,,"['Data not available', 'Oncotype', 'Other', 'Not performed', 'Unknown', 'MammaPrint', '']",,BreastCancerTier3 -Breast Carcinoma Estrogen Receptor Status,Breast Carcinoma Estrogen Receptor Status,BreastCarcinomaEstrogenReceptorStatus,Text term to represent the overall result of Estrogen Receptor (ER) testing in a participant with breast cancer,False,,"['Equivocal', 'Performed but Not Available', 'Not Performed', 'Positive', 'Unknown', 'Indeterminate', 'Negative', 'Borderline', '']",,BreastCancerTier3 -Breast Carcinoma Histology Category,Breast Carcinoma Histology Category,BreastCarcinomaHistologyCategory,Classification of the type of invasive breast carcinoma diagnosed based on histologic attributes.,False,,"['Invasive mammary carcinoma NOS', 'Infiltrating ductal carcinoma', 'Other', 'Invasive mixed ductal and lobular carcinoma', 'Infiltrating lobular carcinoma', '']",,BreastCancerTier3 -BIRADS Mammography Breast Density Category,BIRADS Mammography Breast Density Category,BIRADSMammographyBreastDensityCategory,The category that describes the relative amount of different tissues present in the breast on a mammogram based on the updated 2015 edition of the American College of Radiology's Breast Imaging Reporting and Data System (BI-RADS) reporting guidelines.,False,,"['Extremely dense', 'Data not available', 'Heterogeneously dense', 'Unknown', 'Predominantly fatty', 'Scattered fibroglandular densities', '']",,BreastCancerTier3 -Stop Days from Index,Stop Days from Index,StopDaysfromIndex,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'",False,,,,BreastCancerTier3 -Breast Carcinoma PR Status Percentage Value,Breast Carcinoma PR Status Percentage Value,BreastCarcinomaPRStatusPercentageValue,A numerical quantity measured or assigned or computed which captures the progesterone receptor level measured in a participant with breast cancer,False,,,,BreastCancerTier3 -Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,BreastCancerTier3 -HER2 Breast Carcinoma Copy Number Total,HER2 Breast Carcinoma Copy Number Total,HER2BreastCarcinomaCopyNumberTotal,"Result of HER2 Copy Number testing (in a participant with breast cancer), expressed as a range of values.",False,,,,BreastCancerTier3 -Breast Carcinoma ER Staining Intensity,Breast Carcinoma ER Staining Intensity,BreastCarcinomaERStainingIntensity,Text term to indicate the ER staining intensity on pathology assessment in a participant with breast cancer,False,,"['Weak-Moderate', 'Weak-Strong', 'Strong', 'Other', 'Unknown', 'Moderate', 'Moderate-Strong', 'Weak', '']",,BreastCancerTier3 -Oncotype Risk Group,Oncotype Risk Group,OncotypeRiskGroup,Text term that represents the risk group for breast cancer as determined by assessment of the Oncotype recurrence score.,False,,"['High risk', 'Data not available', 'Unknown', 'Low risk', 'Intermediate risk', '']",,BreastCancerTier3 -Oncotype Score,Oncotype Score,OncotypeScore,OncotypeDX recurrence score,False,,,,BreastCancerTier3 -Multicentric Breast Carcinoma Present Indicator,Multicentric Breast Carcinoma Present Indicator,MulticentricBreastCarcinomaPresentIndicator,A response to indicate if there is breast cancer characterized by the presence of multiple cancerous tumors that originate from different clones and usually located in different quadrants of the breast.,False,,"['No', 'Unknown', 'Data not available', 'Yes', '']",,BreastCancerTier3 -Breast Cancer Allred Estrogen Receptor Score,Breast Cancer Allred Estrogen Receptor Score,BreastCancerAllredEstrogenReceptorScore,"The numeric Allred score, that is cell staining percentage plus intensity, to determine estrogen receptor status.",False,,"['4', '1', '5', '6', 'Unknown', '2', '7', '10', '3', '8', '0', '']",,BreastCancerTier3 -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,BreastCancerTier3 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BreastCancerTier3 -Breast Cancer Assessment Tests,Breast Cancer Assessment Tests,BreastCancerAssessmentTests,Text term to identify assessment tests done in participants during diagnosis,False,,"['HER2 IHC', 'Data not available', 'HER2 FISH-CISH', 'Estrogen receptor IHC', 'Other', 'HER2 FISH', 'Unknown', 'Progesterone receptor IHC', '']",,BreastCancerTier3 -Invasive Lobular Breast Carcinoma Histologic Category,Invasive Lobular Breast Carcinoma Histologic Category,InvasiveLobularBreastCarcinomaHistologicCategory,The histologic subtype for an infiltrating lobular carcinoma of the breast.,False,,"['Data not available', 'Classical type', 'Pleomorphic type', 'Alveolar type', 'Unknown', '']",,BreastCancerTier3 -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,NeuroblastomaandGliomaTier3 -Glioma Specific Metastasis Sites,Glioma Specific Metastasis Sites,GliomaSpecificMetastasisSites,Evidence of active brain metastasis including leptomeningeal involvement,False,,"['Leptomeningeal', 'Bone marrow', 'Other', 'Not Applicable', 'CSF', 'Brain', 'Spine', '']",,NeuroblastomaandGliomaTier3 -Supra Tentorial Ependymoma Molecular Subgroup,Supra Tentorial Ependymoma Molecular Subgroup,SupraTentorialEpendymomaMolecularSubgroup,Text term to identify the molecular subgroup in a supra tentorial ependymoma,False,,"['Unknown', 'ST-EPN-RELA', 'Not Applicable', 'ST-EPN-YAP1', '']",,NeuroblastomaandGliomaTier3 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,NeuroblastomaandGliomaTier3 -Glioma Specific Radiation Field,Glioma Specific Radiation Field,GliomaSpecificRadiationField,A description of the location on or within the CNS where radiation was administered in a partcipant with glioma,False,,"['Focal-tumor bed', 'Unknown', 'Not Applicable', 'Craniospinal', '']",,NeuroblastomaandGliomaTier3 -Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,NeuroblastomaandGliomaTier3 -Stop Days from Index,Stop Days from Index,StopDaysfromIndex,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'",False,,,,NeuroblastomaandGliomaTier3 -Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,NeuroblastomaandGliomaTier3 -Neuroblastoma MYCN Gene Amplification Status,Neuroblastoma MYCN Gene Amplification Status,NeuroblastomaMYCNGeneAmplificationStatus,Neuroblastoma MYCN amplification or over-expression status,False,,"['Unknown', 'Amplified', 'Not done', 'Not amplified', '']",,NeuroblastomaandGliomaTier3 -CNS Tumor Primary Anatomic Site,CNS Tumor Primary Anatomic Site,CNSTumorPrimaryAnatomicSite,Primary tumor location in the central nervous system that comprise the tissues of the central nervous system (brain and spinal cord)-not covered in Tiers 1 and 2,False,,"['Ventricles', 'Spinal cord-Cervical', 'Spinal cord-Lumbar', 'Optic pathway', 'Other locations NOS', 'Meninges/Dura', 'Other lymph nodes', 'Spinal cord-Thoracic', 'Paraspinal ganglion', 'Basal ganglia', 'Hippocampus', 'Thalamus', 'Suprasellar/Hypothalamic/Pituitary', 'Brain stem-Midbrain/Tectum', 'Cerebellar/Posterior fossa', 'Intracranial/Leptomeningeal', 'Brainstem-Pons', 'Brain stem-Medulla', '']",,NeuroblastomaandGliomaTier3 -Infra Tentorial Ependymoma Molecular Subgroup,Infra Tentorial Ependymoma Molecular Subgroup,InfraTentorialEpendymomaMolecularSubgroup,Text term to identify the molecular subgroup in a infra tentorial ependymoma,False,,"['PF-EPN-A', 'Not Applicable', 'PF-EPN-B', 'Unknown', 'Myxopapillary ependymoma', '']",,NeuroblastomaandGliomaTier3 -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,AcuteLymphoblasticLeukemiaTier3 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,AcuteLymphoblasticLeukemiaTier3 -NCI ALL Risk Group,NCI ALL Risk Group,NCIALLRiskGroup,The NCI risk group assigned to a patient at initial diagnosis with Acute Lymphoblastic Leukemia.,False,,"['Unknown', 'NCI Standard Risk', 'NCI High Risk', '']",,AcuteLymphoblasticLeukemiaTier3 -Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,AcuteLymphoblasticLeukemiaTier3 -Stop Days from Index,Stop Days from Index,StopDaysfromIndex,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'",False,,,,AcuteLymphoblasticLeukemiaTier3 -MRD ALL Diagnostic Sensitivity,MRD ALL Diagnostic Sensitivity,MRDALLDiagnosticSensitivity,The assay sensitivity results of a diagnostic assessment of Minimal Residual Disease in patients diagnosed with Acute Lymphoblastic Leukemia.,False,,"['Unknown', 'Indeterminate', 'Optimal', 'Suboptimal', '']",,AcuteLymphoblasticLeukemiaTier3 -CNS Leukemia Status,CNS Leukemia Status,CNSLeukemiaStatus,The status of central nervous system leukemia at the time of diagnosis.,False,,"['CNS 2c', 'CNS 2', 'CNS 1', 'Unknown', 'CNS 3b', 'CNS 2a', 'CNS 2b', 'CNS 3c', 'Not evaluated', 'CNS 3a', 'CNS 3', '']",,AcuteLymphoblasticLeukemiaTier3 -Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,AcuteLymphoblasticLeukemiaTier3 -Specimen Blast Count Percentage Value,Specimen Blast Count Percentage Value,SpecimenBlastCountPercentageValue,"The value, in percent(%) of the medical procedure that involves testing a sample of blood for blast cells, immature (undifferentiated) cells during diagnosis",False,,,,AcuteLymphoblasticLeukemiaTier3 -Ovarian Cancer Platinum Status,Ovarian Cancer Platinum Status,OvarianCancerPlatinumStatus,Text term to indicate the status of treatment with platinum in participant with ovarian cancer,False,,"['Platinum-sensitive', 'Platinum-resistant', 'Data not available', 'Platinum-refractory', 'Unknown', '']",,OvarianCancerTier3 -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,OvarianCancerTier3 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,OvarianCancerTier3 -Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,OvarianCancerTier3 -Stop Days from Index,Stop Days from Index,StopDaysfromIndex,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'",False,,,,OvarianCancerTier3 -Ovarian Cancer Surgical Outcome,Ovarian Cancer Surgical Outcome,OvarianCancerSurgicalOutcome,Text term that describes the kind of surgical treatment administered.,False,,"['Data not available', 'R0 resection', 'Optimal cytoreduction', 'Other', 'Unknown', 'Sub-optimal cytoreduction', '']",,OvarianCancerTier3 -Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,OvarianCancerTier3 -Ovarian Cancer Histologic Subtype,Ovarian Cancer Histologic Subtype,OvarianCancerHistologicSubtype,Text term to describe the histological subtype of ovarian cancer in the participant,False,,"['Low-grade serous', 'Germ cell', 'High-grade endometrioid', 'Mucinous', 'Data not available', 'Other', 'Clear cell', 'Unknown', 'Sex-cord stromal', 'Low-grade endometrioid', 'High-grade serous', '']",,OvarianCancerTier3 -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,ProstateCancerTier3 -Seminal Vesicle Invasion,Seminal Vesicle Invasion,SeminalVesicleInvasion,An anatomic position identifying a side of the body where local spread of malignant neoplasm is found to infiltrate tissue in the saclike glandular diverticulum on the ductus deferens in a male.,False,,"['None', 'Both sides', 'Not Reported', 'Unknown', 'Left', 'Right', '']",,ProstateCancerTier3 -Location Nature Positive Margins,Location Nature Positive Margins,LocationNaturePositiveMargins,Location and nature of positive margins,False,,"['Left Positive in an area of intraprostatic incision (II)', 'Right Positive where it is difficult to distinguish EPE vs II', 'Vas deferens', 'Right Anterior', 'Left Lateral', 'Right Lateral', 'Left Focal', 'Right Apex', 'Left Apex', 'Right Focal', 'Right Positive in an area of intraprostatic incision (II)', 'Unknown', 'Left Positive in an area of extraprostatic extension (EPE)', 'Right Positive in an area of extraprostatic extension (EPE)', 'Bladder neck (block PUM)', 'Left Posterior', 'Left Extensive', 'Not Reported', 'Left Posterolateral', 'Left Anterior', 'Apical margin (block DUM)', 'Left Positive where it is difficult to distinguish EPE vs II', 'Right Posterior', 'Right Mid', 'Left Mid', 'Right Posterolateral', 'Right Base', 'Left Base', 'Right Extensive', '']",,ProstateCancerTier3 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ProstateCancerTier3 -Prostate Carcinoma Histologic Type,Prostate Carcinoma Histologic Type,ProstateCarcinomaHistologicType,The diagnostic subclassification of an invasive prostate carcinoma.,False,,"['Undifferentiated carcinoma NOS', 'Acinar prostate adenocarcinoma-signet-ring variant', 'Prostatic small cell carcinoma', 'Acinar prostate mucinous adenocarcinoma', 'Other', 'Prostatic duct adenocarcinoma', 'Prostatic adenosquamous carcinoma', 'Prostatic adenocarcinoma (conventional NOS)', 'Acinar prostate mucinous (colloid) adenocarcinoma', 'Acinar prostate adenocarcinoma-sarcomatoid variant', '']",,ProstateCancerTier3 -Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,ProstateCancerTier3 -Stop Days from Index,Stop Days from Index,StopDaysfromIndex,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'",False,,,,ProstateCancerTier3 -Prostate Cancer Cytologic Morphologic Subtypes,Prostate Cancer Cytologic Morphologic Subtypes,ProstateCancerCytologicMorphologicSubtypes,Text term that describes various morphological and cytological subtypes in protate tumors.,False,,"['Not Reported', 'prostatic atypical adenomatous hyperplasia (adenosis or AAH)', 'prostatic clear cell cribiform hyperplasia', 'High grade prostatic intraepithelial neoplasia (HGPIN)/ (PIN II & PIN III)', 'Other', 'Low grade prostatic intraepithelial neoplasia (PIN)/(PIN I)', 'Unknown', 'prostatic basal cell hyperplasia', '']",,ProstateCancerTier3 -Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,ProstateCancerTier3 -Prostate Cancer Local Extent,Prostate Cancer Local Extent,ProstateCancerLocalExtent,The response used to categorize the local extent of disease for prostate cancer.,False,,"['Extraprostatic extension', 'Unknown', 'Organ Confined', 'Not Reported', '']",,ProstateCancerTier3 -Location Extent Extraprostatic Extension,Location Extent Extraprostatic Extension,LocationExtentExtraprostaticExtension,Location and extent of extraprostatic extension,False,,"['Right Anterior', 'Left Lateral', 'Right Lateral', 'Left Focal', 'Right Apex', 'Left Apex', 'Right Focal', 'Unknown', 'Right Non-focal (established)', 'Left Non-focal (established)', 'Not Reported', 'Left Posterior', 'Left Posterolateral', 'Left Anterior', 'Right Posterior', 'Right Mid', 'Left Mid', 'Right Posterolateral', 'Right Base', 'Left Base', '']",,ProstateCancerTier3 -Additonal Findings Uninvolved Prostate,Additonal Findings Uninvolved Prostate,AdditonalFindingsUninvolvedProstate,"Additional findings, uninvolved prostate",False,,"['High-grade prostatic intraepithelial neoplasia (PIN)', 'Not Reported', 'Inflammation', 'Benign prostatic hyperplasia (BPH)', 'Other', 'Unknown', 'Prostatic Intraductal adenocarcinoma', '']",,ProstateCancerTier3 -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,SarcomaTier3 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,SarcomaTier3 -Sarcoma Tumor Extension Type,Sarcoma Tumor Extension Type,SarcomaTumorExtensionType,The field to indicate the organs and structures to which the tumor has become adherent or has invaded.,False,,"['Extraosseous', 'Not Reported', 'Intracranial', 'Thoracic cavity', 'Other', 'Parameningeal', 'Unknown', 'Lymph nodes', '']",,SarcomaTier3 -Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,SarcomaTier3 -Stop Days from Index,Stop Days from Index,StopDaysfromIndex,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'",False,,,,SarcomaTier3 -Sarcoma Subtype,Sarcoma Subtype,SarcomaSubtype,"The subtype related to the scientific determination and investigation, analysis and recognition of the presence and nature of disease, condition, or injury from expressed signs and symptoms of tissue growth resulting from uncontrolled cell proliferation.",False,,"['Other Synovial Sarcoma Or Malignant Peripheral Nerve Sheath Tumor Sarcoma', 'Gastrointestinal Stromal Tumor', 'Not Reported', 'Undifferentiated pleomorphic sarcoma', 'Other', 'Unknown', 'Liposarcoma', 'Leiomyosarcoma (uterine or extra-uterine)', 'undifferentiated pleomorphic sarcoma or malignant fibrous histiosarcoma', '']",,SarcomaTier3 -Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,SarcomaTier3 -Sarcoma Diagnosis Classification Category,Sarcoma Diagnosis Classification Category,SarcomaDiagnosisClassificationCategory,"High level grouping to describe a diagnostic grouping or category for sarcoma, a malignant mesenchymal cell tumor most commonly arising from muscle, fat, fibrous tissue, bone, cartilage, and blood vessels.",False,,"['Not Reported', 'Unknown', 'Soft Tissue Sarcoma', 'Musculoskeletal Sarcoma', 'Bone Sarcoma', '']",,SarcomaTier3 -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,PancreaticCancerTier3 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,PancreaticCancerTier3 -Pancreatic IPMN Pathology Epithelial Subtype,Pancreatic IPMN Pathology Epithelial Subtype,PancreaticIPMNPathologyEpithelialSubtype,The Intraductal Papillary Mucinous Neoplasm (IPMN) epithelial cell subtype based on the gross and microscopic examination of a pancreatic neoplasm specimen,False,,"['Intestinal', 'Not Reported', 'Intraductal Tubopapillary', 'Pancreatobiliary', 'Oncocytic', 'Other', 'Unknown', 'Gastric Foveolar', '']",,PancreaticCancerTier3 -Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,PancreaticCancerTier3 -Stop Days from Index,Stop Days from Index,StopDaysfromIndex,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'",False,,,,PancreaticCancerTier3 -Pancreatic Duct Final Pathology Type,Pancreatic Duct Final Pathology Type,PancreaticDuctFinalPathologyType,The final pathology result of the pancreatic duct communication type.,False,,"['None', 'Not Reported', 'Not Specified', 'Side-Branch', 'Main Duct', 'Mixed', '']",,PancreaticCancerTier3 -Pancreas Precancer Histopathologic Grade,Pancreas Precancer Histopathologic Grade,PancreasPrecancerHistopathologicGrade,The grade of precancerous pancreatic tissue based on microscopic study of characteristic tissue abnormalities by employing various cytochemical and immunocytochemical stains.,False,,"['PanIN 1', 'IPMN-Borderline', 'PanIN 1A', 'IPMN-Invasive carcinoma', 'Not Reported', 'PanIN 1B', 'PanIN 3', 'PanIN 2', 'Unknown', 'IPMN-Carcinoma in situ', 'IPMN-Adenoma', '']",,PancreaticCancerTier3 -Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,PancreaticCancerTier3 -Melanoma Lesion Size,Melanoma Lesion Size,MelanomaLesionSize,"Diameter of lesion determined on skin examination (pre-bx), in mm",False,,,,MelanomaTier3 -Cutaneous Melanoma Ulceration,Cutaneous Melanoma Ulceration,CutaneousMelanomaUlceration,Description of extent of disruption to the surface of the skin caused by the cutaneous melanoma.,False,,"['Absent', 'Unknown', 'Not Reported', 'Present', '']",,MelanomaTier3 -History of Atypical Nevi,History of Atypical Nevi,HistoryofAtypicalNevi,Patient has a history of atypical nevi,False,,"['Yes (less than 50)', 'Yes (more than 50)', 'Not Reported', 'No', 'Unknown', '']",,MelanomaTier3 -Cutaneous Melanoma Tumor Infiltrating Lymphocytes,Cutaneous Melanoma Tumor Infiltrating Lymphocytes,CutaneousMelanomaTumorInfiltratingLymphocytes,Description of degree of lymphocytic infiltration surrounding and disrupting tumor cells of the vertical growth phase in a cutaneous melanoma.,False,,"['Brisk', 'Absent', 'Unknown', 'Nonbrisk', '']",,MelanomaTier3 -Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,MelanomaTier3 -History of Tanning Bed Use,History of Tanning Bed Use,HistoryofTanningBedUse,History of tanning bed use of the patient,False,,"['Not Reported', 'Never', 'Less than 10 times', '50-100 times', '10-50 times', 'More than 100 times', '']",,MelanomaTier3 -Cutaneous Melanoma Surgical Margins,Cutaneous Melanoma Surgical Margins,CutaneousMelanomaSurgicalMargins,Text term to indicate presence of tumor at resection margins,False,,"['Positive', 'Unknown', 'Not Reported', 'Negative', '']",,MelanomaTier3 -Stop Days from Index,Stop Days from Index,StopDaysfromIndex,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'",False,,,,MelanomaTier3 -Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,MelanomaTier3 -Cutaneous Melanoma Additional Findings,Cutaneous Melanoma Additional Findings,CutaneousMelanomaAdditionalFindings,Significant pathologic finding present in addition to the cutaneous melanoma.,False,,"['Solar Elastosis', 'Nevus Remnant', 'Vascular Proliferation', 'Not Applicable', 'Other', 'Actinic Keratosis', 'Nesting Melanoma', 'Unknown', 'Fibrosing Regression', 'Pagetoid Spread', '']",,MelanomaTier3 -Immediate Family History Melanoma,Immediate Family History Melanoma,ImmediateFamilyHistoryMelanoma,Text that describes the age at which the family member was diagnosed with melanoma skin cancer in relationship to their 50th birthday.,False,,"['Unknown', 'Not before age 50', 'Before age 50', '']",,MelanomaTier3 -Melanoma Biopsy Resection Sites,Melanoma Biopsy Resection Sites,MelanomaBiopsyResectionSites,Biopsy resection sites specific to melanoma (not covered in Tiers 1 and 2),False,,"['Skin of scrotum', 'Skin of ear', 'Skin of lower limb and hip', 'Skin of breast', 'skin of trunk-other', 'Skin of scalp', 'Skin of penis', 'Not Reported', 'Skin NOS', 'Skin of neck', 'Skin of lip', 'Skin of back', 'Skin of upper limb and shoulder', 'Skin of sole', 'Skin of vulva', 'Skin of chest', 'Skin of other parts of face', 'Skin of abdomen', 'Skin of palm', 'Skin of nose', 'Skin of eye lid', 'skin other', '']",,MelanomaTier3 -History of Chronic UV Exposure,History of Chronic UV Exposure,HistoryofChronicUVExposure,History of chronic UV exposure,False,,"['None', 'Not Reported', 'Outdoor occupational', 'Outdoor recreational', 'Therapeutic', '']",,MelanomaTier3 -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,MelanomaTier3 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MelanomaTier3 -Cutaneous Melanoma Tumor Regression Range,Cutaneous Melanoma Tumor Regression Range,CutaneousMelanomaTumorRegressionRange,Description of the degree to which tumor cells are replaced by lymphocytic inflammation with or without dermal melanophages and fibrosis._Range; the difference between the lowest and highest numerical values.,False,,"['Present involving 75% or more', 'Absent', 'Present involving less than 75%', 'Unknown', '']",,MelanomaTier3 -Fitzpatrick Skin Tone,Fitzpatrick Skin Tone,FitzpatrickSkinTone,The Fitzpatrick classification of skin phototype,False,,"['Not Reported', 'III', 'V', 'Unknown', 'I', 'VI', 'II', 'IV', '']",,MelanomaTier3 -History of Blistering Sunburn,History of Blistering Sunburn,HistoryofBlisteringSunburn,Patient has history of blistering sunburn,False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,MelanomaTier3 -Melanoma Specimen Clark Level Value,Melanoma Specimen Clark Level Value,MelanomaSpecimenClarkLevelValue,Definition of the Clark level or depth of involvement of a melanoma in the skin or a specimen.,False,,"['III', 'V', 'Unknown', 'I', 'No Source Documentation', 'II', 'IV', '']",,MelanomaTier3 -Ischemic Temperature,Ischemic Temperature,IschemicTemperature,Specify whether specimen experienced warm or cold ischemia.,False,,"['4C wet ice', 'Ambient air', 'Cold Ischemia', 'Warm Ischemia', 'Unknown', 'Liquid Nitrogen', 'Negative -20C', 'Dry Ice', '']",,SRRSBiospecimen -Additional Topography,Additional Topography,AdditionalTopography,Topography not included in the ICD-O-3 Topography codes.,False,,"['Hilar Airway', 'Skin of scrotum', 'Skin of ear', 'Skin of lower limb and hip', 'Skin of breast', 'Skin of scalp', 'Skin of penis', 'Not Reported', 'Skin NOS', 'Skin of neck', 'Skin of lip', 'Skin of back', 'Skin of trunk', 'Skin of upper limb and shoulder', 'Skin of sole', 'Skin of vulva', 'Skin of chest', 'Skin of other parts of face', 'Skin of abdomen', 'Peri-tumoral Airway', 'Skin of palm', 'Skin of nose', 'Skin of eye lid', '']",,SRRSBiospecimen -Fixative Type,Fixative Type,FixativeType,Text term to identify the type of fixative used to preserve a tissue specimen,True,,"['95% Ethanol', 'Dimidoester', 'Acetone', 'RNAlater', 'Polaxamer', 'Glutaraldehyde', 'Cryo-store', 'Carbodiimide', 'OCT media', 'None', 'Formalin', 'Methacarn', 'Unknown', 'NP40 lysis buffer', 'PAXgene tissue', 'Para-benzoquinone', 'Alcohol', 'TCL lysis buffer', 'Dimethylacetamide', 'Saline', 'Other', ""Carnoy's Fixative""]",,SRRSBiospecimen -Biospecimen Type,Biospecimen Type,BiospecimenType,Biospecimen Type,True,,"['Bone Marrow Biospecimen Type', 'Tissue Biospecimen Type', 'Stool Biospecimen Type', 'Fluids Biospecimen Type', 'Cells Biospecimen Type', 'Urine Biospecimen Type', 'Blood Biospecimen Type', 'Ascites Biospecimen Type', 'Analyte Biospecimen Type', 'Mouth Rinse Biospecimen Type', 'Sputum Biospecimen Type']",,SRRSBiospecimen -Preservation Method,Preservation Method,PreservationMethod,Text term that represents the method used to preserve the sample.,True,,"['Negative 80 Deg C', 'Formalin fixed-unbuffered', 'Formalin fixed-buffered', 'Formalin fixed paraffin embedded - FFPE', 'Fresh dissociated and single cell sorted', 'Fresh', 'Frozen', 'Cryopreservation in liquid nitrogen - dead tissue', 'Unknown', 'Liquid Nitrogen', 'OCT', 'Cryopreserved', 'Methacarn fixed paraffin embedded - MFPE', 'Not Reported', 'Cryopreservation in dry ice - dead tissue', 'Snap Frozen', 'Fresh dissociated and single cell sorted into plates', 'Fresh dissociated and single cell sorted into plates in NP40 buffer', 'Fresh dissociated', 'Cryopreservation in liquid nitrogen - live cells']",,SRRSBiospecimen -Histologic Morphology Code,Histologic Morphology Code,HistologicMorphologyCode,"Histologic Morphology Code, based on ICD-O-3. Any valid ICD-O-3 morphology code. See https://seer.cancer.gov/icd-o-3/ and https://seer.cancer.gov/icd-o-3/sitetype.icdo3.20200629.xlsx. Examples: 80510",True,,,,SRRSBiospecimen -HTAN Parent ID,HTAN Parent ID,HTANParentID,HTAN ID of parent from which the biospecimen was obtained. Parent could be another biospecimen or a research participant.,True,,,,SRRSBiospecimen -Source HTAN Biospecimen ID,Source HTAN Biospecimen ID,SourceHTANBiospecimenID,This is the HTAN ID that may have been assigned to the biospecimen at the site of biospecimen origin (e.g. BU).,False,,,,SRRSBiospecimen -HTAN Biospecimen ID,HTAN Biospecimen ID,HTANBiospecimenID,HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,SRRSBiospecimen -Collection Days from Index,Collection Days from Index,CollectionDaysfromIndex,Number of days from the research participant's index date that the biospecimen was obtained.,True,,,,SRRSBiospecimen -Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,SRRSBiospecimen -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,SRRSBiospecimen -Storage Method,Storage Method,StorageMethod,The method by which a biomaterial was stored after preservation or before another protocol was used.,True,,"['RNAlater at 25C', '4C in vacuum chamber', 'RNAlater at 4C', 'Frozen at -80C', 'Cut slide', 'Frozen at -70C', 'Fresh', 'Frozen in vapor phase', 'Not Applicable', 'Ambient temperature', 'Refrigerated at 4 degrees', 'Unknown', 'Paraffin block', 'Refrigerated vacuum chamber', 'Frozen in liquid nitrogen', 'Desiccant at 4C', 'RNAlater at -20C', 'Frozen at -150C']",,SRRSBiospecimen -Processing Days from Index,Processing Days from Index,ProcessingDaysfromIndex,Number of days from the research participant's index date that the biospecimen was processed,True,,,,SRRSBiospecimen -Ischemic Time,Ischemic Time,IschemicTime,"Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value.",False,,,,SRRSBiospecimen -Acquisition Method Type,Acquisition Method Type,AcquisitionMethodType,Records the method of acquisition or source for the specimen under consideration.,True,,"['Blood draw', 'Core needle biopsy', 'Lymphadenectomy - Regional Nodes', 'Biopsy', 'Endoscopic biopsy', 'Shave Biopsy', 'Other Acquisition Method', 'Re-excision', 'BAL (bronchial alveolar lavage)', 'Not specified', 'Induced sputum', 'Cytobrush', 'Sentinel Node Biopsy', 'Surgical Resection', 'Excision', 'Fine Needle Aspirate', 'Punch Biopsy', 'Non induced sputum', 'Fluid collection', 'Forceps biopsy', 'Autopsy']",,SRRSBiospecimen -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,SRRSBiospecimen -Adjacent Biospecimen IDs,Adjacent Biospecimen IDs,AdjacentBiospecimenIDs,"List of HTAN Identifiers (separated by commas) of adjacent biospecimens cut from the same sample; for example HTA3_3000_3, HTA3_3000_4, ...",False,,,,SRRSBiospecimen -Collection Media,Collection Media,CollectionMedia,Material Specimen is collected into post procedure,False,,"['None', 'PBS', 'PBS+Serum', 'RPMI', 'DMEM+Serum', 'RPMI+Serum', 'DMEM', '']",,SRRSBiospecimen -Preinvasive Morphology,Preinvasive Morphology,PreinvasiveMorphology,"Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the HTAN",False,,"['Melanoma in situ - superficial spreading', 'Invasive melanoma - other', 'Benign tumor NOS', 'No diagnosis possible', 'Melanoma in situ - lentigo maligna type', 'Normal WDA', 'Persistent melanoma in situ', 'Atypical adenomatous hyperplasia', 'Squamous Carcinoma in situ', 'Invasive melanoma - nevoid', 'Invasive melanoma - nodular type', 'Severe dysplasia', 'Reserve cell hyperplasia', 'Melanocytic hyperplasia', 'Squamous metaplasia - immature', 'Melanoma in situ - acral-lentiginous', 'Melanoma in situ - arising in a giant congenital nevus', 'Atypical melanocytic proliferation', 'Carcinoma NOS', 'Mild dysplasia', 'Squamous metaplasia - mature', 'Moderate dysplasia', 'Invasive melanoma - acral lentiginous', 'Melanoma in situ - not otherwise classified', 'Adenocarcinoma in situ - mucinous', 'Invasive melanoma - desmoplastic', 'Hamartoma', 'Scar - no residual melanoma', 'Invasive melanoma - superficial spreading', 'Adenocarcinoma in situ - non mucinous', 'Invasive melanoma - lentigo maligna', '']",,SRRSBiospecimen -Topography Code,Topography Code,TopographyCode,"Topography Code, indicating site within the body, based on ICD-O-3.",False,,"['8140/3', '9571/3', '9063/3', '9194/3', '9261/3', '8280/0', '8315/3', '9442/1', '8072/3', '8221/0', '8540/3', '9840/3', '8453/0', '8631/3', '9502/0', '8912/3', '8723/0', '8741/2', '9728/3', '8761/0', '8802/3', '8098/3', '9042/3', '8052/3', '8835/1', '9103/0', '8905/0', '8004/3', '8480/0', '8841/1', '9174/1', '9659/3', '9807/3', '8121/0', '8588/3', '8380/0', '8392/0', '8472/1', '9812/3', '8830/3', '8390/3', '9130/3', '9242/3', '9301/0', '8453/3', '9302/3', '9837/3', '8091/3', '8980/3', '9680/3', '8970/3', '8408/3', '8508/3', '8936/1', '8576/3', '8584/3', '8711/0', '8589/3', '9170/3', '8650/0', '8622/1', '8011/3', '9054/0', '8012/3', '9350/1', '9719/3', '9508/3', '9752/1', '9833/3', '8094/3', '8163/2', '9504/3', '9140/3', '8551/3', '9490/3', '8806/3', '9450/3', '8681/1', '8152/3', '8592/1', '9741/1', '8880/0', '8174/3', '8721/3', '8800/3', '8500/2', '8693/3', '8080/2', '8803/3', '8381/1', '8902/3', '9766/1', '8842/3', '8441/2', '8001/3', '8503/3', '8930/0', '8150/0', '9051/0', '9250/3', '8806/6', '8220/3', '9390/1', '9431/1', '9476/3', '9871/3', '8340/3', 'Unknown', '9120/0', '8720/6', '8280/3', '8336/0', '8504/2', '8714/3', '9542/3', '8904/0', '9654/3', '9755/3', '9065/3', '8521/3', '9911/3', '8121/3', '8981/3', '9655/3', '9391/3', '9590/3', '8815/1', '8290/0', '8973/3', '9051/3', '9423/3', '9767/1', '9735/3', '9898/3', '8723/3', '8350/3', '8311/1', '9989/3', '8583/1', '8172/3', '8580/0', '9071/3', '8634/1', '9013/0', '8375/0', '8230/2', '8850/3', '9740/1', '8052/2', '8210/2', '8247/3', '8800/9', '8031/3', '8051/0', '9805/3', '9987/3', '8281/0', '9174/0', '8660/0', '8010/2', '9320/0', '9717/3', '8405/0', '9945/3', '9530/1', '9733/3', '8402/3', '9432/1', '8210/3', '8339/3', '8332/3', '8163/3', '9764/3', '9984/3', '8270/3', '8831/0', '9311/0', '8085/3', '8102/0', '8250/1', '8092/3', '8854/3', '8076/2', '9501/0', '8931/3', '8650/1', '8770/0', '9872/3', '8050/3', '9000/3', '8594/1', '9041/3', '8810/1', '9441/3', '9020/3', '8960/3', '9827/3', '8130/2', '8173/3', '8801/6', '8920/3', '8728/1', '9760/3', '9460/3', '8814/3', '8220/0', '8852/3', '9200/0', '8170/3', '8641/0', '8812/0', '8824/1', '8780/3', '9836/3', '8474/3', '9150/3', '8471/0', '8896/3', '8261/3', '9826/3', '8041/3', '8310/0', '8140/2', '9161/1', '8103/0', '9670/3', '8155/1', '9820/3', '8856/0', '9424/3', '8073/3', '8936/0', '8720/3', '8441/6', '8102/3', '9122/0', '8692/1', '8460/0', '8522/3', '9182/3', '9351/1', '9664/3', '8210/0', '8966/0', '8825/0', '9832/3', '8740/0', '8149/0', '9540/0', '8010/0', '8081/2', '8982/0', '9290/3', '8272/0', '9302/0', '8330/0', '9754/3', '8463/1', '8582/3', '8347/3', '9186/3', '9341/3', '9064/2', '9712/3', '9083/3', '8231/3', '9085/3', '8580/3', '8811/1', '9962/3', '8201/2', '9531/0', '8147/3', '8840/0', '8722/0', '9173/0', '8090/3', '9091/1', '8900/0', '9421/1', '9530/0', '9982/3', '8346/3', '8374/0', '8200/3', '8761/3', '8940/3', '9580/3', '9651/3', '9875/3', '9110/3', '8257/3', '9230/3', '9946/3', '8690/1', '8160/0', '9086/3', '9395/3', '9055/0', '9965/3', '9252/3', '8982/3', '8242/3', '8713/0', '8000/3', '8512/3', '9040/0', '9520/3', '8070/2', '8965/0', '9270/0', '8254/3', '9474/3', '9110/1', '8571/3', '8312/3', '9691/3', '8213/3', '8371/0', '8100/0', '8601/0', '9015/1', '9385/3', '9503/3', '9180/0', '9831/3', '8245/3', '9430/3', '9975/3', '9121/0', '8241/3', '8550/1', '9420/3', '9191/0', '9870/3', '8380/1', '9980/3', '8161/0', '8043/3', '8246/3', '8642/1', '8156/1', '9014/3', '8310/6', '9130/1', '8190/0', '8561/0', '9220/1', '9865/3', '8319/3', '8408/0', '9992/3', '8900/3', '9101/3', '8345/3', '8712/0', '8842/0', '9753/1', '9372/3', '9352/1', '9661/3', '8086/3', '8240/1', '9475/3', '8881/0', '8474/1', '8959/1', '8990/1', '8313/3', '8409/0', '9251/3', '9410/3', '9716/3', '9180/6', '9141/0', '8380/3', '9801/3', '8602/0', '9653/3', '9053/3', '8590/1', '9440/3', '8078/3', '8381/3', '8046/6', '8893/0', '9532/0', '9665/3', '9690/3', '8093/3', '8451/1', '8890/0', '8730/3', '8983/3', '9000/0', '9541/0', '8634/3', '8772/0', '9310/0', '9726/3', '8333/3', '8967/0', '9490/0', '8935/1', '9971/3', '9105/3', '8314/3', '8610/0', '8853/3', '9132/0', '8507/2', '8391/0', '8593/1', '8077/0', '8935/3', '9401/3', '8824/0', '8633/1', '8892/0', '8311/3', '8857/0', '8521/1', '9150/1', '9195/3', '8040/0', '8740/3', '8245/1', '8265/3', '8407/3', '9762/3', '8390/0', '8325/0', '8870/0', '8045/3', '8810/0', '8272/3', '9718/3', '8076/3', '8263/0', '9684/3', '9275/0', '9330/3', '9142/0', '9866/3', '8041/6', '8680/1', '8840/3', '9835/3', '8246/6', '8890/1', '8161/3', '8805/3', '9731/3', '8021/3', '8250/3', '8162/3', '8334/0', '8250/2', '9597/3', '9535/0', '9705/3', '8140/33', '9250/1', '9273/0', '9231/3', '8200/0', '8825/1', '8631/1', '9650/3', '9400/3', '8525/3', '9596/3', '8920/6', '8827/1', '8013/3', '8373/0', '8897/1', '8011/0', '9102/3', '9698/3', '8801/3', '9506/1', '8823/0', '9050/0', '8420/0', '8935/0', '9170/0', '9732/3', '9510/0', '8746/3', '9948/3', '8320/3', '8895/3', '8144/3', '8502/3', '8972/3', '8964/3', '8519/2', '8895/0', '9185/3', '9560/1', '8473/1', '9724/3', '8140/0', '9442/3', '9161/0', '9741/3', '9382/3', '8407/0', '8300/0', '8573/3', '8800/0', '9440/6', '8725/0', '9702/3', '8150/1', '8826/0', '9052/0', '8974/1', '9814/3', '9210/1', '8131/3', '8204/0', '9758/3', '9131/0', '8052/0', '8410/0', '8700/3', '8120/2', '8158/1', '8936/3', '8750/0', '9811/3', '9876/3', '8010/9', '8372/0', '8450/0', '8523/3', '8550/3', '9813/3', '8581/1', '8053/0', '8140/1', '8821/1', '9570/0', '8153/3', '8001/1', '8252/3', '8620/1', '9687/3', '8682/1', '9860/3', '8313/1', '8400/1', '8452/3', '9084/0', '9062/3', '9480/3', '8862/0', '8600/0', '8152/1', '8190/3', '8120/3', '8271/0', '8462/1', '8560/3', '9100/1', '9390/3', '9580/0', '9817/3', '9689/3', '8441/0', '8830/1', '8959/0', '9970/1', '8213/0', '9110/0', '8097/3', '8023/3', '9014/1', '8000/1', '8811/3', '8383/3', '9136/1', '8461/0', '9171/0', '8513/3', '8323/3', '8921/3', 'Not Reported', '9241/0', '8950/3', '8249/3', '9365/3', '9342/3', '8256/3', '8261/0', '8040/1', '8408/1', '8522/6', '9370/3', '9514/1', '9679/3', '8772/3', '9560/0', '8322/3', '9040/3', '9384/1', '9015/0', '8005/3', '9510/3', '9561/3', '8744/3', '9708/3', '9740/3', '9874/3', '9701/3', '9363/0', '8560/0', '8077/2', '8120/1', '9180/3', '9090/3', '8728/0', '8442/1', '8580/1', '8480/3', '8631/0', '8894/3', '9090/0', '9160/0', '8450/3', '8249/6', '8770/3', '9800/3', '8344/3', '8722/3', '8504/3', '8774/3', '8481/3', '8022/3', '8000/9', '8384/3', '9125/0', '8263/3', '9221/3', '9220/0', '8215/3', '8852/0', '9493/0', '9920/3', '8461/6', '8330/3', '9727/3', '8003/3', '8951/3', '8010/3', '8820/0', '8148/2', '8514/3', '8140/6', '9963/3', '8010/6', '8773/3', '9675/3', '8482/6', '9472/3', '8522/2', '9072/3', '9015/3', '8581/3', '8983/0', '8822/1', '9084/3', '8180/3', '9910/3', '9582/0', '9678/3', '8074/3', '9873/3', '8240/6', '9193/3', '8260/0', '8623/1', '8311/6', '8584/1', '8825/3', '8343/2', '8861/0', '8480/1', '8500/3', '8501/2', '8000/0', '8211/0', '8582/1', '9012/0', '8402/0', '9502/3', '9806/3', '9507/0', '8142/3', '8401/3', '9073/1', '8453/2', '9280/0', '9512/3', '9699/3', '9940/3', '9742/3', '8123/3', '8380/2', '8342/3', '8990/0', '8243/3', '9192/3', '8452/1', '8600/3', '8720/0', '8154/3', '8240/3', '8400/0', '9364/3', '9412/1', '8490/3', '8550/0', '9270/3', '8155/3', '8110/0', '8130/3', '8860/0', '9540/3', '9175/0', '9282/0', '8317/3', '9150/0', '9260/3', '8251/0', '8461/3', '8910/3', '9445/3', '9834/3', '8991/3', '8762/1', '9272/0', '9700/3', '9172/0', '9863/3', '8855/3', '9221/0', '8480/6', '8850/1', '9360/1', '8934/3', '8804/6', '8460/3', '8813/0', '8335/3', '8630/0', '9187/3', '9986/3', '8071/2', '8810/3', '9538/1', '9030/0', '9133/1', '8370/3', '8141/3', '8323/0', '8095/3', '9991/3', '8401/0', '8051/3', '9184/3', '9281/0', '9390/0', '8381/0', '8790/0', '9509/1', '9230/0', '9539/1', '8261/2', '8321/0', '8290/3', '9124/3', '9765/1', '9540/1', '9759/3', '8000/6', '9930/3', '9010/0', '8409/3', '8507/3', '8130/1', '8260/3', '8971/3', '8804/3', '9373/0', '8670/0', '9534/0', '8620/3', '9688/3', '8727/0', '8585/3', '8891/0', '8510/3', '8046/3', '9591/3', '8153/1', '8574/3', '8726/0', '8122/3', '8160/3', '9050/3', '8940/0', '9020/1', '8505/0', '8430/3', '9274/0', '9394/1', '8101/0', '9271/0', '8262/3', '8440/3', '8403/3', '9312/0', '9060/3', '9725/3', '9768/1', '8251/3', '9869/3', '8146/0', '9523/3', '9897/3', '8771/0', '9505/3', '8963/3', '8901/3', '9043/3', '9340/0', '9560/3', '8509/3', '8331/3', '8587/0', '9000/1', '9310/3', '9738/3', '8444/1', '8503/2', '8075/3', '9413/0', '9262/0', '9044/3', '9756/3', '8832/3', '8854/0', '8156/3', '8380/6', '9322/0', '9971/1', '8470/0', '8471/3', '8728/3', '8281/3', '8815/3', '8834/1', '9011/0', '9181/3', '8410/3', '9581/3', '8720/2', '8894/0', '8761/1', '8454/0', '9895/3', '8640/1', '8145/3', '8691/1', '9383/1', '8171/3', '8020/6', '8430/1', '9020/0', '9451/3', '9521/3', '8124/3', '8680/0', '9751/1', '8083/3', '8333/0', '8742/2', '8800/6', '9729/3', '8975/1', '9931/3', '8932/0', '8221/3', '9014/0', '9380/3', '8543/3', '8413/3', '8671/0', '9321/0', '8343/3', '8850/0', '9381/3', '9444/1', '8175/3', '9330/0', '8403/0', '9673/3', '8316/3', '9045/3', '9960/3', '8591/1', '8002/3', '9070/3', '8255/3', '8120/0', '8562/3', '8933/3', '8264/0', '9709/3', '8440/0', '8811/0', '8191/0', '9361/1', '8700/0', '9750/3', '8903/0', '8032/3', '9539/3', '9411/3', '8830/0', '9243/3', '9761/3', '9513/3', '8084/3', '9983/3', '9695/3', '9016/0', '8891/3', '8930/3', '9473/3', '8324/0', '8530/3', '8370/1', '8680/3', '8096/0', '8163/0', '9898/1', '9961/3', '9815/3', '8263/2', '8242/1', '9425/3', '8244/3', '8382/3', '8060/0', '8857/3', '9392/3', '8337/3', '9120/3', '9470/3', '8501/3', '9966/3', '9550/0', '9867/3', '9757/3', '8858/3', '9183/3', '9562/0', '8034/3', '9137/3', '8959/3', '9252/0', '8248/1', '8836/1', '9300/0', '9505/1', '9751/3', '8040/3', '8211/3', '8148/0', '8070/3', '8710/3', '9240/3', '9769/1', '8683/0', '8050/2', '8780/0', '9530/3', '9662/3', '8745/3', '8121/1', '8890/3', '8504/0', '9100/0', '8851/0', '8230/3', '8520/3', '8035/3', '9737/3', '8771/3', '8404/0', '8898/1', '9064/3', '8313/0', '8015/3', '8851/3', '9667/3', '8370/0', '8482/3', '8170/0', '8760/0', '8812/3', '8318/3', '9818/3', '9210/0', '9538/3', '8202/0', '9130/0', '8151/0', '8630/3', '9251/1', '9270/1', '9080/1', '8420/3', '8110/3', '8300/3', '9511/3', '9816/3', '8524/3', '8509/2', '8042/3', '9861/3', '8071/3', '8082/3', '8090/1', '8360/1', '9522/3', '9985/3', '8500/6', '8813/3', '8583/3', '8743/3', '9571/0', '8310/3', '8650/3', '9220/3', '8212/0', '9967/3', '8050/0', '8044/3', '8005/0', '9964/3', '8201/3', '8832/0', '8214/3', '9477/3', '9950/3', '8070/33', '8490/6', '9823/3', '9080/3', '9135/1', '8506/0', '8960/1', '9290/0', '9671/3', '9200/1', '8041/34', '8742/3', '9501/3', '9537/0', '9061/3', '8020/3', '9341/1', '9478/3', '8270/0', '8520/2', '9080/0', '8575/3', '9663/3', '8586/3', '8621/1', '8361/0', '9734/3', '8670/3', '8322/0', '8572/3', '9714/3', '8730/0', '8471/1', '8406/0', '8143/3', '8443/0', '8470/3', '8503/0', '8400/3', '8741/3', '9808/3', '8630/1', '8541/3', '9362/3', '8833/3', '8990/3', '8001/0', '8253/3', '8585/1', '9652/3', '9052/3', '9104/1', '9396/3', '8033/3', '8570/3', '8950/6', '9533/0', '9393/3', '8632/1', '8542/3', '8460/2', '8693/1', '9896/3', '8070/6', '8711/3', '9100/3', '8150/3', '9491/0', '9371/3', '8341/3', '8441/3', '8640/3', '9500/3', '9123/0', '8030/3', '9082/3', '8014/3', '8330/1', '8151/3', '9055/1', '9133/3', '8941/3', '8522/1', '8552/3', '9081/3', '9809/3', '8470/2', '9492/0', '8147/0', '9471/3', '8815/0', '9891/3', '']",,SRRSBiospecimen -Biospecimen Dimension 3,Biospecimen Dimension 3,BiospecimenDimension3,"Third dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,," If Biospecimen is ""Bone"" OR ""Tissue"" then ""Biospecimen Dimension 3"" is required",SRRSBiospecimen -Portion Weight,Portion Weight,PortionWeight,"Numeric value that represents the sample portion weight, measured in milligrams.",False,True,," If Biospecimen is ""Bone"" OR ""Tissue"" OR ""Urine"" then ""Portion Weight"" is required",SRRSBiospecimen -Site of Resection or Biopsy,Site of Resection or Biopsy,SiteofResectionorBiopsy,"The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",False,True,"['Paraurethral gland', 'Colon NOS', 'Frontal sinus', 'Overlapping lesion of tongue', 'Overlapping lesion of palate', 'Scrotum NOS', 'Bone marrow', 'Axillary tail of breast', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'unknown primary site', 'Broad ligament', 'Lateral floor of mouth', 'Overlapping lesion of vulva', 'Trigone of bladder', 'Lacrimal gland', 'Thorax NOS', 'Ampulla of Vater', 'Myometrium', 'Penis NOS', 'Female genital tract NOS', 'Submandibular gland', 'Anterior 2/3 of tongue NOS', 'Posterior wall of bladder', 'Thymus', 'Endocrine gland NOS', 'Stomach NOS', 'Unknown', 'Cerebrum', 'Splenic flexure of colon', 'Urachus', 'Skin of lip NOS', 'Mucosa of lip NOS', 'Accessory sinus NOS', 'Cortex of adrenal gland', 'Other ill-defined sites', 'Middle lobe lung', 'Pelvis NOS', 'Anus NOS', 'Upper-inner quadrant of breast', 'Posterior mediastinum', 'Esophagus NOS', 'Duodenum', 'Cervical esophagus', 'Optic nerve', 'Long bones of lower limb and associated joints', 'Middle ear', 'Breast NOS', 'Dorsal surface of tongue NOS', 'Lesser curvature of stomach NOS', 'Overlapping lesion of floor of mouth', 'Overlapping lesion of heart mediastinum and pleura', 'Eye NOS', 'Overlapping lesion of esophagus', 'Ciliary body', 'Ureteric orifice', 'Postcricoid region', 'External ear', 'Base of tongue NOS', 'Liver', 'Commissure of lip', 'Cloacogenic zone', 'Lower lobe lung', 'Transverse colon', 'Acoustic nerve', 'Supraglottis', 'Fallopian tube', 'Upper third of esophagus', 'Skin of scalp and neck', 'Choroid', 'Long bones of upper limb scapula and associated joints', 'Overlapping lesion of brain', 'Upper gum', 'Skin NOS', 'Hard palate', 'Ileum', 'Overlapping lesion of colon', 'Ascending colon', 'Lower gum', 'Pelvic bones sacrum coccyx and associated joints', 'Hepatic flexure of colon', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Vestibule of mouth', 'Cervix uteri', 'Bones of skull and face and associated joints', 'Overlapping lesion of lip oral cavity and pharynx', 'Endometrium', 'Sphenoid sinus', 'Overlapping lesion of ill-defined sites', 'Sigmoid colon', 'Peritoneum NOS', 'Specified parts of peritoneum', 'Meckel diverticulum', 'Rectosigmoid junction', 'Kidney NOS', 'Reticuloendothelial system NOS', 'Rectum NOS', 'Pylorus', 'Overlapping lesion of tonsil', 'Pleura NOS', 'Jejunum', 'Vallecula', 'Skin of lower limb and hip', 'Pelvic lymph nodes', 'External lower lip', 'Overlapping lesion of skin', 'Mucosa of upper lip', 'Ovary', 'Cauda equina', 'Lower limb NOS', 'Body of stomach', 'Overlapping lesion of larynx', 'Pancreas NOS', 'Overlapping lesion of lung', 'Overlapping lesion of major salivary glands', 'Uvula', 'Overlapping lesion of hypopharynx', 'Round ligament', 'Corpus uteri', 'Biliary tract NOS', 'Male genital organs NOS', 'Parametrium', 'External lip NOS', 'Overlapping lesion of accessory sinuses', 'Cardia NOS', 'Islets of Langerhans', 'Carotid body', 'Ventral surface of tongue NOS', 'Autonomic nervous system NOS', 'Overlapping lesion of corpus uteri', 'Spinal meninges', 'Posterior wall of nasopharynx', 'Placenta', 'Intrahepatic bile duct', 'Overlapping lesion of digestive system', 'Mediastinum NOS', 'Hematopoietic system NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Major salivary gland NOS', 'Cerebellum NOS', 'Overlapping lesion of stomach', 'Vulva NOS', 'Craniopharyngeal duct', 'Lung NOS', 'Greater curvature of stomach NOS', 'Upper-outer quadrant of breast', 'Gallbladder', 'Thoracic esophagus', 'Lymph nodes of axilla or arm', 'Ventricle NOS', 'Overlapping lesion of biliary tract', 'Hypopharynx NOS', 'Clitoris', 'Exocervix', 'Parietal lobe', 'Waldeyer ring', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Head face or neck NOS', 'Anterior wall of nasopharynx', 'Urethra', 'Overlapping lesion of nasopharynx', 'Maxillary sinus', 'Lymph nodes of inguinal region or leg', 'Ureter', 'Tonsillar pillar', 'Sublingual gland', 'Pituitary gland', 'Gastrointestinal tract NOS', 'Pineal gland', 'Meninges NOS', 'Lingual tonsil', 'Trachea', 'Pyriform sinus', 'Mucosa of lower lip', 'Not Reported', 'Posterior wall of hypopharynx', 'Urinary system NOS', 'Orbit NOS', 'Short bones of lower limb and associated joints', 'Connective subcutaneous and other soft tissues of thorax', 'Upper limb NOS', 'Gastric antrum', 'Lymph node NOS', 'Peripheral nerves and autonomic nervous system of thorax', 'Ill-defined sites within respiratory system', 'Other specified parts of male genital organs', 'Rib sternum clavicle and associated joints', 'Overlapping lesion of bladder', 'Appendix', 'Prostate gland', 'Lymph nodes of multiple regions', 'Lateral wall of nasopharynx', 'Branchial cleft', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Floor of mouth NOS', 'Connective subcutaneous and other soft tissues NOS', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Bladder neck', 'Border of tongue', 'Connective subcutaneous and other soft tissues of abdomen', 'Overlapping lesion of small intestine', 'Lateral wall of bladder', 'Soft palate NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Isthmus uteri', 'Nasal cavity', 'Endocervix', 'Tonsil NOS', 'Glottis', 'Retroperitoneum', 'Peripheral nerves and autonomic nervous system of pelvis', 'Frontal lobe', 'Vagina NOS', 'Undescended testis', 'Laryngeal cartilage', 'Eyelid', 'Hypopharyngeal aspect of aryepiglottic fold', 'Overlapping lesion of other and unspecified parts of mouth', 'Upper lobe lung', 'Lip NOS', 'Lymph nodes of head face and neck', 'Overlapping lesion of brain and central nervous system', 'Overlapping lesion of penis', 'Overlapping lesion of retroperitoneum and peritoneum', 'Parotid gland', 'Dome of bladder', 'Bone of limb NOS', 'Descended testis', 'Vertebral column', 'Fundus uteri', 'Connective subcutaneous and other soft tissues of pelvis', 'Epididymis', 'Intra-abdominal lymph nodes', 'Paraspinal', 'Prepuce', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Pharynx NOS', 'Overlapping lesion of endocrine glands and related structures', 'Gum NOS', 'Spinal cord', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Skin of upper limb and shoulder', 'Nasopharynx NOS', 'Parathyroid gland', 'Bone NOS', 'Mouth NOS', 'Abdomen NOS', 'Conjunctiva', 'Spermatic cord', 'External upper lip', 'Labium minus', 'Renal pelvis', 'Overlapping lesion of lip', 'Short bones of upper limb and associated joints', 'Main bronchus', 'Upper respiratory tract NOS', 'Body of penis', 'Small intestine NOS', 'Central portion of breast', 'Lower-inner quadrant of breast', 'Labium majus', 'Tonsillar fossa', 'Cecum', 'Glans penis', 'Tail of pancreas', 'Lower third of esophagus', 'Body of pancreas', 'Intestinal tract NOS', 'Brain stem', 'Overlapping lesion of rectum anus and anal canal', 'Posterior wall of oropharynx', 'Pancreatic duct', 'Blood', 'Temporal lobe', 'Anterior floor of mouth', 'Nervous system NOS', 'Cornea NOS', 'Palate NOS', 'Occipital lobe', 'Abdominal esophagus', 'Overlapping lesion of pancreas', 'Overlapping lesion of female genital organs', 'Cheek mucosa', 'Retina', 'Overlapping lesion of male genital organs', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Larynx NOS', 'Skin of other and unspecified parts of face', 'Spleen', 'Oropharynx NOS', 'Anal canal', 'Subglottis', 'Cerebral meninges', 'Lateral wall of oropharynx', 'Middle third of esophagus', 'Nipple', 'Medulla of adrenal gland', 'Overlapping lesion of eye and adnexa', 'Olfactory nerve', 'Ethmoid sinus', 'Overlapping lesion of cervix uteri', 'Descending colon', 'Brain NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Anterior wall of bladder', 'Mandible', 'Other specified parts of pancreas', 'Skin of trunk', 'Other specified parts of female genital organs', 'Uterus NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Intrathoracic lymph nodes', 'Heart', 'Adrenal gland NOS', 'Aortic body and other paraganglia', 'Extrahepatic bile duct', 'Overlapping lesion of breast', 'Superior wall of nasopharynx', 'Fundus of stomach', 'Anterior mediastinum', 'Tongue NOS', 'Cranial nerve NOS', 'Head of pancreas', 'Overlapping lesions of oropharynx', 'Overlapping lesion of bones joints and articular cartilage', 'Retromolar area', 'Testis NOS', 'Connective subcutaneous and other soft tissues of head face and neck', 'Bladder NOS', 'Overlapping lesion of urinary organs', 'Lower-outer quadrant of breast', 'Thyroid gland', 'Anterior surface of epiglottis', 'Uterine adnexa', '']"," If Biospecimen is ""Bone"" OR ""Tissue"" OR ""Urine"" then ""Site of Resection or Biopsy"" is required",SRRSBiospecimen -Specimen Laterality,Specimen Laterality,SpecimenLaterality,"For tumors in paired organs, designates the side on which the specimen was obtained.",False,True,"['Not Reported', 'Bilateral', 'Not Applicable', 'Unknown', 'Left', 'Right', '']"," If Biospecimen is ""Bone"" OR ""Tissue"" OR ""Urine"" then ""Specimen Laterality"" is required",SRRSBiospecimen -Tumor Tissue Type,Tumor Tissue Type,TumorTissueType,Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint (add rows to select multiple values along with timepoints),False,True,"['Not analyzed', 'Local recurrence', 'Metastatic', 'Premalignant - in situ', 'primary', 'Post therapy neoadjuvant', 'Normal adjacent', 'Post therapy', 'Normal', 'Recurrent', 'Not Otherwise Specified', 'Premalignant', 'Normal distant', 'Additional Primary', 'Post therapy adjuvant', 'Atypia - hyperplasia', '']"," If Biospecimen is ""Bone"" OR ""Tissue"" OR ""Urine"" then ""Tumor Tissue Type"" is required",SRRSBiospecimen -Biospecimen Dimension 1,Biospecimen Dimension 1,BiospecimenDimension1,"First dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,," If Biospecimen is ""Bone"" OR ""Tissue"" then ""Biospecimen Dimension 1"" is required",SRRSBiospecimen -Total Volume,Total Volume,TotalVolume,Numeric value for the total amount of sample or specimen,False,True,," If Biospecimen is ""Bone"" OR ""Tissue"" OR ""Urine"" then ""Total Volume"" is required",SRRSBiospecimen -Section Number in Sequence,Section Number in Sequence,SectionNumberinSequence,"Numeric value (integer, including ranges) provided to a sample in a series of sections (list all adjacent sections in the Adjacent Biospecimen IDs field)",False,True,," If Biospecimen is ""Bone"" OR ""Tissue"" then ""Section Number in Sequence"" is required",SRRSBiospecimen -Biospecimen Dimension 2,Biospecimen Dimension 2,BiospecimenDimension2,"Second dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,," If Biospecimen is ""Bone"" OR ""Tissue"" then ""Biospecimen Dimension 2"" is required",SRRSBiospecimen -Shipping Condition Type,Shipping Condition Type,ShippingConditionType,Text descriptor of the shipping environment of a biospecimen.,False,True,"['Ambient Pack', 'Other Shipping Environment', 'Ice Pack', 'Cold Pack', 'Liquid Nitrogen', 'Not Shipped', 'Dry Ice', 'Specimen at Room Temperature', '']"," If Biospecimen is ""Blood"" OR ""Analyte"" then ""Shipping Condition Type"" is required",SRRSBiospecimen -Slide Charge Type,Slide Charge Type,SlideChargeType,A description of the charge on the glass slide.,False,True,"['Not applicable', 'Uncharged', 'Charged', 'Other', 'Coverslip', '']"," If Biospecimen is ""Analyte"" then ""Slide Charge Type"" is required",SRRSBiospecimen -Fixation Duration,Fixation Duration,FixationDuration,"The length of time, from beginning to end, required to process or preserve biospecimens in fixative (measured in minutes)",False,True,," If Biospecimen is ""Analyte"" then ""Fixation Duration"" is required",SRRSBiospecimen -Section Thickness Value,Section Thickness Value,SectionThicknessValue,"Numeric value to describe the thickness of a slice to tissue taken from a biospecimen, measured in microns (um).",False,True,," If Biospecimen is ""Analyte"" then ""Section Thickness Value"" is required",SRRSBiospecimen -Sectioning Days from Index,Sectioning Days from Index,SectioningDaysfromIndex,Number of days from the research participant's index date that the biospecimen was sectioned after collection,False,True,," If Biospecimen is ""Analyte"" then ""Sectioning Days from Index"" is required",SRRSBiospecimen -Analyte Type,Analyte Type,AnalyteType,The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen,False,True,"['cfDNA Analyte', 'RNA Analyte', 'PBMCs or Plasma or Serum Analyte', 'PBMCs', 'Plasma', 'DNA Analyte', 'cDNA Libraries Analyte', 'Total RNA Analyte', 'Serum Analyte', 'Tissue Section Analyte', 'Tissue Block Analyte', '']"," If Biospecimen is ""Analyte"" then ""Analyte Type"" is required",SRRSBiospecimen -Acquisition Method Other Specify,Acquisition Method Other Specify,AcquisitionMethodOtherSpecify,A custom acquisition method [Text - max length 100 characters],False,True,," If Acquisition is ""Other Acquisition Method"" then ""Acquisition Method Other Specify"" is required",SRRSBiospecimen -Dimensions Unit,Dimensions Unit,DimensionsUnit,"Unit of measurement used for dimension CDEs in metric system (i.e. cm, mm, etc)",False,,"['cm', 'mm', '']",,SRRSBiospecimen -Total Volume Unit,Total Volume Unit,TotalVolumeUnit,Unit of measurement used for the total amount of sample or specimen,False,,"['mL', 'cubic millimeter', 'square centimeter', '']",,SRRSBiospecimen -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,OtherAssay -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,OtherAssay -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,OtherAssay -File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,OtherAssay -Assay Type,Assay Type,AssayType,"The type and level of assay this metadata applies to (e.g. RPPA, Nanostring DSP, etc.)",True,,,,OtherAssay -Filename,Filename,filename,Name of a file ,True,,,,OtherAssay -Technical Replicate Group,Technical Replicate Group,TechnicalReplicateGroup,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),False,,,,ScRNA-seqLevel1 -End Bias,End Bias,EndBias,"The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript",True,,"['Full Length Transcript', '5 Prime', '3 Prime']",,ScRNA-seqLevel1 -Single Cell Dissociation Days from Index,Single Cell Dissociation Days from Index,SingleCellDissociationDaysfromIndex,Number of days between sample for single cell assay was received in lab and when the sample was dissociated and cells were isolated [number],True,,,,ScRNA-seqLevel1 -Read2,Read2,Read2,Read 2 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,ScRNA-seqLevel1 -File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,ScRNA-seqLevel1 -Dissociation Method,Dissociation Method,DissociationMethod,The tissue dissociation method used for scRNASeq or scATAC-seq assays,True,,"['Enzymatic Digestion', 'Not Applicable', 'Dounce', 'gentleMACS']",,ScRNA-seqLevel1 -Read1,Read1,Read1,Read 1 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,ScRNA-seqLevel1 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScRNA-seqLevel1 -Read Indicator,Read Indicator,ReadIndicator,Indicate if this is Read 1 (R1) or Read 2 (R2),True,,"['R1', 'R1&R2', 'R2']",,ScRNA-seqLevel1 -Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number],False,,,,ScRNA-seqLevel1 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ScRNA-seqLevel1 -Single Cell Isolation Method,Single Cell Isolation Method,SingleCellIsolationMethod,"The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)",True,,"['Nuclei Isolation', 'Droplets', 'Plates', '10x', 'Microfluidics Chip', 'FACS']",,ScRNA-seqLevel1 -Nucleic Acid Capture Days from Index,Nucleic Acid Capture Days from Index,NucleicAcidCaptureDaysfromIndex,Number of days between sample for single cell assay was received in lab and day of nucleic acid capture part of library construction (in number of days since sample received in lab) [number],True,,,,ScRNA-seqLevel1 -Input Cells and Nuclei,Input Cells and Nuclei,InputCellsandNuclei,"Number of cells and number of nuclei input; entry format: number, number",True,,,,ScRNA-seqLevel1 -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ScRNA-seqLevel1 -Library Construction Method,Library Construction Method,LibraryConstructionMethod,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],True,,"['10xV1.1', 'inDropsV2', 'Drop-seq', '10xV1.0', '10xV2', '10xV3', 'TruDrop', 'Smart-SeqV4', 'inDropsV3', '10xV3.1', 'sci-ATAC-seq', 'Smart-seq2', 'CEL-seq2']",,ScRNA-seqLevel1 -Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Single Cell', 'Bulk Nuclei', 'Bulk Whole Cell']",,ScRNA-seqLevel1 -Cryopreserved Cells in Sample,Cryopreserved Cells in Sample,CryopreservedCellsinSample,Indicate if library preparation was based on revived frozen cells.,True,,"['No', 'Yes']",,ScRNA-seqLevel1 -Sequencing Library Construction Days from Index,Sequencing Library Construction Days from Index,SequencingLibraryConstructionDaysfromIndex,Number of days between sample for assay was received in lab and day of sequencing library construction [number],True,,,,ScRNA-seqLevel1 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScRNA-seqLevel1 -Total Number of Input Cells,Total Number of Input Cells,TotalNumberofInputCells,Number of cells loaded/placed on plates,True,,,,ScRNA-seqLevel1 -Spike In,Spike In,SpikeIn,A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix,True,,"['No Spike In', 'ERCC', 'Other Spike In', 'PhiX']",,ScRNA-seqLevel1 -Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Genome Analyzer II', 'Illumina Genome Analyzer IIx', 'Illumina Next Seq 2500', 'Illumina NextSeq', 'PacBio RS', 'Illumina HiSeq X Five', 'AB SOLiD 3', 'Illumina HiSeq 2000', 'Illumina HiSeq 4000', 'Unknown', 'Complete Genomics', 'Ion Torrent S5', 'Not Reported', 'Illumina HiSeq X Ten', '454 GS FLX Titanium', 'Ion Torrent Proton', 'Illumina Next Seq 500', 'NovaSeqS4', 'Illumina MiSeq', 'AB SOLiD 4 AB SOLiD 2', 'Illumina NovaSeq 6000', 'NovaSeq 6000', 'Illumina HiSeq 2500', 'Other', 'Illumina Next Seq 550', 'Ion Torrent PGM']",,ScRNA-seqLevel1 -Reverse Transcription Primer,Reverse Transcription Primer,ReverseTranscriptionPrimer,"An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA",True,,"['Poly-dT', 'Feature barcoding', 'Random', 'Oligo-dT']",,ScRNA-seqLevel1 -Filename,Filename,filename,Name of a file ,True,,,,ScRNA-seqLevel1 -Median UMIs per Cell Number,Median UMIs per Cell Number,MedianUMIsperCellNumber,Number,False,True,," If Read1 is ""Cell Barcode and UMI"" then ""Median UMIs per Cell Number"" is required",ScRNA-seqLevel1 -Cell Barcode Length,Cell Barcode Length,CellBarcodeLength,Length of cell barcode read (in bp): number,False,True,," If Read1 is ""Cell Barcode and UMI"" then ""Cell Barcode Length"" is required",ScRNA-seqLevel1 -Valid Barcodes Cell Number,Valid Barcodes Cell Number,ValidBarcodesCellNumber,Number,False,True,," If Read1 is ""Cell Barcode and UMI"" then ""Valid Barcodes Cell Number"" is required",ScRNA-seqLevel1 -Cell Barcode Offset,Cell Barcode Offset,CellBarcodeOffset,Offset in sequence for cell barcode read (in bp): number,False,True,," If Read1 is ""Cell Barcode and UMI"" then ""Cell Barcode Offset"" is required",ScRNA-seqLevel1 -UMI Barcode Length,UMI Barcode Length,UMIBarcodeLength,Length of UMI barcode read (in bp): number,False,True,," If Read1 is ""Cell Barcode and UMI"" then ""UMI Barcode Length"" is required",ScRNA-seqLevel1 -UMI Barcode Offset,UMI Barcode Offset,UMIBarcodeOffset,"Start position of UMI barcode in the sequence. Values: number, 0 for start of read",False,True,," If Read1 is ""Cell Barcode and UMI"" then ""UMI Barcode Offset"" is required",ScRNA-seqLevel1 -cDNA Offset,cDNA Offset,CDNAOffset,Offset in sequence for cDNA read (in bp): number,False,True,," If Read1 is ""cDNA"" then ""cDNA Offset"" is required",ScRNA-seqLevel1 -cDNA Length,cDNA Length,CDNALength,Length of cDNA read (in bp): number,False,True,," If Read1 is ""cDNA"" then ""cDNA Length"" is required",ScRNA-seqLevel1 -Well Index,Well Index,WellIndex,Indicate if protein expression (EPCAM/CD45) positive/negative data is available for each cell in CEL-seq2 assays,False,True,"['No', 'Yes', '']"," If Library Construction Method is ""CEL-seq2"" then ""Well Index"" is required",ScRNA-seqLevel1 -Empty Well Barcode,Empty Well Barcode,EmptyWellBarcode,Unique cell barcode assigned to empty cells used as controls in CEL-seq2 assays.,False,True,," If Library Construction Method is ""CEL-seq2"" then ""Empty Well Barcode"" is required",ScRNA-seqLevel1 -Spike In Concentration,Spike In Concentration,SpikeInConcentration,The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910],False,True,," If Spike In is ""ERCC"" then ""Spike In Concentration"" is required",ScRNA-seqLevel1 -Feature Reference Id,Feature Reference Id,FeatureReferenceId,"Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]",False,True,," If Reverse Transcription Primer is ""Feature barcoding"" then ""Feature Reference Id"" is required",ScRNA-seqLevel1 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScRNA-seqLevel2 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScRNA-seqLevel2 -Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/),True,,,,ScRNA-seqLevel2 -scRNAseq Workflow Parameters Description,scRNAseq Workflow Parameters Description,ScRNAseqWorkflowParametersDescription,"Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion",True,,,,ScRNA-seqLevel2 -Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,ScRNA-seqLevel2 -Genome Annotation URL,Genome Annotation URL,GenomeAnnotationURL,Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz),True,,,,ScRNA-seqLevel2 -Whitelist Cell Barcode File Link,Whitelist Cell Barcode File Link,WhitelistCellBarcodeFileLink,Link to file listing all possible cell barcodes. URL,True,,,,ScRNA-seqLevel2 -Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz) [URL],True,,,,ScRNA-seqLevel2 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScRNA-seqLevel2 -UMI Tag,UMI Tag,UMITag,"SAM tag for UMI field; please provide a valid UB, UMI",True,,,,ScRNA-seqLevel2 -scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['Cell annotation', 'Cufflinks', 'STARsolo', 'CellRanger', 'SEQC', 'DEXSeq', 'dropEST', 'HTSeq - FPKM', 'Differentiation trajectory analysis', 'Other', 'HCA Optimus']",,ScRNA-seqLevel2 -Checksum,Checksum,Checksum,MD5 checksum of the BAM file,True,,,,ScRNA-seqLevel2 -Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,ScRNA-seqLevel2 -File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,ScRNA-seqLevel2 -Applied Hard Trimming,Applied Hard Trimming,AppliedHardTrimming,TBD,True,,"['No', 'Yes - Applied Hard Trimming']",,ScRNA-seqLevel2 -Cell Barcode Tag,Cell Barcode Tag,CellBarcodeTag,SAM tag for cell barcode field; please provide a valid cell barcode tag,True,,,,ScRNA-seqLevel2 -Filename,Filename,filename,Name of a file ,True,,,,ScRNA-seqLevel2 -Aligned Read Length,Aligned Read Length,AlignedReadLength,Read length used for alignment if hard trimming was applied,False,True,," If Applied Hard Trimming is ""Yes - Applied Hard Trimming"" then ""Aligned Read Length"" is required",ScRNA-seqLevel2 -Linked Matrices,Linked Matrices,LinkedMatrices,All matrices associated with every part of a SingleCellExperiment object. Comma-delimited list of filenames,False,,,,ScRNA-seqLevel3 -Cell Total,Cell Total,CellTotal,Number of sequenced cells. Applies to raw counts matrix only.,True,,,,ScRNA-seqLevel3 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScRNA-seqLevel3 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScRNA-seqLevel3 -Cell Median Number Reads,Cell Median Number Reads,CellMedianNumberReads,Median number of reads per cell. Number,True,,,,ScRNA-seqLevel3 -scRNAseq Workflow Parameters Description,scRNAseq Workflow Parameters Description,ScRNAseqWorkflowParametersDescription,"Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion",True,,,,ScRNA-seqLevel3 -Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,ScRNA-seqLevel3 -Cell Median Number Genes,Cell Median Number Genes,CellMedianNumberGenes,Median number of genes detected per cell. Number,True,,,,ScRNA-seqLevel3 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScRNA-seqLevel3 -scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['Cell annotation', 'Cufflinks', 'STARsolo', 'CellRanger', 'SEQC', 'DEXSeq', 'dropEST', 'HTSeq - FPKM', 'Differentiation trajectory analysis', 'Other', 'HCA Optimus']",,ScRNA-seqLevel3 -Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,ScRNA-seqLevel3 -File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,ScRNA-seqLevel3 -Data Category,Data Category,DataCategory,Specific content type of the data file.,True,,"['Splice Junction Quantification', 'Gene Expression Quantification', 'Isoform Expression Quantification', 'Exon Expression Quantification', 'Gene Expression', 'Other', 'Transcript Expression']",,ScRNA-seqLevel3 -Filename,Filename,filename,Name of a file ,True,,,,ScRNA-seqLevel3 -Matrix Type,Matrix Type,MatrixType,Type of data stored in matrix.,True,,"['Batch Corrected Counts', 'Raw Counts', 'Scaled Counts', 'Normalized Counts']",,ScRNA-seqLevel3 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScRNA-seqLevel4 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScRNA-seqLevel4 -scRNAseq Workflow Parameters Description,scRNAseq Workflow Parameters Description,ScRNAseqWorkflowParametersDescription,"Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion",True,,,,ScRNA-seqLevel4 -Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,ScRNA-seqLevel4 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScRNA-seqLevel4 -scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['Cell annotation', 'Cufflinks', 'STARsolo', 'CellRanger', 'SEQC', 'DEXSeq', 'dropEST', 'HTSeq - FPKM', 'Differentiation trajectory analysis', 'Other', 'HCA Optimus']",,ScRNA-seqLevel4 -Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,ScRNA-seqLevel4 -File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,ScRNA-seqLevel4 -Filename,Filename,filename,Name of a file ,True,,,,ScRNA-seqLevel4 -Kmer Content,Kmer Content,KmerContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkRNA-seqLevel1 -Per Base N Content,Per Base N Content,PerBaseNContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkRNA-seqLevel1 -Library Strand,Library Strand,LibraryStrand,Library stranded-ness.,False,,"['Unstranded', 'Second Stranded', 'Not Applicable', 'First Stranded', '']",,BulkRNA-seqLevel1 -Sequencing Batch ID,Sequencing Batch ID,SequencingBatchID,Links samples to a specific local sequencer run. Can be string or 'null',True,,,,BulkRNA-seqLevel1 -Per Sequence GC Content,Per Sequence GC Content,PerSequenceGCContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkRNA-seqLevel1 -Fragment Mean Length,Fragment Mean Length,FragmentMeanLength,"Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number",False,,,,BulkRNA-seqLevel1 -Adapter Content,Adapter Content,AdapterContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkRNA-seqLevel1 -Library Preparation Kit Vendor,Library Preparation Kit Vendor,LibraryPreparationKitVendor,Vendor of Library Preparation Kit. String,True,,,,BulkRNA-seqLevel1 -To Trim Adapter Sequence,To Trim Adapter Sequence,ToTrimAdapterSequence,Does the user suggest adapter trimming?,False,,"['No', 'Yes - Trim Adapter Sequence', '']",,BulkRNA-seqLevel1 -File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,BulkRNA-seqLevel1 -Adapter Name,Adapter Name,AdapterName,Name of the sequencing adapter. String,False,,,,BulkRNA-seqLevel1 -Fragment Minimum Length,Fragment Minimum Length,FragmentMinimumLength,"Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,BulkRNA-seqLevel1 -RIN,RIN,RIN,A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products. Number,False,,,,BulkRNA-seqLevel1 -Encoding,Encoding,Encoding,Version of ASCII encoding of quality values found in the file. String,False,,,,BulkRNA-seqLevel1 -QC Workflow Version,QC Workflow Version,QCWorkflowVersion,Major version for a workflow. String,False,,,,BulkRNA-seqLevel1 -Basic Statistics,Basic Statistics,BasicStatistics,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkRNA-seqLevel1 -Sequence Length Distribution,Sequence Length Distribution,SequenceLengthDistribution,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkRNA-seqLevel1 -QC Workflow Link,QC Workflow Link,QCWorkflowLink,Link to workflow used. String,False,,,,BulkRNA-seqLevel1 -DV200,DV200,DV200,Represents the percentage of RNA fragments that are >200 nucleotides in size. Number,False,,,,BulkRNA-seqLevel1 -Cell Barcode,Cell Barcode,CellBarcode,TBD,False,,,,BulkRNA-seqLevel1 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkRNA-seqLevel1 -Library Selection Method,Library Selection Method,LibrarySelectionMethod,How RNA molecules are isolated.,True,,"['rRNA Depletion', 'miRNA Size Fractionation', 'Other', 'Random', 'Affinity Enrichment', 'PCR', 'Poly-T Enrichment', 'Hybrid Selection']",,BulkRNA-seqLevel1 -Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,BulkRNA-seqLevel1 -Base Caller Name,Base Caller Name,BaseCallerName,Name of the base caller. String,False,,,,BulkRNA-seqLevel1 -QC Workflow Type,QC Workflow Type,QCWorkflowType,Generic name for the workflow used to analyze a data set. String,False,,,,BulkRNA-seqLevel1 -Per Base Sequence Quality,Per Base Sequence Quality,PerBaseSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkRNA-seqLevel1 -Sequence Duplication Levels,Sequence Duplication Levels,SequenceDuplicationLevels,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkRNA-seqLevel1 -Read Indicator,Read Indicator,ReadIndicator,Indicate if this is Read 1 (R1) or Read 2 (R2),True,,"['R1', 'R1&R2', 'R2']",,BulkRNA-seqLevel1 -Library Preparation Kit Version,Library Preparation Kit Version,LibraryPreparationKitVersion,Version of Library Preparation Kit. String,True,,,,BulkRNA-seqLevel1 -Per Tile Sequence Quality,Per Tile Sequence Quality,PerTileSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkRNA-seqLevel1 -Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number],False,,,,BulkRNA-seqLevel1 -Base Caller Version,Base Caller Version,BaseCallerVersion,Version of the base caller. String,False,,,,BulkRNA-seqLevel1 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,BulkRNA-seqLevel1 -Read Length,Read Length,ReadLength,"The length of the sequencing reads. Can be integer, null",True,,,,BulkRNA-seqLevel1 -Flow,Flow,Flow,TBD,False,,,,BulkRNA-seqLevel1 -Overrepresented Sequences,Overrepresented Sequences,OverrepresentedSequences,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkRNA-seqLevel1 -Per Sequence Quality Score,Per Sequence Quality Score,PerSequenceQualityScore,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkRNA-seqLevel1 -Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Paired End', 'Single Read']",,BulkRNA-seqLevel1 -Transcript Integrity Number,Transcript Integrity Number,TranscriptIntegrityNumber,"Used to describe the quality of the starting material, esp. in regards to FFPE samples. Number",False,,,,BulkRNA-seqLevel1 -Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Single Cell', 'Bulk Nuclei', 'Bulk Whole Cell']",,BulkRNA-seqLevel1 -Percent GC Content,Percent GC Content,PercentGCContent,The overall %GC of all bases in all sequences. Integer,False,,,,BulkRNA-seqLevel1 -Lane Number,Lane Number,LaneNumber,"The basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer",False,,,,BulkRNA-seqLevel1 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkRNA-seqLevel1 -Fragment Standard Deviation Length,Fragment Standard Deviation Length,FragmentStandardDeviationLength,"Standard deviation of the sequenced fragments length (e.g., as predicted by Agilent Bioanalyzer). Number",False,,,,BulkRNA-seqLevel1 -Multiplex Barcode,Multiplex Barcode,MultiplexBarcode,The barcode/index sequence used. Wrong or missing information may affect analysis results. String,False,,,,BulkRNA-seqLevel1 -Per Base Sequence Content,Per Base Sequence Content,PerBaseSequenceContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkRNA-seqLevel1 -Adapter Sequence,Adapter Sequence,AdapterSequence,Base sequence of the sequencing adapter. String,False,,,,BulkRNA-seqLevel1 -Spike In,Spike In,SpikeIn,A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix,True,,"['No Spike In', 'ERCC', 'Other Spike In', 'PhiX']",,BulkRNA-seqLevel1 -Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Genome Analyzer II', 'Illumina Genome Analyzer IIx', 'Illumina Next Seq 2500', 'Illumina NextSeq', 'PacBio RS', 'Illumina HiSeq X Five', 'AB SOLiD 3', 'Illumina HiSeq 2000', 'Illumina HiSeq 4000', 'Unknown', 'Complete Genomics', 'Ion Torrent S5', 'Not Reported', 'Illumina HiSeq X Ten', '454 GS FLX Titanium', 'Ion Torrent Proton', 'Illumina Next Seq 500', 'NovaSeqS4', 'Illumina MiSeq', 'AB SOLiD 4 AB SOLiD 2', 'Illumina NovaSeq 6000', 'NovaSeq 6000', 'Illumina HiSeq 2500', 'Other', 'Illumina Next Seq 550', 'Ion Torrent PGM']",,BulkRNA-seqLevel1 -Library Preparation Kit Name,Library Preparation Kit Name,LibraryPreparationKitName,Name of Library Preparation Kit. String,True,,,,BulkRNA-seqLevel1 -Target Depth,Target Depth,TargetDepth,The targeted read depth prior to sequencing. Integer,False,,,,BulkRNA-seqLevel1 -Fragment Maximum Length,Fragment Maximum Length,FragmentMaximumLength,"Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,BulkRNA-seqLevel1 -Size Selection Range,Size Selection Range,SizeSelectionRange,Range of size selection. String,False,,,,BulkRNA-seqLevel1 -Filename,Filename,filename,Name of a file ,True,,,,BulkRNA-seqLevel1 -Spike In Concentration,Spike In Concentration,SpikeInConcentration,The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910],False,True,," If Spike In is ""ERCC"" then ""Spike In Concentration"" is required",BulkRNA-seqLevel1 -Total Unmapped reads,Total Unmapped reads,TotalUnmappedreads,Number of reads that did not map to genome. Integer,False,,,,BulkRNA-seqLevel2 -Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz) [URL],True,,,,BulkRNA-seqLevel2 -Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,BulkRNA-seqLevel2 -File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,BulkRNA-seqLevel2 -Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,BulkRNA-seqLevel2 -Proportion Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,BulkRNA-seqLevel2 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkRNA-seqLevel2 -Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,BulkRNA-seqLevel2 -Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,BulkRNA-seqLevel2 -Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,BulkRNA-seqLevel2 -Proportion,Proportion,Proportion,TBD,False,,,,BulkRNA-seqLevel2 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkRNA-seqLevel2 -Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,BulkRNA-seqLevel2 -Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,BulkRNA-seqLevel2 -Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,BulkRNA-seqLevel2 -Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/),True,,,,BulkRNA-seqLevel2 -MSI Workflow Link,MSI Workflow Link,MSIWorkflowLink,Link to method workflow (or command) used in estimating the MSI. URL,False,,,,BulkRNA-seqLevel2 -MSI Status,MSI Status,MSIStatus,MSIsensor determination of either microsatellite stability or instability.,False,,"['MSI', 'MSS', 'MSI-low', 'MSI-high', '']",,BulkRNA-seqLevel2 -Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['None', 'STAR 2-Pass Genome', 'Other Alignment Workflow', 'BWA', 'STAR 2-Pass', 'BWA with Mark Duplicates and BQSR', 'BWA-aln', 'STAR 2-Pass Chimeric', 'BWA-mem', 'BWA with BQSR', 'STAR 2-Pass Transcriptome']",,BulkRNA-seqLevel2 -Targets No Coverage,Targets No Coverage,TargetsNoCoverage,TBD,False,,,,BulkRNA-seqLevel2 -Pairs On Diff CHR,Pairs On Diff CHR,PairsOnDiffCHR,Pairs on different chromosomes collected from samtools. Integer,False,,,,BulkRNA-seqLevel2 -Contamination Error,Contamination Error,ContaminationError,Estimation error of cross-sample contamination collected from GATK4. Number,False,,,,BulkRNA-seqLevel2 -Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,BulkRNA-seqLevel2 -Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,BulkRNA-seqLevel2 -MSI Score,MSI Score,MSIScore,Numeric score denoting the aligned reads file's MSI score from MSIsensor. Number,False,,,,BulkRNA-seqLevel2 -Alignment Workflow Url,Alignment Workflow Url,AlignmentWorkflowUrl,Link to workflow used for read alignment. DockStore.org recommended. String,True,,,,BulkRNA-seqLevel2 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkRNA-seqLevel2 -Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,BulkRNA-seqLevel2 -Filename,Filename,filename,Name of a file ,True,,,,BulkRNA-seqLevel2 -Custom Alignment Workflow,Custom Alignment Workflow,CustomAlignmentWorkflow,Specify the name of a custom alignment workflow,False,True,," If Alignment is ""Other Alignment Workflow"" then ""Custom Alignment Workflow"" is required",BulkRNA-seqLevel2 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkRNA-seqLevel3 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkRNA-seqLevel3 -Pseudo Alignment Used,Pseudo Alignment Used,PseudoAlignmentUsed,Pseudo aligners such as Kallisto or Salmon do not produce aligned reads BAM files. True indicates pseudoalignment was used.,True,,"['No', 'Yes - Pseudo Alignment Used']",,BulkRNA-seqLevel3 -Fusion Gene Identity,Fusion Gene Identity,FusionGeneIdentity,The gene symbols of fused genes.,False,,,,BulkRNA-seqLevel3 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkRNA-seqLevel3 -Expression Units,Expression Units,ExpressionUnits,How quantities are corrected for gene length,True,,"['FPKM', 'TPM', 'RPKM', 'NA', 'Other', 'Counts']",,BulkRNA-seqLevel3 -Fusion Gene Detected,Fusion Gene Detected,FusionGeneDetected,Was a fusion gene identified?,False,,"['No', 'Unknown', 'Yes - Fusion Gene Detected', '']",,BulkRNA-seqLevel3 -File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,BulkRNA-seqLevel3 -Data Category,Data Category,DataCategory,Specific content type of the data file.,True,,"['Splice Junction Quantification', 'Gene Expression Quantification', 'Isoform Expression Quantification', 'Exon Expression Quantification', 'Gene Expression', 'Other', 'Transcript Expression']",,BulkRNA-seqLevel3 -Filename,Filename,filename,Name of a file ,True,,,,BulkRNA-seqLevel3 -Matrix Type,Matrix Type,MatrixType,Type of data stored in matrix.,True,,"['Batch Corrected Counts', 'Raw Counts', 'Scaled Counts', 'Normalized Counts']",,BulkRNA-seqLevel3 -Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,False,True,," If Pseudo Alignment Used is ""Yes - Pseudo Alignment Used"" then ""Workflow Link"" is required",BulkRNA-seqLevel3 -Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz) [URL],False,True,," If Pseudo Alignment Used is ""Yes - Pseudo Alignment Used"" then ""Genomic Reference URL"" is required",BulkRNA-seqLevel3 -Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,False,True,," If Pseudo Alignment Used is ""Yes - Pseudo Alignment Used"" then ""Software and Version"" is required",BulkRNA-seqLevel3 -Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/),False,True,," If Pseudo Alignment Used is ""Yes - Pseudo Alignment Used"" then ""Genomic Reference"" is required",BulkRNA-seqLevel3 -Specify Other Fusion Gene,Specify Other Fusion Gene,SpecifyOtherFusionGene,"Specify fusion gene detected, if not in list",False,True,," If Fusion Gene Identity is ""Other Fusion Gene"" then ""Specify Other Fusion Gene"" is required",BulkRNA-seqLevel3 -Sequencing Batch ID,Sequencing Batch ID,SequencingBatchID,Links samples to a specific local sequencer run. Can be string or 'null',True,,,,BulkWESLevel1 -Fragment Mean Length,Fragment Mean Length,FragmentMeanLength,"Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number",False,,,,BulkWESLevel1 -Library Preparation Kit Vendor,Library Preparation Kit Vendor,LibraryPreparationKitVendor,Vendor of Library Preparation Kit. String,True,,,,BulkWESLevel1 -To Trim Adapter Sequence,To Trim Adapter Sequence,ToTrimAdapterSequence,Does the user suggest adapter trimming?,False,,"['No', 'Yes - Trim Adapter Sequence', '']",,BulkWESLevel1 -File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,BulkWESLevel1 -Adapter Name,Adapter Name,AdapterName,Name of the sequencing adapter. String,False,,,,BulkWESLevel1 -Target Capture Kit,Target Capture Kit,TargetCaptureKit,"Description that can uniquely identify a target capture kit. Suggested value is a combination of vendor, kit name, and kit version.",True,,"['SeqCap EZ HGSC VCRome v2.1', 'Custom AmpliSeq Cancer Hotspot GENIE-MDA Augmented Panel v1 - 46 Genes', 'Custom GENIE-DFCI OncoPanel - 275 Genes', 'Custom SeqCap EZ TARGET-OS Panel - 7.0 Mb', 'Not Applicable', 'TruSeq RNA Exome', 'Custom Twist Broad PanCancer Panel - 396 Genes', 'xGen Exome Research Panel v1.0', 'Custom MSK IMPACT Panel - 341 Genes', 'Custom Large Construct Capture TARGET-OS Panel - 8 Genes', 'TruSight Myeloid Sequencing Panel', 'Custom Solid Tumor GENIE-VICC Panel - 34 Genes', 'SureSelect Human All Exon v3', 'SureSelect Human All Exon v5', 'Custom SureSelect CGCI-HTMCP-CC Panel - 19.7 Mb', 'Custom SureSelect CGCI-BLGSP Panel - 4.6 Mb', 'Unknown', 'Custom SeqCap EZ HGSC VCRome v2.1 ER Augmented v1', 'SeqCap EZ Human Exome v2.0', 'Foundation Medicine T7 Panel - 429 Genes', 'Custom GENIE-DFCI Oncopanel - 300 Genes', 'Custom MSK IMPACT Panel - 468 Genes', 'Custom Targets File Provided', 'TruSeq Exome Enrichment - 62 Mb', 'Nextera DNA Exome', 'Custom PGDX SureSelect CancerSelect VAREPOP-APOLLO Panel - 88 Genes', 'Custom Ion AmpliSeq Hotspot GENIE-MOSC3 Augmented Panel - 74 Genes', 'Custom SureSelect CGCI-HTMCP-CC KMT2D And Hotspot Panel - 37.0 Kb', 'Custom Twist Broad Exome v1.0 - 35.0 Mb', 'SureSelect Human All Exon v5 + UTR', 'Custom GENIE-DFCI Oncopanel - 447 Genes', 'Nextera Rapid Capture Exome v1.2', 'Custom HaloPlex DLBCL Panel - 370 Genes', 'Custom SureSelect Human All Exon v1.1 Plus 3 Boosters', 'Custom Myeloid GENIE-VICC Panel - 37 Genes', 'Custom SureSelect TARGET-AML_NBL_WT Panel - 2.8 Mb', 'TruSeq Amplicon Cancer Panel', 'Custom SeqCap EZ HGSC VCRome v2.1 ER Augmented v2', 'Custom SureSelect GENIE-UHN Panel - 555 Genes', 'Custom MSK IMPACT Panel - 410 Genes', 'Foundation Medicine T5a Panel - 322 Genes', 'Ion AmpliSeq Cancer Hotspot Panel v2', 'SureSelect Human All Exon v4', 'SeqCap EZ Human Exome v3.0', 'Custom PGDX SureSelect CancerSelect VAREPOP-APOLLO Panel - 203 Genes', 'Ion AmpliSeq Comprehensive Cancer Panel', 'Custom Personalis ACEcp VAREPOP-APOLLO Panel v2']",,BulkWESLevel1 -Fragment Minimum Length,Fragment Minimum Length,FragmentMinimumLength,"Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,BulkWESLevel1 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkWESLevel1 -Library Selection Method,Library Selection Method,LibrarySelectionMethod,How RNA molecules are isolated.,True,,"['rRNA Depletion', 'miRNA Size Fractionation', 'Other', 'Random', 'Affinity Enrichment', 'PCR', 'Poly-T Enrichment', 'Hybrid Selection']",,BulkWESLevel1 -Base Caller Name,Base Caller Name,BaseCallerName,Name of the base caller. String,False,,,,BulkWESLevel1 -Read Indicator,Read Indicator,ReadIndicator,Indicate if this is Read 1 (R1) or Read 2 (R2),True,,"['R1', 'R1&R2', 'R2']",,BulkWESLevel1 -Library Preparation Kit Version,Library Preparation Kit Version,LibraryPreparationKitVersion,Version of Library Preparation Kit. String,True,,,,BulkWESLevel1 -Base Caller Version,Base Caller Version,BaseCallerVersion,Version of the base caller. String,False,,,,BulkWESLevel1 -Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number],False,,,,BulkWESLevel1 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,BulkWESLevel1 -Read Length,Read Length,ReadLength,"The length of the sequencing reads. Can be integer, null",True,,,,BulkWESLevel1 -Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Paired End', 'Single Read']",,BulkWESLevel1 -Lane Number,Lane Number,LaneNumber,"The basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer",False,,,,BulkWESLevel1 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkWESLevel1 -Fragment Standard Deviation Length,Fragment Standard Deviation Length,FragmentStandardDeviationLength,"Standard deviation of the sequenced fragments length (e.g., as predicted by Agilent Bioanalyzer). Number",False,,,,BulkWESLevel1 -Multiplex Barcode,Multiplex Barcode,MultiplexBarcode,The barcode/index sequence used. Wrong or missing information may affect analysis results. String,False,,,,BulkWESLevel1 -Adapter Sequence,Adapter Sequence,AdapterSequence,Base sequence of the sequencing adapter. String,False,,,,BulkWESLevel1 -Library Preparation Kit Name,Library Preparation Kit Name,LibraryPreparationKitName,Name of Library Preparation Kit. String,True,,,,BulkWESLevel1 -Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Genome Analyzer II', 'Illumina Genome Analyzer IIx', 'Illumina Next Seq 2500', 'Illumina NextSeq', 'PacBio RS', 'Illumina HiSeq X Five', 'AB SOLiD 3', 'Illumina HiSeq 2000', 'Illumina HiSeq 4000', 'Unknown', 'Complete Genomics', 'Ion Torrent S5', 'Not Reported', 'Illumina HiSeq X Ten', '454 GS FLX Titanium', 'Ion Torrent Proton', 'Illumina Next Seq 500', 'NovaSeqS4', 'Illumina MiSeq', 'AB SOLiD 4 AB SOLiD 2', 'Illumina NovaSeq 6000', 'NovaSeq 6000', 'Illumina HiSeq 2500', 'Other', 'Illumina Next Seq 550', 'Ion Torrent PGM']",,BulkWESLevel1 -Flow Cell Barcode,Flow Cell Barcode,FlowCellBarcode,Flow cell barcode. Wrong or missing information may affect analysis results. String,False,,,,BulkWESLevel1 -Target Depth,Target Depth,TargetDepth,The targeted read depth prior to sequencing. Integer,False,,,,BulkWESLevel1 -Fragment Maximum Length,Fragment Maximum Length,FragmentMaximumLength,"Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,BulkWESLevel1 -Size Selection Range,Size Selection Range,SizeSelectionRange,Range of size selection. String,False,,,,BulkWESLevel1 -Filename,Filename,filename,Name of a file ,True,,,,BulkWESLevel1 -Per Base N Content,Per Base N Content,PerBaseNContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkWESLevel2 -Per Sequence GC Content,Per Sequence GC Content,PerSequenceGCContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkWESLevel2 -Total Unmapped reads,Total Unmapped reads,TotalUnmappedreads,Number of reads that did not map to genome. Integer,False,,,,BulkWESLevel2 -Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz) [URL],True,,,,BulkWESLevel2 -Adapter Content,Adapter Content,AdapterContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkWESLevel2 -Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,BulkWESLevel2 -File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,BulkWESLevel2 -Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,BulkWESLevel2 -Encoding,Encoding,Encoding,Version of ASCII encoding of quality values found in the file. String,False,,,,BulkWESLevel2 -QC Workflow Version,QC Workflow Version,QCWorkflowVersion,Major version for a workflow. String,False,,,,BulkWESLevel2 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkWESLevel2 -Proportion Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,BulkWESLevel2 -Basic Statistics,Basic Statistics,BasicStatistics,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkWESLevel2 -Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,BulkWESLevel2 -Proportion Targets No Coverage,Proportion Targets No Coverage,ProportionTargetsNoCoverage,Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number,False,,,,BulkWESLevel2 -Sequence Length Distribution,Sequence Length Distribution,SequenceLengthDistribution,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkWESLevel2 -QC Workflow Link,QC Workflow Link,QCWorkflowLink,Link to workflow used. String,False,,,,BulkWESLevel2 -Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,BulkWESLevel2 -Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,BulkWESLevel2 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkWESLevel2 -Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,BulkWESLevel2 -Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,BulkWESLevel2 -QC Workflow Type,QC Workflow Type,QCWorkflowType,Generic name for the workflow used to analyze a data set. String,False,,,,BulkWESLevel2 -Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,BulkWESLevel2 -Per Base Sequence Quality,Per Base Sequence Quality,PerBaseSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkWESLevel2 -Sequence Duplication Levels,Sequence Duplication Levels,SequenceDuplicationLevels,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkWESLevel2 -Per Tile Sequence Quality,Per Tile Sequence Quality,PerTileSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkWESLevel2 -Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/),True,,,,BulkWESLevel2 -MSI Workflow Link,MSI Workflow Link,MSIWorkflowLink,Link to method workflow (or command) used in estimating the MSI. URL,False,,,,BulkWESLevel2 -MSI Status,MSI Status,MSIStatus,MSIsensor determination of either microsatellite stability or instability.,False,,"['MSI', 'MSS', 'MSI-low', 'MSI-high', '']",,BulkWESLevel2 -Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['None', 'STAR 2-Pass Genome', 'Other Alignment Workflow', 'BWA', 'STAR 2-Pass', 'BWA with Mark Duplicates and BQSR', 'BWA-aln', 'STAR 2-Pass Chimeric', 'BWA-mem', 'BWA with BQSR', 'STAR 2-Pass Transcriptome']",,BulkWESLevel2 -Pairs On Diff CHR,Pairs On Diff CHR,PairsOnDiffCHR,Pairs on different chromosomes collected from samtools. Integer,False,,,,BulkWESLevel2 -Overrepresented Sequences,Overrepresented Sequences,OverrepresentedSequences,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkWESLevel2 -Per Sequence Quality Score,Per Sequence Quality Score,PerSequenceQualityScore,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkWESLevel2 -Contamination Error,Contamination Error,ContaminationError,Estimation error of cross-sample contamination collected from GATK4. Number,False,,,,BulkWESLevel2 -Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,BulkWESLevel2 -Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,BulkWESLevel2 -MSI Score,MSI Score,MSIScore,Numeric score denoting the aligned reads file's MSI score from MSIsensor. Number,False,,,,BulkWESLevel2 -Percent GC Content,Percent GC Content,PercentGCContent,The overall %GC of all bases in all sequences. Integer,False,,,,BulkWESLevel2 -Proportion Coverage 10x,Proportion Coverage 10x,ProportionCoverage10x,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools.",False,,,,BulkWESLevel2 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkWESLevel2 -Per Base Sequence Content,Per Base Sequence Content,PerBaseSequenceContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkWESLevel2 -Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,BulkWESLevel2 -Proportion Coverage 30X,Proportion Coverage 30X,ProportionCoverage30X,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools.",False,,,,BulkWESLevel2 -Filename,Filename,filename,Name of a file ,True,,,,BulkWESLevel2 -Custom Alignment Workflow,Custom Alignment Workflow,CustomAlignmentWorkflow,Specify the name of a custom alignment workflow,False,True,," If Alignment is ""Other Alignment Workflow"" then ""Custom Alignment Workflow"" is required",BulkWESLevel2 -Structural Variant Workflow URL,Structural Variant Workflow URL,StructuralVariantWorkflowURL,Link to workflow document. DockStore.org recommended. URL,True,,,,BulkWESLevel3 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkWESLevel3 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkWESLevel3 -Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/),True,,,,BulkWESLevel3 -Somatic Variants Workflow URL,Somatic Variants Workflow URL,SomaticVariantsWorkflowURL,Generic name for the workflow used to analyze a data set.,True,,,,BulkWESLevel3 -Structural Variant Workflow Type,Structural Variant Workflow Type,StructuralVariantWorkflowType,Generic name for the workflow used to analyze a data set.,False,,"['None', 'Other Structural Variant Workflow Type', 'CNV', 'GATK4', 'BRASS', 'CNVkit', '']",,BulkWESLevel3 -Somatic Variants Workflow Type,Somatic Variants Workflow Type,SomaticVariantsWorkflowType,Generic name for the workflow used to analyze a data set.,False,,"['None', 'Other Somatic Variants Workflow Type', 'GATK4', 'SomaticSniper', 'MuSE', 'VarScan2', 'CaVEMan', 'MuTect2', 'Pindel', '']",,BulkWESLevel3 -Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz) [URL],True,,,,BulkWESLevel3 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkWESLevel3 -Somatic Variants Sample Type,Somatic Variants Sample Type,SomaticVariantsSampleType,Is the sample case or control in somatic variant analysis,True,,"['Case Sample', 'Control Sample', 'Not Applicable']",,BulkWESLevel3 -Germline Variants Workflow URL,Germline Variants Workflow URL,GermlineVariantsWorkflowURL,"Link to workflow document, e.g. Github, DockStore.org recommended",True,,,,BulkWESLevel3 -Germline Variants Workflow Type,Germline Variants Workflow Type,GermlineVariantsWorkflowType,Generic name for the workflow used to analyze a data set,False,,"['None', 'GATK4', 'Other Germline Variants Workflow Type', '']",,BulkWESLevel3 -File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,BulkWESLevel3 -Filename,Filename,filename,Name of a file ,True,,,,BulkWESLevel3 -Custom Structural Variant Workflow Type,Custom Structural Variant Workflow Type,CustomStructuralVariantWorkflowType,Specify the name of a custom workflow name,False,True,," If Structural is ""Other"" then ""Custom Structural Variant Workflow Type"" is required",BulkWESLevel3 -Custom Somatic Variants Workflow Type,Custom Somatic Variants Workflow Type,CustomSomaticVariantsWorkflowType,Specify the name of a custom workflow name,False,True,," If Somatic is ""Other"" then ""Custom Somatic Variants Workflow Type"" is required",BulkWESLevel3 -Custom Germline Variants Workflow Type,Custom Germline Variants Workflow Type,CustomGermlineVariantsWorkflowType,Specify the name of a custom alignment workflow,False,True,," If Germline is ""Other"" then ""Custom Germline Variants Workflow Type"" is required",BulkWESLevel3 -Technical Replicate Group,Technical Replicate Group,TechnicalReplicateGroup,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),False,,,,ScATAC-seqLevel1 -scATACseq Read3,scATACseq Read3,ScATACseqRead3,Read 3 content description,False,,"['DNA Insert', 'Sample Index', 'Cell Barcode and DNA Insert', 'Cell Barcode', 'Sample Index and DNA Insert', '']",,ScATAC-seqLevel1 -File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,ScATAC-seqLevel1 -Dissociation Method,Dissociation Method,DissociationMethod,The tissue dissociation method used for scRNASeq or scATAC-seq assays,True,,"['Enzymatic Digestion', 'Not Applicable', 'Dounce', 'gentleMACS']",,ScATAC-seqLevel1 -Median Fraction of Reads in Peaks,Median Fraction of Reads in Peaks,MedianFractionofReadsinPeaks,Median fraction of reads in peaks (FRIP),True,,,,ScATAC-seqLevel1 -Transposition Reaction,Transposition Reaction,TranspositionReaction,"Name of the transposase, transposon sequences",True,,"['EZ-Tn5', 'In-House', 'Tn5-059', 'Nextera Tn5', 'Tn5']",,ScATAC-seqLevel1 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScATAC-seqLevel1 -Median Percentage of Mitochondrial Reads per Nucleus,Median Percentage of Mitochondrial Reads per Nucleus,MedianPercentageofMitochondrialReadsperNucleus,Contamination from mitochondrial sequences,True,,,,ScATAC-seqLevel1 -scATACseq Read2,scATACseq Read2,ScATACseqRead2,Read 2 content description,True,,"['DNA Insert', 'Sample Index', 'Cell Barcode and DNA Insert', 'Cell Barcode', 'Sample Index and DNA Insert']",,ScATAC-seqLevel1 -Total Number of Passing Nuclei,Total Number of Passing Nuclei,TotalNumberofPassingNuclei,Number of nuclei sequenced,True,,,,ScATAC-seqLevel1 -Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,ScATAC-seqLevel1 -scATACseq Library Layout,scATACseq Library Layout,ScATACseqLibraryLayout,Sequencing read type,True,,['scATACseq Paired End'],,ScATAC-seqLevel1 -Single Nucleus Buffer,Single Nucleus Buffer,SingleNucleusBuffer,Nuclei isolation buffer,True,,"['Omni', 'NIB', '10x']",,ScATAC-seqLevel1 -Nucleus Identifier,Nucleus Identifier,NucleusIdentifier,Unique nuclei barcode; added at transposition step. Determines which nucleus the reads originated from,True,,['Nuclei Barcode'],,ScATAC-seqLevel1 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ScATAC-seqLevel1 -Median Passing Read Percentage,Median Passing Read Percentage,MedianPassingReadPercentage,Non-PCR duplicate nuclear genomic sequence reads not aligning to unanchored contigs out of total reads assigned to the nucleus barcode,True,,,,ScATAC-seqLevel1 -Single Cell Isolation Method,Single Cell Isolation Method,SingleCellIsolationMethod,"The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)",True,,"['Nuclei Isolation', 'Droplets', 'Plates', '10x', 'Microfluidics Chip', 'FACS']",,ScATAC-seqLevel1 -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ScATAC-seqLevel1 -Library Construction Method,Library Construction Method,LibraryConstructionMethod,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],True,,"['10xV1.1', 'inDropsV2', 'Drop-seq', '10xV1.0', '10xV2', '10xV3', 'TruDrop', 'Smart-SeqV4', 'inDropsV3', '10xV3.1', 'sci-ATAC-seq', 'Smart-seq2', 'CEL-seq2']",,ScATAC-seqLevel1 -Threshold for Minimum Passing Reads,Threshold for Minimum Passing Reads,ThresholdforMinimumPassingReads,Threshold for calling cells,True,,,,ScATAC-seqLevel1 -Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Single Cell', 'Bulk Nuclei', 'Bulk Whole Cell']",,ScATAC-seqLevel1 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScATAC-seqLevel1 -scATACseq Read1,scATACseq Read1,ScATACseqRead1,Read 1 content description,True,,"['DNA Insert', 'Sample Index', 'Cell Barcode and DNA Insert', 'Cell Barcode', 'Sample Index and DNA Insert']",,ScATAC-seqLevel1 -Nuclei Barcode Length,Nuclei Barcode Length,NucleiBarcodeLength,Nuclei Barcode Length,True,,,,ScATAC-seqLevel1 -Median Fraction of Reads in Annotated cis DNA Elements,Median Fraction of Reads in Annotated cis DNA Elements,MedianFractionofReadsinAnnotatedcisDNAElements,Median fraction of reads in annotated cis-DNA elements (FRIADE),True,,,,ScATAC-seqLevel1 -Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Genome Analyzer II', 'Illumina Genome Analyzer IIx', 'Illumina Next Seq 2500', 'Illumina NextSeq', 'PacBio RS', 'Illumina HiSeq X Five', 'AB SOLiD 3', 'Illumina HiSeq 2000', 'Illumina HiSeq 4000', 'Unknown', 'Complete Genomics', 'Ion Torrent S5', 'Not Reported', 'Illumina HiSeq X Ten', '454 GS FLX Titanium', 'Ion Torrent Proton', 'Illumina Next Seq 500', 'NovaSeqS4', 'Illumina MiSeq', 'AB SOLiD 4 AB SOLiD 2', 'Illumina NovaSeq 6000', 'NovaSeq 6000', 'Illumina HiSeq 2500', 'Other', 'Illumina Next Seq 550', 'Ion Torrent PGM']",,ScATAC-seqLevel1 -Nuclei Barcode Read,Nuclei Barcode Read,NucleiBarcodeRead,Nuclei Barcode Read,True,,,,ScATAC-seqLevel1 -Filename,Filename,filename,Name of a file ,True,,,,ScATAC-seqLevel1 -Peaks Calling Software,Peaks Calling Software,PeaksCallingSoftware,Generic name of peaks calling tool,False,,,,ScATAC-seqLevel1 -Well Index,Well Index,WellIndex,Indicate if protein expression (EPCAM/CD45) positive/negative data is available for each cell in CEL-seq2 assays,False,True,"['No', 'Yes', '']"," If Library Construction Method is ""CEL-seq2"" then ""Well Index"" is required",ScATAC-seqLevel1 -Empty Well Barcode,Empty Well Barcode,EmptyWellBarcode,Unique cell barcode assigned to empty cells used as controls in CEL-seq2 assays.,False,True,," If Library Construction Method is ""CEL-seq2"" then ""Empty Well Barcode"" is required",ScATAC-seqLevel1 -Total Unmapped reads,Total Unmapped reads,TotalUnmappedreads,Number of reads that did not map to genome. Integer,False,,,,ScATAC-seqLevel2 -Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,ScATAC-seqLevel2 -Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,ScATAC-seqLevel2 -Proportion Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,ScATAC-seqLevel2 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScATAC-seqLevel2 -MapQ30,MapQ30,MapQ30,Number of reads with Quality >= 30.,False,,,,ScATAC-seqLevel2 -Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,ScATAC-seqLevel2 -Proportion Targets No Coverage,Proportion Targets No Coverage,ProportionTargetsNoCoverage,Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number,False,,,,ScATAC-seqLevel2 -Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,ScATAC-seqLevel2 -Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,ScATAC-seqLevel2 -Median Percentage of Mitochondrial Reads per Nucleus,Median Percentage of Mitochondrial Reads per Nucleus,MedianPercentageofMitochondrialReadsperNucleus,Contamination from mitochondrial sequences,True,,,,ScATAC-seqLevel2 -Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,ScATAC-seqLevel2 -Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,ScATAC-seqLevel2 -Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,ScATAC-seqLevel2 -Reference URL,Reference URL,ReferenceURL,TBD,False,,,,ScATAC-seqLevel2 -Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/),True,,,,ScATAC-seqLevel2 -Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['None', 'STAR 2-Pass Genome', 'Other Alignment Workflow', 'BWA', 'STAR 2-Pass', 'BWA with Mark Duplicates and BQSR', 'BWA-aln', 'STAR 2-Pass Chimeric', 'BWA-mem', 'BWA with BQSR', 'STAR 2-Pass Transcriptome']",,ScATAC-seqLevel2 -HTAN Biospecimen ID,HTAN Biospecimen ID,HTANBiospecimenID,HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScATAC-seqLevel2 -Pairs On Diff CHR,Pairs On Diff CHR,PairsOnDiffCHR,Pairs on different chromosomes collected from samtools. Integer,False,,,,ScATAC-seqLevel2 -Contamination Error,Contamination Error,ContaminationError,Estimation error of cross-sample contamination collected from GATK4. Number,False,,,,ScATAC-seqLevel2 -Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,ScATAC-seqLevel2 -Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,ScATAC-seqLevel2 -Genomic,Genomic,Genomic,TBD,False,,,,ScATAC-seqLevel2 -Alignment Workflow Url,Alignment Workflow Url,AlignmentWorkflowUrl,Link to workflow used for read alignment. DockStore.org recommended. String,True,,,,ScATAC-seqLevel2 -Proportion Coverage 10x,Proportion Coverage 10x,ProportionCoverage10x,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools.",False,,,,ScATAC-seqLevel2 -Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,ScATAC-seqLevel2 -Proportion Coverage 30X,Proportion Coverage 30X,ProportionCoverage30X,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools.",False,,,,ScATAC-seqLevel2 -Custom Alignment Workflow,Custom Alignment Workflow,CustomAlignmentWorkflow,Specify the name of a custom alignment workflow,False,True,," If Alignment is ""Other Alignment Workflow"" then ""Custom Alignment Workflow"" is required",ScATAC-seqLevel2 -MACS2 Neg Log10 qvalue Summit,MACS2 Neg Log10 qvalue Summit,MACS2NegLog10qvalueSummit,Negative log10 q-value for the peak summit in MACS2,False,,,,ScATAC-seqLevel3 -Blacklist Ratio,Blacklist Ratio,BlacklistRatio,Ratio of reads in blacklist regions,False,,,,ScATAC-seqLevel3 -MACS2 Start,MACS2 Start,MACS2Start,Genomic starting position in MACS2,False,,,,ScATAC-seqLevel3 -Object ID,Object ID,ObjectID,TBD,False,,,,ScATAC-seqLevel3 -nFeature RNA,nFeature RNA,NFeatureRNA,Number of genes detected in cell,False,,,,ScATAC-seqLevel3 -Nucleosome Signal,Nucleosome Signal,NucleosomeSignal,"Nucleosome signal score (strength of the nucleosome signal per cell, computed as the ratio of fragments between 147 bp and 294 bp (mononucleosome) to fragments < 147 bp (nucleosome-free))",False,,,,ScATAC-seqLevel3 -Passed Filters,Passed Filters,PassedFilters,"Number of non-duplicate, usable read-pairs i.e. fragments",False,,,,ScATAC-seqLevel3 -TSS Percentile,TSS Percentile,TSSPercentile,Percentile rank of TSS score,False,,,,ScATAC-seqLevel3 -LowMapQ,LowMapQ,LowMapQ,Number of read-pairs with <30 mapq on at least one end,False,,,,ScATAC-seqLevel3 -MACS2 Strand,MACS2 Strand,MACS2Strand,DNA stand aligned with in MACS2,False,,,,ScATAC-seqLevel3 -Duplicate Read-Pairs,Duplicate Read-Pairs,DuplicateRead-Pairs,Number of duplicate read-pairs,False,,,,ScATAC-seqLevel3 -MACS2 Neg Log10 pvalue Summit,MACS2 Neg Log10 pvalue Summit,MACS2NegLog10pvalueSummit,Negative log10 p-value for the peak summit in MACS2,False,,,,ScATAC-seqLevel3 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScATAC-seqLevel3 -DNase Sensitive Region Fragments,DNase Sensitive Region Fragments,DNaseSensitiveRegionFragments,Number of fragments overlapping with DNase sensitive regions,False,,,,ScATAC-seqLevel3 -Blacklist Region Fragments,Blacklist Region Fragments,BlacklistRegionFragments,Number of fragments overlapping blacklisted regions,False,,,,ScATAC-seqLevel3 -Unmapped Read-Pairs,Unmapped Read-Pairs,UnmappedRead-Pairs,Number of read-pairs with at least one end not mapped,False,,,,ScATAC-seqLevel3 -Chimeric Read-Pairs,Chimeric Read-Pairs,ChimericRead-Pairs,Number of chimerically mapped read-pairs,False,,,,ScATAC-seqLevel3 -TSS Fragments,TSS Fragments,TSSFragments,Number of fragments overlapping with TSS regions,False,,,,ScATAC-seqLevel3 -Seurat Clusters,Seurat Clusters,SeuratClusters,Clusters of cells by a shared nearest neighbor (SNN) modularity optimization based clustering algorithm,False,,,,ScATAC-seqLevel3 -MACS2 Score,MACS2 Score,MACS2Score,Peak score (proportional to q-value) in MACS2,False,,,,ScATAC-seqLevel3 -Peak Region Cutsites,Peak Region Cutsites,PeakRegionCutsites,Number of ends of fragments in peak regions,False,,,,ScATAC-seqLevel3 -On Target Fragments,On Target Fragments,OnTargetFragments,"Number of fragments overlapping any of TSS, enhancer, promoter and DNase hypersensitivity sites (counted with multiplicity)",False,,,,ScATAC-seqLevel3 -Nucleosome Percentile,Nucleosome Percentile,NucleosomePercentile,Percentile rank of nucleosome score,False,,,,ScATAC-seqLevel3 -Pct Reads in Peaks,Pct Reads in Peaks,PctReadsinPeaks,Percentage of reads in peaks,False,,,,ScATAC-seqLevel3 -HTAN Biospecimen ID,HTAN Biospecimen ID,HTANBiospecimenID,HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScATAC-seqLevel3 -MACS2 End,MACS2 End,MACS2End,Genomic ending position in MACS2,False,,,,ScATAC-seqLevel3 -Peak Region Fragments,Peak Region Fragments,PeakRegionFragments,Number of fragments overlapping peaks,False,,,,ScATAC-seqLevel3 -MACS2 Seqnames,MACS2 Seqnames,MACS2Seqnames,Chromosome id,False,,,,ScATAC-seqLevel3 -MACS2 Relative Summit Position,MACS2 Relative Summit Position,MACS2RelativeSummitPosition,Position of the peak summit related to the start position in MACS2,False,,,,ScATAC-seqLevel3 -nCount Peaks,nCount Peaks,NCountPeaks,TBD,False,,,,ScATAC-seqLevel3 -MACS2 Fold Change,MACS2 Fold Change,MACS2FoldChange,Fold enrichment for this peak summit against random Poisson distribution with local lambda in MACS2,False,,,,ScATAC-seqLevel3 -TSS Enrichment,TSS Enrichment,TSSEnrichment,Transcription start site (TSS) enrichment score,False,,,,ScATAC-seqLevel3 -MACS2 Name,MACS2 Name,MACS2Name,Name of the peak in MACS2,False,,,,ScATAC-seqLevel3 -nFeature Peaks,nFeature Peaks,NFeaturePeaks,TBD,False,,,,ScATAC-seqLevel3 -Mitochondrial Read-Pairs,Mitochondrial Read-Pairs,MitochondrialRead-Pairs,Number of read-pairs mapping to mitochondria and non-nuclear contigs,False,,,,ScATAC-seqLevel3 -Enhancer Region Fragments,Enhancer Region Fragments,EnhancerRegionFragments,Number of fragments overlapping enhancer regions,False,,,,ScATAC-seqLevel3 -nCount RNA,nCount RNA,NCountRNA,Total number of fragments in genes,False,,,,ScATAC-seqLevel3 -MACS2 Width,MACS2 Width,MACS2Width,Width of the peak in bases in MACS2,False,,,,ScATAC-seqLevel3 -Total Read-Pairs,Total Read-Pairs,TotalRead-Pairs,Total read-pairs,False,,,,ScATAC-seqLevel3 -Promoter Region Fragments,Promoter Region Fragments,PromoterRegionFragments,Number of fragments overlapping promoter regions,False,,,,ScATAC-seqLevel3 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScATAC-seqLevel4 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScATAC-seqLevel4 -Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,ScATAC-seqLevel4 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScATAC-seqLevel4 -scATACseq Workflow Type,scATACseq Workflow Type,ScATACseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,,,ScATAC-seqLevel4 -Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,ScATAC-seqLevel4 -File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,ScATAC-seqLevel4 -scATACseq Workflow Parameters Description,scATACseq Workflow Parameters Description,ScATACseqWorkflowParametersDescription,Parameters used to run the scATAC-seq workflow. ,True,,,,ScATAC-seqLevel4 -Filename,Filename,filename,Name of a file ,True,,,,ScATAC-seqLevel4 -Imaging Assay Type,Imaging Assay Type,ImagingAssayType,Type of imaging assay,True,,"['CyCIF', 't-CyCIF', 'MxIF', 'MERFISH', 'IHC', 'MIBI', 'H&E', 'Not Applicable', 'GeoMX-DSP', 'IMC', 'CODEX', 'SABER', 'ExSeq', 'mIHC']",,ImagingLevel1 -Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ImagingLevel1 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ImagingLevel1 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ImagingLevel1 -Pre-processing Completed,Pre-processing Completed,Pre-processingCompleted,Pre-processing steps completed to convert level 1 raw data to a single level 2 image,True,,"['None', 'Illumination correction', 'Channel/Cycle Registration', 'Other', 'Tile Stitching', 'TMA de-arraying']",,ImagingLevel1 -Comment,Comment,Comment,Free text field (generally for QC comment),False,,,,ImagingLevel1 -Pre-processing Required,Pre-processing Required,Pre-processingRequired,Pre-processing steps required to convert level 1 raw data to a single level 2 image,True,,"['None', 'Illumination correction', 'Channel/Cycle Registration', 'Other', 'Tile Stitching', 'TMA de-arraying']",,ImagingLevel1 -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ImagingLevel1 -Commit SHA,Commit SHA,CommitSHA,"Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]",False,,,,ImagingLevel1 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel1 -File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,ImagingLevel1 -Filename,Filename,filename,Name of a file ,True,,,,ImagingLevel1 -WorkingDistance,WorkingDistance,WorkingDistance,"The working distance of the lens, expressed as a floating point number. Floating point > 0.",False,,,,ImagingLevel2 -Imaging Assay Type,Imaging Assay Type,ImagingAssayType,Type of imaging assay,True,,"['CyCIF', 't-CyCIF', 'MxIF', 'MERFISH', 'IHC', 'MIBI', 'H&E', 'Not Applicable', 'GeoMX-DSP', 'IMC', 'CODEX', 'SABER', 'ExSeq', 'mIHC']",,ImagingLevel2 -FOVX,FOVX,FOVX,Field of view X dimension. Floating point,False,,,,ImagingLevel2 -Image ID,Image ID,ImageID,"Unique internal image identifier. eg ""Image:0"". (To be extracted from OME-XML)",True,,,,ImagingLevel2 -PhysicalSizeZUnit,PhysicalSizeZUnit,PhysicalSizeZUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),True,,"['Å', 'cm', 'nm', 'mm', 'µm']",,ImagingLevel2 -PhysicalSizeYUnit,PhysicalSizeYUnit,PhysicalSizeYUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),True,,"['Å', 'cm', 'nm', 'mm', 'µm']",,ImagingLevel2 -PlaneCount,PlaneCount,PlaneCount,"Number of Z-planes (not to be confused with downsampled ""pyramid""). Integer >=1",True,,,,ImagingLevel2 -FOVYUnit,FOVYUnit,FOVYUnit,Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['Å', 'cm', 'nm', 'mm', 'µm', '']",,ImagingLevel2 -Frame Averaging,Frame Averaging,FrameAveraging,"Number of frames averaged together (if no averaging, set to 1). Integer >= 1",False,,,,ImagingLevel2 -Tseries,Tseries,Tseries,Does data file contain a time-series of images,True,,"['No', 'Yes']",,ImagingLevel2 -Objective,Objective,Objective,Objective,False,,,,ImagingLevel2 -File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,ImagingLevel2 -FOV number,FOV number,FOVnumber,Index of FOV (as it pertains to its sequence order). Integer >= 1,False,,,,ImagingLevel2 -Pixels BigEndian,Pixels BigEndian,PixelsBigEndian,Boolean (True/False),True,,"['False', 'True']",,ImagingLevel2 -FOVY,FOVY,FOVY,Field of view Y dimension. Floating point value,False,,,,ImagingLevel2 -SizeC,SizeC,SizeC,Number of channels. Integer >= 1,True,,,,ImagingLevel2 -PhysicalSizeX,PhysicalSizeX,PhysicalSizeX,Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.,True,,,,ImagingLevel2 -SizeY,SizeY,SizeY,Size of image: Y dimension (in pixels). Integer >= 1,True,,,,ImagingLevel2 -SizeT,SizeT,SizeT,Number of time points. Integer >= 1,True,,,,ImagingLevel2 -LensNA,LensNA,LensNA,The numerical aperture of the lens. Floating point value > 0.,False,,,,ImagingLevel2 -Comment,Comment,Comment,Free text field (generally for QC comment),False,,,,ImagingLevel2 -Microscope,Microscope,Microscope,"Microscope type (manufacturer, model, etc) used for this experiment",True,,,,ImagingLevel2 -WorkingDistanceUnit,WorkingDistanceUnit,WorkingDistanceUnit,The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['Å', 'cm', 'nm', 'mm', 'µm', '']",,ImagingLevel2 -Immersion,Immersion,Immersion,Immersion medium,False,,"['Air', 'Water', 'Other', 'Oil', '']",,ImagingLevel2 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel2 -Zstack,Zstack,Zstack,Does data file contain a Z-stack of images,True,,"['No', 'Yes']",,ImagingLevel2 -NominalMagnification,NominalMagnification,NominalMagnification,The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units),True,,,,ImagingLevel2 -Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ImagingLevel2 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ImagingLevel2 -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ImagingLevel2 -PixelType,PixelType,PixelType,"Data type for each pixel value. E.g. ""uint16""",True,,"['double', 'uint32', 'uint16', 'int16', 'float', 'int8', 'int32', 'uint8', 'bit']",,ImagingLevel2 -Channel Metadata Filename,Channel Metadata Filename,ChannelMetadataFilename,Full path within Synapse project of uploaded companion CSV file containing channel-level metadata details,True,,,,ImagingLevel2 -PhysicalSizeXUnit,PhysicalSizeXUnit,PhysicalSizeXUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['Å', 'cm', 'nm', 'mm', 'µm', '']",,ImagingLevel2 -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,ImagingLevel2 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ImagingLevel2 -FOVXUnit,FOVXUnit,FOVXUnit,Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['Å', 'cm', 'nm', 'mm', 'µm', '']",,ImagingLevel2 -DimensionOrder,DimensionOrder,DimensionOrder,The order in which the individual planes of data are interleaved.,True,,"['ZYX', 'XYCZT', 'XYTZC', 'XYZTC', 'XYZCT', 'XYCTZ']",,ImagingLevel2 -SizeX,SizeX,SizeX,Size of image: X dimension (in pixels). Integer >= 1,True,,,,ImagingLevel2 -SizeZ,SizeZ,SizeZ,Size of image: Z dimension (in pixels). Integer >= 1,True,,,,ImagingLevel2 -Passed QC,Passed QC,PassedQC,Did all channels pass QC (if not add free text Comment),True,,"['No - Channels QC', 'Yes']",,ImagingLevel2 -PhysicalSizeY,PhysicalSizeY,PhysicalSizeY,Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.,True,,,,ImagingLevel2 -Pyramid,Pyramid,Pyramid,Does data file contain pyramid of images,True,,"['No', 'Yes']",,ImagingLevel2 -PhysicalSizeZ,PhysicalSizeZ,PhysicalSizeZ,Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.,True,,,,ImagingLevel2 -Filename,Filename,filename,Name of a file ,True,,,,ImagingLevel2 -Parameter file,Parameter file,Parameterfile,Path in Syanpse to a text file listing algorithm version numbers and relevant parameters needed to reproduce the analysis,False,,,,ImagingLevel3Segmentation -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ImagingLevel3Segmentation -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ImagingLevel3Segmentation -Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ImagingLevel3Segmentation -Commit SHA,Commit SHA,CommitSHA,"Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]",False,,,,ImagingLevel3Segmentation -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel3Segmentation -Imaging Object Class,Imaging Object Class,ImagingObjectClass,Defines the structure that the mask delineates,True,,"['plasma membrane', 'cytoplasm', 'nucleus', 'Imaging Object Class Other', 'whole cell']",,ImagingLevel3Segmentation -Number of Objects,Number of Objects,NumberofObjects, The number of objects (eg cells) described,True,,,,ImagingLevel3Segmentation -File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,ImagingLevel3Segmentation -Filename,Filename,filename,Name of a file ,True,,,,ImagingLevel3Segmentation -Imaging Segmentation Data Type,Imaging Segmentation Data Type,ImagingSegmentationDataType,Specifies how the segmentation is stored,True,,"['Point', 'Polygon', 'Mask', 'Probability Map', 'Outline']",,ImagingLevel3Segmentation -Imaging Object Class Description,Imaging Object Class Description,ImagingObjectClassDescription,Free text description of object class [string],False,True,," If Imaging Object Class is ""Imaging Object Class Other"" then ""Imaging Object Class Description"" is required",ImagingLevel3Segmentation -WorkingDistance,WorkingDistance,WorkingDistance,"The working distance of the lens, expressed as a floating point number. Floating point > 0.",False,,,,ImagingLevel3Image -Imaging Assay Type,Imaging Assay Type,ImagingAssayType,Type of imaging assay,True,,"['CyCIF', 't-CyCIF', 'MxIF', 'MERFISH', 'IHC', 'MIBI', 'H&E', 'Not Applicable', 'GeoMX-DSP', 'IMC', 'CODEX', 'SABER', 'ExSeq', 'mIHC']",,ImagingLevel3Image -FOVX,FOVX,FOVX,Field of view X dimension. Floating point,False,,,,ImagingLevel3Image -Frame Averaging,Frame Averaging,FrameAveraging,"Number of frames averaged together (if no averaging, set to 1). Integer >= 1",False,,,,ImagingLevel3Image -Tseries,Tseries,Tseries,Does data file contain a time-series of images,True,,"['No', 'Yes']",,ImagingLevel3Image -Objective,Objective,Objective,Objective,False,,,,ImagingLevel3Image -File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,ImagingLevel3Image -FOV number,FOV number,FOVnumber,Index of FOV (as it pertains to its sequence order). Integer >= 1,False,,,,ImagingLevel3Image -FOVY,FOVY,FOVY,Field of view Y dimension. Floating point value,False,,,,ImagingLevel3Image -HTAN Parent Channel Metadata ID,HTAN Parent Channel Metadata ID,HTANParentChannelMetadataID,TBD,False,,,,ImagingLevel3Image -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ImagingLevel3Image -LensNA,LensNA,LensNA,The numerical aperture of the lens. Floating point value > 0.,False,,,,ImagingLevel3Image -Comment,Comment,Comment,Free text field (generally for QC comment),False,,,,ImagingLevel3Image -Microscope,Microscope,Microscope,"Microscope type (manufacturer, model, etc) used for this experiment",True,,,,ImagingLevel3Image -Immersion,Immersion,Immersion,Immersion medium,False,,"['Air', 'Water', 'Other', 'Oil', '']",,ImagingLevel3Image -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel3Image -Zstack,Zstack,Zstack,Does data file contain a Z-stack of images,True,,"['No', 'Yes']",,ImagingLevel3Image -NominalMagnification,NominalMagnification,NominalMagnification,The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units),True,,,,ImagingLevel3Image -Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ImagingLevel3Image -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ImagingLevel3Image -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ImagingLevel3Image -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ImagingLevel3Image -Passed QC,Passed QC,PassedQC,Did all channels pass QC (if not add free text Comment),True,,"['No - Channels QC', 'Yes']",,ImagingLevel3Image -Pyramid,Pyramid,Pyramid,Does data file contain pyramid of images,True,,"['No', 'Yes']",,ImagingLevel3Image -Filename,Filename,filename,Name of a file ,True,,,,ImagingLevel3Image -WorkingDistanceUnit,WorkingDistanceUnit,WorkingDistanceUnit,The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['Å', 'cm', 'nm', 'mm', 'µm', '']",,ImagingLevel3Image -FOVXUnit,FOVXUnit,FOVXUnit,Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['Å', 'cm', 'nm', 'mm', 'µm', '']",,ImagingLevel3Image -FOVYUnit,FOVYUnit,FOVYUnit,Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['Å', 'cm', 'nm', 'mm', 'µm', '']",,ImagingLevel3Image -Lot,Lot,Lot,Lot number from vendor,False,,,,ImagingLevel3Channels -Fluorophore,Fluorophore,Fluorophore,Fluorescent dye label (eg Alexa Fluor 488),False,,,,ImagingLevel3Channels -Catalog Number,Catalog Number,CatalogNumber,Catalog Number,False,,,,ImagingLevel3Channels -Metal Isotope Element,Metal Isotope Element,MetalIsotopeElement,Element abbreviation. eg “La” or “Nd”,False,,"['Rh', 'Pd', 'Fe', 'Nd', 'Sb', 'Zn', 'Ca', 'Ga', 'Au', 'B', 'Ti', 'Sr', 'Pm', 'Nb', 'Mt', 'Ge', 'Pr', 'Ce', 'Cd', 'Hf', 'Cu', 'Fr', 'In', 'Cr', 'H', 'Ar', 'Th', 'Rg', 'Ts', 'Pt', 'md', 'Lv', 'P', 'Li', 'Be', 'Cn', 'Eu', 'Nh', 'I', 'Y', 'Fm', 'Fl', 'Os', 'Ir', 'N', 'Db', 'Si', 'U', 'S', 'Mo', 'Dy', 'Cf', 'At', 'Tl', 'Ru', 'Sn', 'Yb', 'Se', 'Te', 'Mg', 'Ba', 'Ho', 'Hg', 'Pu', 'K', 'Xe', 'Lr', 'Ag', 'Zr', 'Ra', 'Kr', 'Re', 'Al', 'No', 'Bh', 'Er', 'Cs', 'Sm', 'Mc', 'Ni', 'Br', 'F', 'V', 'Rf', 'Pb', 'Gd', 'Na', 'Sc', 'He', 'La', 'W', 'O', 'Tb', 'As', 'Np', 'Co', 'Rb', 'Bi', 'Ac', 'Cl', 'am', 'Bk', 'Og', 'Mn', 'Po', 'Tm', 'Pa', 'Sg', 'Tc', 'Ne', 'Rn', 'Lu', 'Hs', 'Es', 'C', 'Ta', 'Ds', '']",,ImagingLevel3Channels -Cycle Number,Cycle Number,CycleNumber,The cycle # in which the co-listed reagent(s) was(were) used. Integer >= 1 (up to number of cycles),False,,,,ImagingLevel3Channels -Concentration,Concentration,Concentration,Concentration (eg 10ug/mL),False,,,,ImagingLevel3Channels -Channel Name,Channel Name,ChannelName,This must match the corresponding field in the OME-XML / TIFF header. (eg 'Blue' or 'CD45' or “E-cadherin”),True,,,,ImagingLevel3Channels -Clone,Clone,Clone,Clone,False,,,,ImagingLevel3Channels -Emission Bandwidth,Emission Bandwidth,EmissionBandwidth,Nominal width of emission spectrum (nm),False,,,,ImagingLevel3Channels -Vendor,Vendor,Vendor,Vendor,False,,,,ImagingLevel3Channels -Excitation Bandwidth,Excitation Bandwidth,ExcitationBandwidth,Nominal width of excitation spectrum (nm),False,,,,ImagingLevel3Channels -Channel Passed QC,Channel Passed QC,ChannelPassedQC,Identify stains that did not pass QC but are included in the dataset.,True,,"['No - Channel Failed QC', 'Yes']",,ImagingLevel3Channels -Dilution,Dilution,Dilution,Dilution (eg 1:1000),False,,,,ImagingLevel3Channels -Channel ID,Channel ID,ChannelID,This must match the corresponding field in the OME-XML / TIFF header. (eg 'Channel:0:1'),True,,,,ImagingLevel3Channels -Target Name,Target Name,TargetName,Short descriptive name (abbreviation) for this target (antigen),True,,,,ImagingLevel3Channels -Oligo Barcode Upper Strand,Oligo Barcode Upper Strand,OligoBarcodeUpperStrand,Oligo Barcode - Upper Strand,False,,,,ImagingLevel3Channels -Antibody Name,Antibody Name,AntibodyName,"Antibody Name (free text (eg “Keratin”, “CD163”, “DNA”))",True,,,,ImagingLevel3Channels -Emission Wavelength,Emission Wavelength,EmissionWavelength,Center/peak of the emission spectrum (nm),False,,,,ImagingLevel3Channels -Antibody Role,Antibody Role,AntibodyRole," ""Is this antibody acting as a primary or secondary antibody""",True,,"['secondary', 'primary']",,ImagingLevel3Channels -Oligo Barcode Lower Strand,Oligo Barcode Lower Strand,OligoBarcodeLowerStrand,Oligo Barcode - Lower Strand,False,,,,ImagingLevel3Channels -RRID identifier,RRID identifier,RRIDidentifier,Research Resource Identifier (eg “RRID: AB_394606”),True,,,,ImagingLevel3Channels -Excitation Wavelength,Excitation Wavelength,ExcitationWavelength,Center/peak of the excitation spectrum (nm),False,,,,ImagingLevel3Channels -HTAN Channel Metadata ID,HTAN Channel Metadata ID,HTANChannelMetadataID,HTAN ID for this channel metadata table (same for all rows),True,,,,ImagingLevel3Channels -Metal Isotope Mass,Metal Isotope Mass,MetalIsotopeMass,Element mass number,False,,,,ImagingLevel3Channels -Sub Cycle Number,Sub Cycle Number,SubCycleNumber,Sub cycle number,False,,,,ImagingLevel3Channels -Channel QC Faliure Type,Channel QC Faliure Type,ChannelQCFaliureType,TBD,False,True,," If Channel Passed QC is ""No - Channel Failed QC"" then ""Channel QC Faliure Type"" is required",ImagingLevel3Channels -Parameter file,Parameter file,Parameterfile,Path in Syanpse to a text file listing algorithm version numbers and relevant parameters needed to reproduce the analysis,False,,,,ImagingLevel4 -HTAN Parent Channel Metadata ID,HTAN Parent Channel Metadata ID,HTANParentChannelMetadataID,TBD,False,,,,ImagingLevel4 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ImagingLevel4 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ImagingLevel4 -Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ImagingLevel4 -Number of Features,Number of Features,NumberofFeatures, The number of features (eg channels) described,True,,,,ImagingLevel4 -Commit SHA,Commit SHA,CommitSHA,"Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]",False,,,,ImagingLevel4 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel4 -Imaging Object Class,Imaging Object Class,ImagingObjectClass,Defines the structure that the mask delineates,True,,"['plasma membrane', 'cytoplasm', 'nucleus', 'Imaging Object Class Other', 'whole cell']",,ImagingLevel4 -Number of Objects,Number of Objects,NumberofObjects, The number of objects (eg cells) described,True,,,,ImagingLevel4 -File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,ImagingLevel4 -Imaging Summary Statistic,Imaging Summary Statistic,ImagingSummaryStatistic, Function used to summarize object/feature intensity,False,,"['Median', 'Mean', 'Not Specified', '']",,ImagingLevel4 -Filename,Filename,filename,Name of a file ,True,,,,ImagingLevel4 -Imaging Object Class Description,Imaging Object Class Description,ImagingObjectClassDescription,Free text description of object class [string],False,True,," If Imaging Object Class is ""Imaging Object Class Other"" then ""Imaging Object Class Description"" is required",ImagingLevel4 -Imaging Assay Type,Imaging Assay Type,ImagingAssayType,Type of imaging assay,True,,"['CyCIF', 't-CyCIF', 'MxIF', 'MERFISH', 'IHC', 'MIBI', 'H&E', 'Not Applicable', 'GeoMX-DSP', 'IMC', 'CODEX', 'SABER', 'ExSeq', 'mIHC']",,SRRSImagingLevel2 -Image ID,Image ID,ImageID,"Unique internal image identifier. eg ""Image:0"". (To be extracted from OME-XML)",True,,,,SRRSImagingLevel2 -PhysicalSizeYUnit,PhysicalSizeYUnit,PhysicalSizeYUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),True,,"['Å', 'cm', 'nm', 'mm', 'µm']",,SRRSImagingLevel2 -PlaneCount,PlaneCount,PlaneCount,"Number of Z-planes (not to be confused with downsampled ""pyramid""). Integer >=1",True,,,,SRRSImagingLevel2 -Frame Averaging,Frame Averaging,FrameAveraging,"Number of frames averaged together (if no averaging, set to 1). Integer >= 1",False,,,,SRRSImagingLevel2 -Tseries,Tseries,Tseries,Does data file contain a time-series of images,True,,"['No', 'Yes']",,SRRSImagingLevel2 -Objective,Objective,Objective,Objective,False,,,,SRRSImagingLevel2 -File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,SRRSImagingLevel2 -Pixels BigEndian,Pixels BigEndian,PixelsBigEndian,Boolean (True/False),True,,"['False', 'True']",,SRRSImagingLevel2 -SizeC,SizeC,SizeC,Number of channels. Integer >= 1,True,,,,SRRSImagingLevel2 -PhysicalSizeX,PhysicalSizeX,PhysicalSizeX,Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.,True,,,,SRRSImagingLevel2 -SizeY,SizeY,SizeY,Size of image: Y dimension (in pixels). Integer >= 1,True,,,,SRRSImagingLevel2 -SizeT,SizeT,SizeT,Number of time points. Integer >= 1,True,,,,SRRSImagingLevel2 -Microscope,Microscope,Microscope,"Microscope type (manufacturer, model, etc) used for this experiment",True,,,,SRRSImagingLevel2 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,SRRSImagingLevel2 -Zstack,Zstack,Zstack,Does data file contain a Z-stack of images,True,,"['No', 'Yes']",,SRRSImagingLevel2 -NominalMagnification,NominalMagnification,NominalMagnification,The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units),True,,,,SRRSImagingLevel2 -Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,SRRSImagingLevel2 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,SRRSImagingLevel2 -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,SRRSImagingLevel2 -PixelType,PixelType,PixelType,"Data type for each pixel value. E.g. ""uint16""",True,,"['double', 'uint32', 'uint16', 'int16', 'float', 'int8', 'int32', 'uint8', 'bit']",,SRRSImagingLevel2 -Channel Metadata Filename,Channel Metadata Filename,ChannelMetadataFilename,Full path within Synapse project of uploaded companion CSV file containing channel-level metadata details,True,,,,SRRSImagingLevel2 -PhysicalSizeXUnit,PhysicalSizeXUnit,PhysicalSizeXUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['Å', 'cm', 'nm', 'mm', 'µm', '']",,SRRSImagingLevel2 -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,SRRSImagingLevel2 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,SRRSImagingLevel2 -DimensionOrder,DimensionOrder,DimensionOrder,The order in which the individual planes of data are interleaved.,True,,"['ZYX', 'XYCZT', 'XYTZC', 'XYZTC', 'XYZCT', 'XYCTZ']",,SRRSImagingLevel2 -SizeX,SizeX,SizeX,Size of image: X dimension (in pixels). Integer >= 1,True,,,,SRRSImagingLevel2 -SizeZ,SizeZ,SizeZ,Size of image: Z dimension (in pixels). Integer >= 1,True,,,,SRRSImagingLevel2 -Passed QC,Passed QC,PassedQC,Did all channels pass QC (if not add free text Comment),True,,"['No - Channels QC', 'Yes']",,SRRSImagingLevel2 -PhysicalSizeY,PhysicalSizeY,PhysicalSizeY,Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.,True,,,,SRRSImagingLevel2 -Pyramid,Pyramid,Pyramid,Does data file contain pyramid of images,True,,"['No', 'Yes']",,SRRSImagingLevel2 -Filename,Filename,filename,Name of a file ,True,,,,SRRSImagingLevel2 -Comment,Comment,Comment,Free text field (generally for QC comment),False,True,," If Passed QC is ""No - Channels QC"" then ""Comment"" is required",SRRSImagingLevel2 -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,RPPALevel2 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,RPPALevel2 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,RPPALevel2 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,RPPALevel2 -Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,RPPALevel2 -HTAN RPPA Antibody Table,HTAN RPPA Antibody Table,HTANRPPAAntibodyTable,A table containing antibody level metadata for RPPA,False,,,,RPPALevel2 -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,RPPALevel2 -File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",False,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf', '']",,RPPALevel2 -Assay Type,Assay Type,AssayType,"The type and level of assay this metadata applies to (e.g. RPPA, Nanostring DSP, etc.)",True,,,,RPPALevel2 -Filename,Filename,filename,Name of a file ,False,,,,RPPALevel2 -Phosphoprotein Flag,Phosphoprotein Flag,PhosphoproteinFlag,A flag the denotes if an antibody targets a phosphoprotein.,False,,"['False', 'True', '']",,RPPALevel2 -RPPA Validation Status,RPPA Validation Status,RPPAValidationStatus,Valid = RPPA and WB correlation > 0.7; Use with Caution = RPPA and WB correlation < 0.7; Under Evaluation = Antibody has given mixed results and/or evaluated by another lab; We are in the process of (re)validating; Used for QC = These antibodies are used for tissue sample quality control (QC),False,,"['Under Evaluation', 'Used for QC', 'Valid', 'Use with Caution', '']",,RPPALevel2 -GENCODE Gene Symbol Target,GENCODE Gene Symbol Target,GENCODEGeneSymbolTarget,The comma separated list of gene symbols targeted by the antibody.,False,,,,RPPALevel2 -UNIPROT Protein ID Target,UNIPROT Protein ID Target,UNIPROTProteinIDTarget,TBD,False,,,,RPPALevel2 -Catalog Number,Catalog Number,CatalogNumber,Catalog Number,False,,,,RPPALevel2 -Species,Species,Species,Host animal.,False,,"['Mouse', 'Goat', 'Rabbit', '']",,RPPALevel2 -Clone,Clone,Clone,Clone,False,,,,RPPALevel2 -HTAN RPPA Antibody Table ID,HTAN RPPA Antibody Table ID,HTANRPPAAntibodyTableID,HTAN identifier associated with RPPA antibody level metadata. Identical for every row of the table.,False,,,,RPPALevel2 -Ab Name Reported on Dataset,Ab Name Reported on Dataset,AbNameReportedonDataset,The antibody name.,False,,,,RPPALevel2 -Phospho Site,Phospho Site,PhosphoSite,The protein site for a phosphoprotein targeting antibody. Report AA and site (i.e. S442),False,,,,RPPALevel2 -Internal Ab ID,Internal Ab ID,InternalAbID,TBD,False,,,,RPPALevel2 -RPPA Dilution,RPPA Dilution,RPPADilution,The dilution ratio.,False,,,,RPPALevel2 -Clonality,Clonality,Clonality,The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Clonal', 'Non-clonal', '']",,RPPALevel2 -Vendor,Vendor,Vendor,Vendor,False,,,,RPPALevel2 -Notes,Notes,Notes,TBD,False,,,,RPPALevel2 -Phosphoprotein Flag,Phosphoprotein Flag,PhosphoproteinFlag,A flag the denotes if an antibody targets a phosphoprotein.,True,,"['False', 'True']",,HTANRPPAAntibodyTable -RPPA Validation Status,RPPA Validation Status,RPPAValidationStatus,Valid = RPPA and WB correlation > 0.7; Use with Caution = RPPA and WB correlation < 0.7; Under Evaluation = Antibody has given mixed results and/or evaluated by another lab; We are in the process of (re)validating; Used for QC = These antibodies are used for tissue sample quality control (QC),False,,"['Under Evaluation', 'Used for QC', 'Valid', 'Use with Caution', '']",,HTANRPPAAntibodyTable -GENCODE Gene Symbol Target,GENCODE Gene Symbol Target,GENCODEGeneSymbolTarget,The comma separated list of gene symbols targeted by the antibody.,True,,,,HTANRPPAAntibodyTable -UNIPROT Protein ID Target,UNIPROT Protein ID Target,UNIPROTProteinIDTarget,TBD,False,,,,HTANRPPAAntibodyTable -Catalog Number,Catalog Number,CatalogNumber,Catalog Number,False,,,,HTANRPPAAntibodyTable -Species,Species,Species,Host animal.,True,,"['Mouse', 'Goat', 'Rabbit']",,HTANRPPAAntibodyTable -Clone,Clone,Clone,Clone,False,,,,HTANRPPAAntibodyTable -HTAN RPPA Antibody Table ID,HTAN RPPA Antibody Table ID,HTANRPPAAntibodyTableID,HTAN identifier associated with RPPA antibody level metadata. Identical for every row of the table.,True,,,,HTANRPPAAntibodyTable -Ab Name Reported on Dataset,Ab Name Reported on Dataset,AbNameReportedonDataset,The antibody name.,True,,,,HTANRPPAAntibodyTable -Phospho Site,Phospho Site,PhosphoSite,The protein site for a phosphoprotein targeting antibody. Report AA and site (i.e. S442),False,,,,HTANRPPAAntibodyTable -Internal Ab ID,Internal Ab ID,InternalAbID,TBD,False,,,,HTANRPPAAntibodyTable -RPPA Dilution,RPPA Dilution,RPPADilution,The dilution ratio.,False,,,,HTANRPPAAntibodyTable -Clonality,Clonality,Clonality,The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Clonal', 'Non-clonal', '']",,HTANRPPAAntibodyTable -Vendor,Vendor,Vendor,Vendor,False,,,,HTANRPPAAntibodyTable -Notes,Notes,Notes,TBD,False,,,,HTANRPPAAntibodyTable -File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,HTANRPPAAntibodyTable -Filename,Filename,filename,Name of a file ,True,,,,HTANRPPAAntibodyTable +,Attribute,Label,Description,Required,Valid Values,Component +Survival Outcome,Survival Outcome,SurvivalOutcome,Text term that describes the last known status of an individual.,False,"['Distant met recurrence/progression', 'unknown tumor status', 'Tumor free', 'Deceased', 'With tumor', 'Loco-regional recurrence/progression', 'Not Applicable', 'Not Reported', 'Not Allowed To Collect', 'Biochemical evidence of disease without structural correlate', '']",Biospecimen +Tumor Grade,Tumor Grade,TumorGrade,"Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.",False,"['G2', 'G4', 'unknown', 'G1', 'Intermediate Grade', 'G3', 'Not Applicable', 'High Grade', 'GB', 'Not Reported', 'GX', 'Low Grade', '']",Biospecimen +Biospecimen Tumor Type,Biospecimen Tumor Type,BiospecimenTumorType,"The type of tumor associated with the specimen. Multiple values permitted, comma separated.",False,"['Non-Functioning Pituitary Gland Adenoma', 'Soft Tissue Sarcoma', 'Myeloproliferative Neoplasm', 'Ewing Sarcoma', 'High Grade Ovarian Serous Adenocarcinoma', 'Histiocytic Sarcoma', 'Central Nervous System Neoplasm', 'Myeloid Leukemia', 'Uveal Neoplasm', 'Atypical Teratoid/Rhabdoid Tumor', 'T-Cell Lymphoma', 'Meningioma', 'Sinonasal Squamous Cell Carcinoma', 'Leiomyoma', 'Cerebellar Neoplasm', 'Neurofibroma', 'Cervical Small Cell Carcinoma', 'Castration-Resistant Prostate Carcinoma', 'Pan-cancer', 'Medulloblastoma', 'Rhabdomyosarcoma', 'Pituitary Gland Adenoma', 'Pancreatic Adenocarcinoma', 'Lung Small Cell Carcinoma', 'Schwannoma', 'Combined Hepatocellular Carcinoma and Cholangiocarcinoma', 'Invasive Ductal Breast Carcinoma', 'T Acute Lymphoblastic Leukemia', 'Malignant Skin Neoplasm', 'Acute Myeloid Leukemia', 'Thyroid Gland Anaplastic Carcinoma', 'Lymphoma', 'Breast Adenocarcinoma', 'Colorectal Adenocarcinoma', 'Pending Annotation', 'Leukemia', 'Rosette-Forming Glioneuronal Tumor', 'Dysembryoplastic Neuroepithelial Neoplasm', 'Multiple Myeloma', 'Breast Carcinoma', 'Malignant Ovarian Neoplasm', 'Glioblastoma', 'Skin Carcinoma', 'Skin Neoplasm', 'Pancreatic Neuroendocrine Carcinoma', 'Lung Neoplasm', 'Plasmacytoma', 'Lung Adenocarcinoma', 'Testicular Embryonal Carcinoma', 'Non-Hodgkin Lymphoma', 'Biliary Tract Carcinoma', 'Acute Monocytic Leukemia', 'Follicular Lymphoma', 'Precursor B-cell lymphoblastic leukemia', 'Not Applicable', 'Urothelial Carcinoma', 'Ovarian Neoplasm', 'Primary Myelofibrosis', 'Synovial Sarcoma', 'Neuroendocrine Neoplasm', 'Uterine Adenosarcoma', 'Plexiform Neurofibroma', 'Head and Neck Carcinoma', 'Cervical Neoplasm', 'Bone Neoplasm', 'Chronic Myeloid Leukemia', 'Liver and Intrahepatic Bile Duct Carcinoma', 'Intrahepatic Cholangiocarcinoma', 'Choriocarcinoma', 'Central Nervous System Cavernous Hemangioma', 'B-Cell Non-Hodgkin Lymphoma', 'Primary Central Nervous System Lymphoma', 'Prostate Carcinoma', 'Breast Neoplasm', 'Fibrosarcoma', 'Cholangiocarcinoma', 'Mesothelioma', 'Hodgkin Lymphoma', 'Renal Cell Carcinoma', 'Gastric Neoplasm', 'Triple-Negative Breast Carcinoma', 'Intestinal Neoplasm', 'Colorectal Carcinoma', 'Lung Squamous Cell Carcinoma', 'Malignant Peripheral Nerve Sheath Tumor', 'Pancreatic Carcinoma', 'Uveal Melanoma', 'Gastrointestinal Stromal Neoplasm', 'Cutaneous Melanoma', 'Head and Neck Squamous Cell Carcinoma', 'Barrett Esophagus', 'Ovarian Adenosarcoma', 'Angiosarcoma', 'Malignant Digestive System Neoplasm', 'Acinar Cell Carcinoma', 'B Acute Lymphoblastic Leukemia', 'Craniopharyngioma', 'Gallbladder Carcinoma', 'Pheochromocytoma', 'Malignant Peritoneal Neoplasm', 'Sarcoma', 'Serous Tubal Intraepithelial Carcinoma', 'Chronic Lymphocytic Leukemia', 'Cutaneous T Cell Lymphoma', 'Acute Lymphoblastic Leukemia', 'Esophageal Adenocarcinoma', 'Colorectal Neoplasm', 'Fibroepithelial Polyp', 'Glioma', 'Esophageal Squamous Cell Carcinoma', 'Carcinoma In Situ', 'Low Grade Glioma', 'Myoepithelioma', 'Malignant Glioma', 'Malignant Neoplasm', 'Esophageal Carcinoma', 'Retinoblastoma', 'Chondroblastoma', 'Plasmablastic Lymphoma', 'Hepatocellular Carcinoma', 'Cervical Carcinoma', 'Rectal Adenocarcinoma', 'Colorectal Adenoma', 'Bladder Neoplasm', 'Gastric Carcinoma', 'Pancreatic Ductal Adenocarcinoma', 'Plexiform Schwannoma', 'Luminal A Breast Carcinoma', 'Ductal Breast Carcinoma In Situ', 'Mantle Cell Lymphoma', 'Thyroid Gland Noninvasive Follicular Neoplasm with Papillary-Like Nuclear Features', 'Giant Cell Tumor', 'Basal Cell Neoplasm', 'Kaposi Sarcoma', 'Bladder Carcinoma', 'Teratoma', 'Carcinoma', 'Cellular Schwannoma', 'Ovarian Carcinoma', 'Endometrial Neoplasm', 'Prostate Adenocarcinoma', 'Astrocytoma', 'Oral Cavity Squamous Cell Carcinoma', 'Malignant Genitourinary System Neoplasm', 'Ovarian Serous Adenocarcinoma', 'Penile Carcinoma', 'Gastroesophageal Adenocarcinoma', 'Squamous Cell Carcinoma', 'Liver and Intrahepatic Bile Duct Neoplasm', 'Thyroid Gland Carcinoma', 'Lymphoid Leukemia', 'Extraventricular Neurocytoma', 'Neuroblastoma', 'Lung Non-Small Cell Carcinoma', 'Diffuse Large B-Cell Lymphoma', 'Nasopharyngeal Carcinoma', 'Myeloid Neoplasm', 'Acute Promyelocytic Leukemia', 'Clear Cell Renal Cell Carcinoma', 'Oral Cavity Neoplasm', 'Lung Carcinoma', 'Osteosarcoma', 'Colon Carcinoma', 'Malignant Brain Neoplasm', 'Adenocarcinoma', 'Brain Neoplasm', 'Prostate Neoplasm', 'Ependymoma', 'Fibrolamellar Carcinoma', 'Pilocytic Astrocytoma', 'Mycosis Fungoides', 'Colon Adenocarcinoma', 'Vascular Neoplasm', 'Basal-Like Breast Carcinoma', 'Gastroesophageal Junction Adenocarcinoma', 'Endometrial Carcinoma', 'Malignant Pancreatic Neoplasm', 'Oropharyngeal Neoplasm', 'Salivary Gland Adenoid Cystic Carcinoma', 'Melanoma', 'Head and Neck Neoplasm', 'Not-Applicable', 'Pancreatic Neoplasm', 'Marginal Zone Lymphoma', 'Gastric Adenocarcinoma', 'Neuroepithelial Neoplasm', '']",Biospecimen +Health Care Site,Health Care Site,HealthCareSite,The health care site at which the biospecimen sample was collected.,False,,Biospecimen +Biospecimen_id,Biospecimen_id,BiospecimenId,"Unique row identifier, used as a primary key for record updates",True,,Biospecimen +Component,Component,Component,"Category of metadata (e.g. Tools, Publications, etc.); provide the same one for all items/rows.",True,,Biospecimen +Biospecimen Species,Biospecimen Species,BiospecimenSpecies,The species from which the biospecimen originates,True,"['Human', 'Chicken', 'Yeast', 'Trichoplax adhaerens', 'Boar', 'Rhesus monkey', 'Rat', 'Armadillo', 'African Bush Elephant', 'unknown', 'Escherichia coli', 'Cow', 'Dog', 'Multispecies', 'Cat', 'Asian Elephant', 'Opossum', 'Horse', 'Fruit Fly', 'Rabbit', 'Guinea Pig', 'Zebrafish', 'Worm', 'Sheep', 'Mouse', 'Unspecified']",Biospecimen +Age at Sample Collection,Age at Sample Collection,AgeatSampleCollection,"Age at the time the biospecimen was collected, expressed in number of years since birth.",False,,Biospecimen +Tumor Subtype,Tumor Subtype,TumorSubtype,"The subtype related to the scientific determination and investigation, analysis and recognition of the presence and nature of disease, condition, or injury from expressed signs and symptoms of tissue growth resulting from uncontrolled cell proliferation.",False,"['LumB', 'TNBC', 'LumA', 'Not Applicable', 'HER2', '']",Biospecimen +Known Metastasis Sites,Known Metastasis Sites,KnownMetastasisSites,The text term(s) used to describe the anatomic site(s) of metastasis associated with the patient's malignant disease.,False,,Biospecimen +Timepoint,Timepoint,Timepoint,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",False,,Biospecimen +Biospecimen ID,Biospecimen ID,BiospecimenID,ID associated with a biosample,True,,Biospecimen +Individual ID,Individual ID,IndividualID,ID associated with a study participant,True,,Biospecimen +Biospecimen Type,Biospecimen Type,BiospecimenType,The type of biospecimen,True,"['Urine', 'Tissue', 'Blood', 'Analyte', 'Mouth Rinse', 'Sputum', 'Stool', 'Bone Marrow', 'Cells', 'Fluids', 'Ascites']",Biospecimen +Site of Resection or Biopsy,Site of Resection or Biopsy,SiteofResectionorBiopsy,The text term used to describe the anatomic site of the resection or biopsy of the patient's malignant disease.,False,"['Artery', 'Trachea', 'Tongue', 'Intestine', 'Lymphoid Tissue', 'Blood', 'Eye', 'Gastroesophageal Junction', 'Cervix Uteri', 'Lymphatic System', 'Endocervix', 'Thymus', 'Omentum', 'Olfactory Mucosa', 'Adrenal Gland', 'Kidney', 'Ovary', 'Vascular Endothelium', 'Placenta', 'Pending Annotation', 'Epithelium', 'Salivary Gland', 'Lung', 'Ear', 'Hippocampus', 'Pituitary Gland', 'Duodenum', 'Lymph Node', 'Pharynx', 'Foreskin', 'Adipose Tissue', 'Hematopoietic System', 'Genitourinary', 'Synovial Membrane', 'Not Applicable', 'Fallopian Tube', 'Aorta', 'Vertebra', 'Blood Vessel', 'Spinal Cord', 'Stomach', 'Cancer-Associated Fibroblast', 'Endothelium', 'Testis', 'Mammary Gland', 'Pleura', 'Gastrointestinal Tract', 'Joint', 'Periodontal Ligament', 'Vagina', 'Frontal Lobe', 'Breast', 'Bile Duct', 'Hair Follicle', 'Skin', 'Cardia', 'Ligament', 'Rectum', 'Caecum', 'Main Bronchus', 'Respiratory System', 'Embryonic Heart', 'Meninges', 'Brain', 'Alveolus', 'Intra-Abdominal Lymph Nodes', 'Uterus', 'Liver', 'Bone', 'Mesenchyme', 'Head and Neck', 'Heart Muscle', 'Embryo', 'Thyroid Gland', 'Cartilage', 'Abdominal Esophagus', 'Nervous System', 'Reproductive System', 'Intrathoracic Lymph Nodes', 'Peritoneum', 'Heart', 'Peripheral Blood Mononuclear Cell', 'Muscle', 'Prostate Gland', 'Mucosa', 'Connective and Soft Tissue', 'Larynx', 'Sclera', 'Unspecified', 'Nasal Cavity', 'Small Intestine', 'Endometrium', 'Esophagus', 'Tonsil', 'Gonad', 'Choroid', 'Sinonasal Tract', 'Lymph Nodes of Axilla or Arm', 'Pelvic Lymph Nodes', 'Oral Cavity', 'Colon', 'Lymph', 'Ascending Colon', 'Bladder', 'Spleen', 'Umbilical Cord', 'Peripheral Nerves', 'Lymph Nodes of Inguinal Region or Leg', 'Vein', 'Pancreas', 'Oral Mucosa', 'Bone Marrow', 'Cornea', 'Tendon', '']",Biospecimen +Biospecimen Composition,Biospecimen Composition,BiospecimenComposition,"The text term used to describe the type(s) of tissue contained in the biospecimen. Multiple values permitted, comma separated.",False,,Biospecimen +Preservation Method,Preservation Method,PreservationMethod,Text term that represents the method used to preserve the sample.,False,"['Cryopreservation in liquid nitrogen - live cells', 'Frozen', 'Liquid Nitrogen', 'Fresh dissociated and single cell sorted', 'unknown', 'Cryopreservation in dry ice - dead tissue', 'Fresh dissociated', 'Snap Frozen', 'Fresh', 'Cryopreserved', 'Cryopreservation in liquid nitrogen - dead tissue', 'Formalin fixed paraffin embedded - FFPE', 'Formalin fixed-buffered', 'Fresh dissociated and single cell sorted into plates', 'Negative 80 Deg C', 'Methacarn fixed paraffin embedded - MFPE', 'Not Reported', 'Formalin fixed-unbuffered', 'Fresh dissociated and single cell sorted into plates in NP40 buffer', 'OCT', '']",Biospecimen +Site of Origin,Site of Origin,SiteofOrigin,"The text term used to describe the anatomic site of origin, of the patient's malignant disease.",False,"['Artery', 'Trachea', 'Tongue', 'Intestine', 'Lymphoid Tissue', 'Blood', 'Eye', 'Gastroesophageal Junction', 'Cervix Uteri', 'Lymphatic System', 'Endocervix', 'Thymus', 'Omentum', 'Olfactory Mucosa', 'Adrenal Gland', 'Kidney', 'Ovary', 'Vascular Endothelium', 'Placenta', 'Pending Annotation', 'Epithelium', 'Salivary Gland', 'Lung', 'Ear', 'Hippocampus', 'Pituitary Gland', 'Duodenum', 'Lymph Node', 'Pharynx', 'Foreskin', 'Adipose Tissue', 'Hematopoietic System', 'Genitourinary', 'Synovial Membrane', 'Not Applicable', 'Fallopian Tube', 'Aorta', 'Vertebra', 'Blood Vessel', 'Spinal Cord', 'Stomach', 'Cancer-Associated Fibroblast', 'Endothelium', 'Testis', 'Mammary Gland', 'Pleura', 'Gastrointestinal Tract', 'Joint', 'Periodontal Ligament', 'Vagina', 'Frontal Lobe', 'Breast', 'Bile Duct', 'Hair Follicle', 'Skin', 'Cardia', 'Ligament', 'Rectum', 'Caecum', 'Main Bronchus', 'Respiratory System', 'Embryonic Heart', 'Meninges', 'Brain', 'Alveolus', 'Intra-Abdominal Lymph Nodes', 'Uterus', 'Liver', 'Bone', 'Mesenchyme', 'Head and Neck', 'Heart Muscle', 'Embryo', 'Thyroid Gland', 'Cartilage', 'Abdominal Esophagus', 'Nervous System', 'Reproductive System', 'Intrathoracic Lymph Nodes', 'Peritoneum', 'Heart', 'Peripheral Blood Mononuclear Cell', 'Muscle', 'Prostate Gland', 'Mucosa', 'Connective and Soft Tissue', 'Larynx', 'Sclera', 'Unspecified', 'Nasal Cavity', 'Small Intestine', 'Endometrium', 'Esophagus', 'Tonsil', 'Gonad', 'Choroid', 'Sinonasal Tract', 'Lymph Nodes of Axilla or Arm', 'Pelvic Lymph Nodes', 'Oral Cavity', 'Colon', 'Lymph', 'Ascending Colon', 'Bladder', 'Spleen', 'Umbilical Cord', 'Peripheral Nerves', 'Lymph Nodes of Inguinal Region or Leg', 'Vein', 'Pancreas', 'Oral Mucosa', 'Bone Marrow', 'Cornea', 'Tendon', '']",Biospecimen +Sex,Sex,Sex,Biological sex associated with the specimen donor,False,"['Other', 'M', 'unknown', 'F', '']",Biospecimen +Study Investigator,Study Investigator,StudyInvestigator,Investigator(s) associated with the project. Multiple names should be provided as a comma-separated list.,True,,Study +PersonView Key,PersonView Key,PersonViewKey,"Unique PersonView_id foreign key(s) that group the resource with other components, as part of the same person-associated studies. Please provide multiple values as a comma-separated list.",False,,Study +GrantView Key,GrantView Key,GrantViewKey,"Unique GrantView_id foreign key(s) that group the resource with other components, as part of the same grant-associated collection. Please provide multiple values as a comma-separated list.",False,,Study +ProjectView Key,ProjectView Key,ProjectViewKey,"Unique ProjectView_id foreign key(s) that group the resource with other components, as part of the same grant-associated studies. Please provide multiple values as a comma-separated list.",False,,Study +Study_id,Study_id,StudyId,A unique primary key that enables record updates using schematic.,True,,Study +Component,Component,Component,"Category of metadata (e.g. Tools, Publications, etc.); provide the same one for all items/rows.",True,,Study +Study Name,Study Name,StudyName,Name of the study,True,,Study +Study Reuse Statement,Study Reuse Statement,StudyReuseStatement,"The funder-, contributor-, patient-, etc., derived content that includes terms, conditions, or statements associated with accessing and reusing the resource(s).",False,,Study +Study Description,Study Description,StudyDescription,"Description of the study, including the types of experimental assays, model systems, types of analysis, etc.",True,,Study +Grant Theme Name,Grant Theme Name,GrantThemeName,Theme(s) associated with the grant. 1...*,True,,GrantView +Embargo End Date,Embargo End Date,EmbargoEndDate,Date at which an embargo on related resources had lifted,False,,GrantView +NIH RePORTER Link,NIH RePORTER Link,NIHRePORTERLink,Link to the search results for this grant number on the NIH Reporter website,True,,GrantView +Duration of Funding,Duration of Funding,DurationofFunding,"Duration of the funding period, in years",False,,GrantView +Grant Name,Grant Name,GrantName,Name of the grant,True,,GrantView +Grant Institution Name,Grant Institution Name,GrantInstitutionName,The full name of the institution(s) associated with the grant. (e.g. Harvard University). 1...*,True,,GrantView +Grant Number,Grant Number,GrantNumber,"Number of the grant (i.e. ""CA------"" format)",True,,GrantView +Grant Type,Grant Type,GrantType,Type of grant,True,"['R21', 'R37', 'U54', 'R01', 'U01', 'U24']",GrantView +Grant Synapse Team,Grant Synapse Team,GrantSynapseTeam,"The Synapse team associated with the grant, created by the MC2 Center",False,,GrantView +Grant Abstract,Grant Abstract,GrantAbstract,Abstract for the grant,True,,GrantView +Component,Component,Component,"Category of metadata (e.g. Tools, Publications, etc.); provide the same one for all items/rows.",True,,GrantView +Grant Institution Alias,Grant Institution Alias,GrantInstitutionAlias,The alias of the institution(s) associated with the grant (e.g. UCSD). 1...*,True,,GrantView +Grant Consortium Name,Grant Consortium Name,GrantConsortiumName,Consortium(s) associated with the grant. 1...1,True,"['CCBIR', 'CSBC', 'PS-ON', 'TEC', 'PDMC', 'Sage Bionetworks', 'ICBP', 'MetNet', 'NCI Clinical and Translational Exploratory/Developmental Studies', 'HTAN', 'NCI']",GrantView +Grant Investigator,Grant Investigator,GrantInvestigator,Investigator(s) associated witht the grant. 1...*,True,,GrantView +Grant Start Date,Grant Start Date,GrantStartDate,The start date of the grant YYYY-MM-DD format,True,,GrantView +Grant Synapse Project,Grant Synapse Project,GrantSynapseProject,"The Synapse project associated with the grant, created by the MC2 Center",False,,GrantView +GrantView_id,GrantView_id,GrantViewId,A unique primary key that enables record updates using schematic.,True,,GrantView +File Description,File Description,FileDescription,Description of the file.,False,,FileView +File Species,File Species,FileSpecies,"The species the data was collected on. Multiple values permitted, comma separated.",True,,FileView +Biospecimen Key,Biospecimen Key,BiospecimenKey,Unique Biospecimen_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list.,False,,FileView +FileView_id,FileView_id,FileViewId,A unique primary key that enables record updates using schematic.,True,,FileView +DatasetView Key,DatasetView Key,DatasetViewKey,Unique DatasetView_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list.,False,,FileView +Data Use Codes,Data Use Codes,DataUseCodes,"DUO code - A data item that is used to indicate consent permissions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used.",False,,FileView +File Assay,File Assay,FileAssay,The assay the file is representative of.,True,"['Deep Mutational Scanning', 'Multiplexed Immunofluorescence', 'Micropipette Aspiration', 'Electron Diffraction', 'QFISH', 'Multi-Angle Light Scattering', 'Gene Silencing', 'Whole Exome Sequencing', 'Vibrational Spectroscopy', 'Bioluminescence Imaging', 'Confocal Reflectance Quantitative Phase Microscopy', 'Global Chromatin Profiling', 'Comparative Genomic Hybridization', 'Hydrophilic Interaction Chromatography', 'Intravital Microscopy', 'siRNA', 'SDS-PAGE', 'In Situ Hybridization', 'Allograft', 'PlateSeq', 'Surveyor Nuclease Assay', 'Computed Tomography', 'Not Applicable', 'ImmunoFISH', 'Gas Chromatography Mass Spectrometry', 'Wound-Healing Assay', 'Magnetic Tweezers', 'Antitumor Drug Screening Assay', 'Virus Plaque Assay', 'TUNEL assay', 'Barcode-Seq', 'Optogenetic Assay', 'Forster Resonance Energy Transfer', 'Cell Adhesion Assay', 'Enzyme Activity Assay', 'Cytometric Bead Array Assay', 'Optical Stretcher', 'Plasmid Construction', 'Dynamic Contrast-Enhanced Magnetic Resonance Imaging', 'DNA Gene-Expression Microarray', 'High Throughput Screening', 'Synthesis', 'Tiling Array', 'Modeling', 'Bioelectrochemical Analysis', 'Mint-ChIP', 'Magnetic Twisting Cytometry', 'Phylogenetic Analysis', 'DBiT-Seq', 'Scanning Angle Interference Microscopy', 'Reverse-Phase High-Performance liquid Chromatography', '3C', 'Fluorescent Cell Barcoding', 'Fluorescence Activated Cell Sorting', 'Luciferase Reporter Assay', 'Field-Emission Scanning Electron Microscopy', 'Single-Molecule Localization Microscopy', 'Circular Dichroism Spectroscopy', 'DNase-Seq', 'Gene Set Enrichment Analysis', 'TIRF Microscopy', 'Patient Derived Xenograft', 'Mammosphere Formation Assay', 'Fluorescence Imaging', 'Immunohistochemistry Staining Method', 'Computational Modeling', 'Target Engagement Assay', 'MeRIP-Seq', 'Reduced Representation Bisulfite Sequencing', 'NanoString Digital Spatial Profiling', 'Transwell Assay', 'Reverse Phase Protein Array', 'ATAC-Seq', 'Whole Genome Sequencing', 'Suspended Microchannel Resonator', 'Cell Cycle Assay', 'Small-Angle X-ray Scattering', 'cDNA Array', 'RAS Protein Family Activation Assay', 'Tissue Microarray', 'Differential Scanning Fluorimetry', 'Computational Tool', 'Autoradiography', 'Surface Plasmon Resonance', 'Global Run-On Sequencing', 'Southern Blotting', 'Gene Ontology Enrichment Analysis', 'Unspecified', 'Von Kossa Staining', 'Electron Paramagnetic Resonance Spectroscopy', 'Mass Cytometry', 'Nm-seq', 'Proteomics Assay', 'Nuclear Magnetic Resonance', 'Atomic Force Microscopy', 'Hi-C', 'Cell Viability Assay', 'Scratch Assay', 'Fluorescence Lifetime Imaging Microscopy', 'Fourier-Transform Infrared Spectroscopy', 'Single-Molecule Tracking', '16S Ribosomal Gene Sequencing Assay', '5C', 'Photolithography', 'Bio-Layer Interferometry', 'MEMA Cell Growth Assay', 'Luminescent Cell Viability Assay', 'Colorimetric Cell Viability Assay', 'Clonality Analysis', 'Nanopore Sequencing', 'RNA Sequencing', 'Western Blotting', 'Survival Analysis', 'Shotgun Mass Spectrometry', 'Paraquat Survival Assay', 'Tandem Mass Tagging', 'Optical Tweezers', 'Microscopy', 'Deep Learning', 'Picrosirius Staining', 'Phagocytosis Assay', 'Nanopatterning', 'Transmission Electron Microscopy', 'Clinical Study', 'mRNA Sequencing', 'Thin-Layer Chromatography', 'Lattice Light Sheet Microscopy', 'Visium Spatial Gene Expression', 'Co-culture Assay', 'Imaging Mass Cytometry', 'eCLIP-Seq', 'Inductively-Coupled Plasma Mass Spectrometry', 'MicroRNA Expression Array', 'Nested PCR', 'Differential Interference Contrast Microscopy', 'Metabolite Profiling Assay', 'scSLAM-seq', 'DRIP-seq', 'Traction Force Microscopy', 'Quantitative Multiplex Immunofluorescence', 'Atomic Absorption Spectrophotometry', 'Stimulated Raman Scattering', 'qPCR', 'X-Ray Micro-Computed Tomography', 'Angiogenesis Assay', 'Optical Mapping', 'PET-CT', 'Artificial Intelligence', 'ChIP-qPCR assay', 'Bicinchoninic Acid Assay', 'MULTI-Seq', 'Immobilized Metal Affinity Chromatography', 'Microfluidics', 'Dye Endocytosis Assay', 'L1000 mRNA Profiling Assay', 'Fourier Transform Ion Cyclotron Resonance Mass Spectrometry', 'MicroRNA Sequencing', 'Tandem Mass Spectrometry', 'Immunofluorescent Staining Method', 'Image Cytometry', 'ChIP-Seq', 'Cell-spreading Assay', 'Scanning Electron Microscopy', '10x Multiome', 'Soft Agar Assay', 'Second-Harmonic Imaging Microscopy', 'Dideoxy Chain Termination DNA Sequencing', 'CRISPR', 'X-Ray Diffraction', 'Tissue Engineering', 'Next Generation Sequencing', 'Multiplexed Ion Beam Imaging', 'Fluorescence Correlation Spectroscopy', 'Hydrogels', 'Statistical Modeling', 'DNA Sequencing', 'Methylation-Specific PCR', 'High-Content Screen', 'Single Nucleus RNA-Sequencing', 'Methyl Binding Domain Sequencing', 'HL-Chip', 'ChIA-PET', 'Optical Coherence Tomography', 'Epidemiological Method', 'Nano-hmC-Seal', 'Ribosomal P Protein Antibody Measurement', 'UV Photocrosslinking', 'Targeted Transcriptome Sequencing', 'In Vivo Bioluminescence', 'Isothermal Titration Calorimetry', 'Immunoprecipitation', 'Gelatin Zymography', 'Synthetic Genetic Array', '3C-qPCR', 'Binding Assay', 'Fluorescent In Situ Sequencing', 'Chimeric Antigen Receptor T-Cell Therapy', 'Murine Model', 'Immunoassay', 'Flow Cytometry', 'ATP Bioluminescence Assay', 'Drop-Seq', 'Magnetic Resonance Imaging', 'Permeability Assay', 'Stochastic Optical Reconstruction Microscopy', 'Thermal Shift Assay', 'Affinity Purification Mass Spectrometry', 'Dynamic Light Scattering', 'Single Cell Gel Electrophoresis', 'Knife-Edge Scanning Microscopy', 'RIP-Seq', 'RT-PCR', 'Pending Annotation', 'Magnetically Activated Cell Sorting', 'Raman Spectroscopy', 'CUT&RUN', 'Dynamic Susceptibility Contrast-Enhanced Magnetic Resonance Imaging', 'Data Integration', '3D Cell Culture', 'Cerenkov Luminescence Imaging', 'Cell Proliferation Assay', 'Targeted Error Correction Sequencing', 'Fluorescence Recovery After Photo-Bleaching', 'TCR Sequencing', 'Immunocytochemistry', 'Cross-Linking Immunoprecipitation High-throughput Sequencing', 'Chemotaxis Assay', 'Microcontact Printing', 'Quantitative Point Accumulation for Imaging in Nanoscale Topography', 'RNAi Screen', 'UPLC-MSMS', 'scCGI-seq', 'Spectroscopy', 'Electrospray Ionization Time-of-Flight Mass Spectrometry', 'Diffusion Weighted Imaging', 'Immunotherapy', '3D Bioprinting', 'In Vitro Selection', 'Time-Correlated Single Photon Counting', 'Dark Field Microscopy', 'Direct Long-Read RNA Sequencing', 'Hematoxylin and Eosin Staining Method', 'Cell Fractionation', 'FAIRE-Seq', 'Tuba-Seq', 'Brightfield Microscopy', 'In Vitro Cell Killing Assay', 'Brillouin Microscopy', 'smFISH', 'Imaging', 'Chemiluminescent Assay', 'Fluorescent Antibody Procedure', 'Liquid Chromatography Mass Spectrometry', 'Organoid', 'Electron Microscopy', 'TRAP Staining', 'Monolayer Stress Microscopy', 'Xenograft', 'Questionnaire', 'Cryo-Electron Tomography', ""3' RNA-seq"", 'Targeted Therapy Agent', 'HiChIP', 'Micropipette Adhesion Assay', 'TAB-Seq', 'CITE-seq', 'Ultrasound Imaging', 'Photoacoustic Imaging', 'Label-free Protein Quantification by LC/MS', 'Precision Run-On Sequencing', 'Metastatic Colonization Assay', 'Cell Culture', 'Desorption Electrospray Ionization', 'Atomic Absorption Spectroscopy', 'Size Exclusion Chromatography', 'Total Internal Reflection Fluorescence Microscopy', 'Migration Assay', 'Co-Immunoprecipitation', 'FISH', 'Karyotyping', 'Collision-Induced Dissociation', 'Viral Transduction', 'Multiplexed Error-Robust Fluorescence In Situ Hybridization', 'Cyclic Immunofluorescence', 'Micro-computed Tomography', 'Single Cell ATAC-Seq', 'Invasion Assay', 'RIP', 'Positron Emission Tomography', 'Dual-Luciferase Reporter Assay', 'Low-Vacuum Scanning Electron Microscopy', 'Multi-Isotope Mass Spectrometry', 'Transcription profiling by NanoString', 'Stimulated Emission Depletion Microscopy', 'Co-Immunoprecipitation Mass Spectrometry', 'DNA Methylation Array', 'Targeted Genome Sequencing', 'Mass Spectrometry', 'Point Accumulation for Imaging in Nanoscale Topography', 'Reporter Gene Assay', 'Multiscale Light Sheet Microscopy', 'Partial Wave Spectroscopy', 'HPLC-MSMS', 'Molecular Simulations', 'Cytokine Expression Profile', 'Rheometry', 'Cell-free Circulating Tumor DNA Assay', 'Multiphoton Microscopy', 'scNT-Seq', 'Genotyping', 'Trichrome Staining Method', 'Dynamic Force Spectroscopy', 'Human Induced Pluripotent Stem Cell-derived Cardiomyocytes Culture', 'CASFISH', 'Structural Variant Analysis', 'CLIP-qPCR', 'Cryo-Electron Microscopy', 'Bisulfite Sequencing', 'Single-Cell BCR Sequencing', '4C', 'Cross-Linking Mass Spectrometry', 'Multiparametric Magnetic Resonance Imaging', 'Multiplexed Immunohistochemistry', 'Interference Reflection Microscopy', 'Widefield Fluorescence Microscopy', 'MeDIP', 'Single-Cell TCR Sequencing', 'In Vitro Model', 'Amplicon Sequencing', 'Single-Cell Barcode Chip', 'Whole Genome Bisulfite Sequencing', 'CellTiter-Glo Luminescent Cell Viability Assay', 'Liquid Chromatography/Tandem Mass Spectrometry', 'Nanowire', 'RT-qPCR', 'Proximity Ligation Assay', 'CUT&Tag-Sequencing', 'Enzyme-Linked Immunospot Assay', 'MNase-Seq', 'Endotoxin Assay', 'PCR', 'Sirius Red Staining', 'Time Lapse Microscopy', 'Alcian Blue Staining Method', 'Ribo-Seq', 'Graphite Furnace Atomic Absorption Spectrometry', 'Electrophoretic Mobility Shift Assay', 'seqFISH', 'Optical Emission Spectroscopy', 'In-Cell Western Assay', 'Droplet Digital PCR', 'Pull-Down Assay', 'In Vitro Translation', 'Focused Ion Beam Scanning Electron Microscopy', 'Single Molecule Forster Resonance Energy Transfer', 'Single Cell RNA-Sequencing', 'Efferocytosis Assay', 'Synaptophysin Staining Method', 'Apoptosis Assay', 'snRNA-seq', 'shRNA', 'Confocal Microscopy', 'X-Ray Crystallography', 'Energy-Dispersive X-Ray Spectroscopy', 'Mathematical Modeling', 'Single Cell Cytokine Detection Chip Assay', 'Single Cell DNA Sequencing', 'Macrophage Polarization Assay', 'smRNA-seq', '10-cell RNA Sequencing', 'Fluorescence Microscopy', 'ELISA', 'MALDI-TOF Mass Spectrometry', 'ChIP-PCR', 'Super-Resolution Microscopy', 'Single Nucleotide Polymorphism Array', 'Cytochemical Stain', 'Cytotoxicity Assay']",FileView +File Design,File Design,FileDesign,The overall design of the dataset or file.,False,,FileView +File Alias,File Alias,FileAlias,"Alias of the file. Must be unique. Can be the GEO identifier such as GSE12345, or a DOI. No Greek Letters.",True,,FileView +File Tumor Type,File Tumor Type,FileTumorType,"The tumor type(s), if applicable, of the data collected. Multiple values permitted, comma separated.",False,,FileView +File Level,File Level,FileLevel,The processing level the file can be mapped to.,True,"['Level 3', 'Level 1', 'Auxilliary', 'Not Applicable', 'Level 4', 'Level 2']",FileView +Filename,Filename,Filename,Name of a file,True,,FileView +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,FileView +Component,Component,Component,"Category of metadata (e.g. Tools, Publications, etc.); provide the same one for all items/rows.",True,,FileView +Study Key,Study Key,StudyKey,"The unique Study_id foreign keys associated with the resource, found in the grant Study information. Used to group the resource with other components. Please provide multiple values as a comma-separated list.",False,,FileView +File Tissue,File Tissue,FileTissue,"Tissue type(s) associated with the file. Multiple values permitted, comma separated.",False,,FileView +File Url,File Url,FileUrl,The url of where the file is stored.,True,,FileView +Biospecimen Key,Biospecimen Key,BiospecimenKey,Unique Biospecimen_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list.,False,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles +Slide ID,Slide ID,SlideID,"For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide.",True,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles +Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles +VisiumRNALevel3 Key,VisiumRNALevel3 Key,VisiumRNALevel3Key,Unique VisiumRNALevel3_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,False,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles +Visium File Type,Visium File Type,VisiumFileType,The file type generated for the visium experiment.,True,"['json scale factors', 'probe dataset csv', 'features', 'high res image', 'fiducial image jpg', 'reference png', 'detected jpg', 'low res image', 'filtered mex', 'detected image png', 'reference jpg', 'barcodes', 'qc result html', 'tissue_positions', 'fiducial image png', 'unfiltered mex']",10xVisiumSpatialTranscriptomics-AuxiliaryFiles +VisiumRNALevel2 Key,VisiumRNALevel2 Key,VisiumRNALevel2Key,Unique VisiumRNALevel2_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,False,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles +VisiumAux_id,VisiumAux_id,VisiumAuxId,"Unique row identifier, used as a primary key for record updates",True,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles +Capture Area,Capture Area,CaptureArea,"Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.",False,"['D', 'A', 'D1', 'B1', 'A1', 'C1', 'C', 'B', '']",10xVisiumSpatialTranscriptomics-AuxiliaryFiles +VisiumRNALevel4 Key,VisiumRNALevel4 Key,VisiumRNALevel4Key,Unique VisiumRNALevel4_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,False,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles +Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. URL,False,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles +Component,Component,Component,"Category of metadata (e.g. Tools, Publications, etc.); provide the same one for all items/rows.",True,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles +VisiumRNALevel1 Key,VisiumRNALevel1 Key,VisiumRNALevel1Key,Unique VisiumRNALevel1_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,False,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles +Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),False,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles +Filename,Filename,Filename,Name of a file,True,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles +Permeabilization Time,Permeabilization Time,PermeabilizationTime,Fixed and stained tissue sections are permeabilized for different times. Each Capture Area captures polyadenylated mRNA from the attached tissue section. Measure is provided in minutes.,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Spatial Read1,Spatial Read1,SpatialRead1,Read 1 content description,True,"['Spatial Barcode and UMI', 'cDNA']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Slide Version,Slide Version,SlideVersion,Version of imaging slide used. Slide version is critical for the analysis of the sequencing data as different slides have different capture area layouts.,True,"['V3', 'V1', 'V4', 'V2']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Spatial Read2,Spatial Read2,SpatialRead2,Read 2 content description,True,"['Spatial Barcode and UMI', 'cDNA']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Component,Component,Component,"Category of metadata (e.g. Tools, Publications, etc.); provide the same one for all items/rows.",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Spatial Library Construction Method,Spatial Library Construction Method,SpatialLibraryConstructionMethod,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],True,"['Smart-seq2', '10xV1.1', 'Drop-seq', 'inDropsV3', 'TruDrop', 'inDropsV2', '10xV1.0', '10xV3', 'Nextera XT', 'Smart-SeqV4', '10xV2', '10xV3.1']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Biospecimen Key,Biospecimen Key,BiospecimenKey,Unique Biospecimen_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list.,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +File Alias,File Alias,FileAlias,"Alias of the file. Must be unique. Can be the GEO identifier such as GSE12345, or a DOI. No Greek Letters.",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable',False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Sequencing Library Construction Days from Index,Sequencing Library Construction Days from Index,SequencingLibraryConstructionDaysfromIndex,Number of days between sample for assay was received in lab and day of sequencing library construction [number]. If not applicable please enter 'Not Applicable',True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,"['R2', 'R1', 'R1&R2', 'I1', 'Other']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +VisiumRNALevel1_id,VisiumRNALevel1_id,VisiumRNALevel1Id,"Unique row identifier, used as a primary key for record updates",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Slide ID,Slide ID,SlideID,"For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide.",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +DV200,DV200,DV200,Represents the percentage of RNA fragments that are >200 nucleotides in size. Number,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +End Bias,End Bias,EndBias,"The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript",True,"['3 Prime', 'Full Length Transcript', '5 Prime']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +RIN,RIN,RIN,A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products. Number,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Filename,Filename,Filename,Name of a file,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Reverse Transcription Primer,Reverse Transcription Primer,ReverseTranscriptionPrimer,"An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA",True,"['Oligo-dT', 'Random', 'Feature barcoding', 'Poly-dT']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,"['Illumina NextSeq', 'Illumina Genome Analyzer II', 'Illumina HiSeq X Ten', 'PacBio RS', 'GridION', 'Revio', 'Other', 'Illumina Next Seq 500', 'Illumina Genome Analyzer IIx', 'Illumina Next Seq 550', 'unknown', 'NovaSeq 6000', 'Illumina HiSeq 4000', 'Ion Torrent Proton', 'AB SOLiD 2', 'Complete Genomics', 'NovaSeqS4', 'Ion Torrent S5', 'Illumina HiSeq 2000', 'Illumina NextSeq 1000', 'Illumina HiSeq 2500', 'Illumina Next Seq 2500', 'Ultima Genomics UG100', 'Illumina MiSeq', 'PacBio Sequel2', 'Not Reported', 'Illumina NovaSeq 6000', 'AB SOLiD 3', 'Oxford Nanopore minION', 'Illumina HiSeq X Five', '454 GS FLX Titanium', 'Ion Torrent PGM', 'Illumina NextSeq 2000', 'AB SOLiD 4', 'PromethION']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Capture Area,Capture Area,CaptureArea,"Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.",False,"['D', 'A', 'D1', 'B1', 'A1', 'C1', 'C', 'B', '']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Image Re-orientation,Image Re-orientation,ImageRe-orientation,"To ensure good fiducial alignment and tissue spots detection, it is important to correct for this shift in orientation.",False,"['False', 'True', '']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Whitelist Spatial Barcode File Link,Whitelist Spatial Barcode File Link,WhitelistSpatialBarcodeFileLink,Link to file listing all possible spatial barcodes. URL,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence; ftp or reference URL will be accepted.,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +Component,Component,Component,"Category of metadata (e.g. Tools, Publications, etc.); provide the same one for all items/rows.",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +Spatial Barcode Tag,Spatial Barcode Tag,SpatialBarcodeTag,"SAM tag for spot barcode field; please provide a valid tag-type pair, consisting of a tag (e.g. CB or CR) and type (e.g. Z) separated by a colon.",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +Biospecimen Key,Biospecimen Key,BiospecimenKey,Unique Biospecimen_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list.,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +File Alias,File Alias,FileAlias,"Alias of the file. Must be unique. Can be the GEO identifier such as GSE12345, or a DOI. No Greek Letters.",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +Checksum,Checksum,Checksum,TBD,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +VisiumRNALevel1 Key,VisiumRNALevel1 Key,VisiumRNALevel1Key,Unique VisiumRNALevel1_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +VisiumRNALevel2_id,VisiumRNALevel2_id,VisiumRNALevel2Id,"Unique row identifier, used as a primary key for record updates",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +UMI Tag,UMI Tag,UMITag,"SAM tag for the UMI field; please provide a valid tag-type pair, consisting of a tag (e.g. UB or UR) and type (e.g. Z) separated by a colon.",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +Applied Hard Trimming,Applied Hard Trimming,AppliedHardTrimming,Was Hard Trimming applied,True,"['False', 'True']",10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. URL,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +Filename,Filename,Filename,Name of a file,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +Genome Annotation URL,Genome Annotation URL,GenomeAnnotationURL,Link to the human genome annotation (GTF) file; ftp or reference URL will be accepted.,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +Capture Area,Capture Area,CaptureArea,"Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.",False,"['D', 'A', 'D1', 'B1', 'A1', 'C1', 'C', 'B', '']",10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +Mean Reads per Spatial Spot,Mean Reads per Spatial Spot,MeanReadsperSpatialSpot,"The number of reads, both under and outside of tissue, divided by the number of barcodes associated with a spot under tissue.",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +VisiumRNALevel3_id,VisiumRNALevel3_id,VisiumRNALevel3Id,"Unique row identifier, used as a primary key for record updates",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +Sequencing Saturation,Sequencing Saturation,SequencingSaturation,"The fraction of reads originating from an already-observed UMI. This is a function of library complexity and sequencing depth. More specifically, this is the fraction of confidently mapped, valid spot-barcode, valid UMI reads that had a non-unique (spot-barcode, UMI, gene).",False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +Spots under tissue,Spots under tissue,Spotsundertissue,The number of barcodes associated with a spot under tissue.,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +Visium File Type,Visium File Type,VisiumFileType,The file type generated for the visium experiment.,True,"['json scale factors', 'probe dataset csv', 'features', 'high res image', 'fiducial image jpg', 'reference png', 'detected jpg', 'low res image', 'filtered mex', 'detected image png', 'reference jpg', 'barcodes', 'qc result html', 'tissue_positions', 'fiducial image png', 'unfiltered mex']",10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +Component,Component,Component,"Category of metadata (e.g. Tools, Publications, etc.); provide the same one for all items/rows.",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +Biospecimen Key,Biospecimen Key,BiospecimenKey,Unique Biospecimen_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list.,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +VisiumAux Key,VisiumAux Key,VisiumAuxKey,Unique VisiumAux_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +File Alias,File Alias,FileAlias,"Alias of the file. Must be unique. Can be the GEO identifier such as GSE12345, or a DOI. No Greek Letters.",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +Median UMI Counts per Spot,Median UMI Counts per Spot,MedianUMICountsperSpot,The median number of UMI counts per tissue covered spot.,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. URL,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +Proportion Reads Mapped to Transcriptome,Proportion Reads Mapped to Transcriptome,ProportionReadsMappedtoTranscriptome,Fraction of reads that mapped to a unique gene in the transcriptome. The read must be consistent with annotated splice junctions. These reads are considered for UMI counting.,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +Filename,Filename,Filename,Name of a file,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +Median Number Genes per Spatial Spot,Median Number Genes per Spatial Spot,MedianNumberGenesperSpatialSpot,The median number of genes detected per spot under tissue-associated barcode. Detection is defined as the presence of at least 1 UMI count.,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +VisiumRNALevel2 Key,VisiumRNALevel2 Key,VisiumRNALevel2Key,Unique VisiumRNALevel2_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +Capture Area,Capture Area,CaptureArea,"Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.",False,"['D', 'A', 'D1', 'B1', 'A1', 'C1', 'C', 'B', '']",10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +Biospecimen Key,Biospecimen Key,BiospecimenKey,Unique Biospecimen_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list.,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 +Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 +VisiumRNALevel3 Key,VisiumRNALevel3 Key,VisiumRNALevel3Key,Unique VisiumRNALevel3_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 +Visium Workflow Type,Visium Workflow Type,VisiumWorkflowType,Generic name for the workflow used to analyze the visium data set.,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 +Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. URL,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 +Component,Component,Component,"Category of metadata (e.g. Tools, Publications, etc.); provide the same one for all items/rows.",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 +VisiumRNALevel4_id,VisiumRNALevel4_id,VisiumRNALevel4Id,"Unique row identifier, used as a primary key for record updates",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 +Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 +Visium Workflow Parameters Description,Visium Workflow Parameters Description,VisiumWorkflowParametersDescription,Parameters used to run the workflow.,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 +Filename,Filename,Filename,Name of a file,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 diff --git a/files/Merged/deprecated/HTAN_attribute_table.csv b/files/Merged/deprecated/HTAN_attribute_table.csv new file mode 100644 index 0000000..f96ed55 --- /dev/null +++ b/files/Merged/deprecated/HTAN_attribute_table.csv @@ -0,0 +1,1194 @@ +,Attribute,Label,Description,Required,Cond_Req,Valid Values,Conditional Requirements,Component +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,Patient +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Patient +Days to Birth,Days to Birth,DaystoBirth,Number of days between the date used for index and the date from a person's date of birth represented as a calculated negative number of days.,False,,,,Demographics +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,Demographics +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Demographics +Weeks Gestation at Birth,Weeks Gestation at Birth,WeeksGestationatBirth,Numeric value used to describe the number of weeks starting from the approximate date of the biological mother's last menstrual period and ending with the birth of the patient.,False,,,,Demographics +Vital Status,Vital Status,VitalStatus,The survival state of the person registered on the protocol.,True,,"['Alive', 'Unknown', 'Dead', 'Not Reported']",,Demographics +Age Is Obfuscated,Age Is Obfuscated,AgeIsObfuscated,The age of the patient has been modified for compliance reasons. The actual age differs from what is reported. Other date intervals for this patient may also be modified.,False,,"['False', 'True', '']",,Demographics +Race,Race,Race,"An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation withina a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution.",True,,"['white', 'Not Reported', 'american indian or alaska native', 'asian', 'Other', 'Unknown', 'native hawaiian or other pacific islander', 'not allowed to collect', 'black or african american']",,Demographics +Occupation Duration Years,Occupation Duration Years,OccupationDurationYears,The number of years a patient worked in a specific occupation.,False,,,,Demographics +Year Of Birth,Year Of Birth,YearOfBirth,Numeric value to represent the calendar year in which an individual was born.,False,,,,Demographics +Gender,Gender,Gender,"Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.]",True,,"['Not Reported', 'unspecified', 'Unknown', 'female', 'male']",,Demographics +Premature At Birth,Premature At Birth,PrematureAtBirth,The yes/no/unknown indicator used to describe whether the patient was premature (less than 37 weeks gestation) at birth.,False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,Demographics +Ethnicity,Ethnicity,Ethnicity,"An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.",True,,"['Not Reported', 'Unknown', 'hispanic or latino', 'not hispanic or latino', 'not allowed to collect']",,Demographics +Country of Residence,Country of Residence,CountryofResidence,Country of Residence at enrollment,False,,"['Belize', 'Monaco', 'Bahrain', 'Iraq', 'South Africa', 'Vietnam', 'Niue', 'Poland', 'Albania', 'Burundi', 'Spain', 'Bhutan', 'Saudi Arabia', 'Madagascar', 'Gambia', 'Switzerland', 'Laos', 'Saint Lucia', 'Myanmar', 'Mayotte', 'Guadeloupe', 'South Korea', 'Tokelau', 'Syria', 'Pakistan', 'Isle of Man', 'Yemen', 'Svalbard & Jan Mayen Islands', 'Jersey', 'Bosnia and Herzegovina', 'Eritrea', 'Guinea', 'Philippines', 'Guinea-Bissau', 'Azerbaijan', 'Somalia', 'Sudan', 'Cambodia', 'Cuba', 'Rwanda', 'Tonga', 'Saint Kitts and Nevis', 'Finland', 'Paraguay', 'Malawi', 'Falkland Islands (Malvinas)', 'Federated States of Micronesia', 'Niger', 'Colombia', 'Democratic Republic of the Congo', 'North Macedonia', 'Haiti', 'Timor-Leste', 'Austria', 'Chad', 'Iceland', 'Dominica', 'Malta', 'Denmark', 'Kosovo', 'Martinique', 'Bangladesh', 'San Marino', 'South Sudan', 'Georgia', 'Nigeria', 'Gibraltar', 'Nauru', 'Tajikistan', 'Montserrat', 'Sweden', 'Antigua and Barbuda', 'Indonesia', 'Sri Lanka', 'Greece', 'Gabon', 'Japan', 'Mauritania', 'Nicaragua', 'China', 'Cape Verde', 'Grenada', 'French Polynesia', 'Moldova', 'Cayman Islands', 'Dominican Republic', 'Liechtenstein', 'Senegal', 'Holy See', 'Mali', 'Vanuatu', 'India', 'Bermuda', 'Netherlands', 'Ireland', 'Zambia', 'North Korea', 'Macau', 'Romania', 'Solomon Islands', 'Suriname', 'Nepal', 'Croatia', 'Reunion', 'Ghana', 'Saint Helena Ascension and Tristan da Cunha', 'Israel', 'Faroe Islands', 'Greenland', 'State of Palestine', 'Wallis and Futuna', 'Ecuador', 'French Guiana', 'Angola', 'Aruba', 'Guyana', 'Kuwait', 'Taiwan', 'Singapore', 'Togo', 'Andorra', 'Lebanon', 'Northern Mariana Islands', 'Armenia', 'Iran', 'New Zealand', 'Bolivia', 'Cameroon', 'Norway', 'Panama', 'Papua New Guinea', 'Qatar', 'Tanzania', 'Portugal', 'Slovakia', 'Equatorial Guinea', 'Estonia', 'Mongolia', 'Chile', 'Burkina Faso', 'Ethiopia', 'Hungary', 'Djibouti', 'Kenya', 'Kiribati', 'Botswana', 'Australia', 'Guam', 'Congo', 'Belarus', 'Uruguay', 'Czech Republic (Czechia)', 'Lesotho', 'United Kingdom', 'Lithuania', 'Russia', 'Thailand', 'Oman', 'Benin', 'Tunisia', 'Uganda', 'Namibia', 'Honduras', 'Algeria', 'Turkey', 'Morocco', 'Barbados', 'Sierra Leone', 'Venezuela', 'Saint Pierre and Miquelon', 'Kyrgyzstan', 'Trinidad and Tobago', 'Serbia', 'Peru', 'Comoros', 'Canada', 'Hong Kong', 'Liberia', 'Malaysia', 'Puerto Rico', 'Brazil', 'Virgin Islands British', 'Zimbabwe', 'Latvia', 'Eswatini', ""Cote d'Ivoire"", 'United Arab Emirates', 'Bahamas', 'Curacao', 'Slovenia', 'Central African Republic', 'Guatemala', 'Jordan', 'Egypt', 'Germany', 'Mozambique', 'Fiji', 'Turkmenistan', 'Mexico', 'Brunei', 'France', 'Kazakhstan', 'Argentina', 'Uzbekistan', 'Samoa', 'Bulgaria', 'Virgin Islands U.S.', 'Maldives', 'Cyprus', 'Costa Rica', 'Italy', 'Libya', 'Jamaica', 'Tuvalu', 'United States', 'Saint Vincent and the Grenadines', 'Palau', 'Western Sahara', 'Guernsey', 'Mauritius', 'El Salvador', 'Afghanistan', 'Belgium', 'Luxembourg', 'Ukraine', 'Marshall Islands', 'Montenegro', 'Cook Islands', 'Seychelles', 'Sao Tome and Principe', 'New Caledonia', 'Anguilla', '']",,Demographics +Year of Death,Year of Death,YearofDeath,Numeric value to represent the year of the death of an individual.,False,True,," If Vital Status is ""Dead"" then ""Year of Death"" is required",Demographics +Cause of Death Source,Cause of Death Source,CauseofDeathSource,The text term used to describe the source used to determine the patient's cause of death.,False,True,"['Medical Record', 'Not Reported', 'Unknown', 'Death Certificate', 'Autopsy', 'Social Security Death Index', '']"," If Vital Status is ""Dead"" then ""Cause of Death Source"" is required",Demographics +Cause of Death,Cause of Death,CauseofDeath,The cause of death,False,True,"['Cancer Related', 'Not Reported', 'Renal Disorder NOS', 'Not Applicable', 'Spinal Muscular Atrophy', 'End-stage Renal Disease', 'Not Cancer Related', 'Unknown', 'Infection', 'Surgical Complications', 'Cardiovascular Disorder NOS', 'Toxicity', '']"," If Vital Status is ""Dead"" then ""Cause of Death"" is required",Demographics +Days to Death,Days to Death,DaystoDeath,Number of days between the date used for index and the date from a person's date of death represented as a calculated number of days.,False,True,," If Vital Status is ""Dead"" then ""Days to Death"" is required",Demographics +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,FamilyHistory +Relative with Cancer History,Relative with Cancer History,RelativewithCancerHistory,The yes/no/unknown indicator used to describe whether any of the patient's relatives have a history of cancer.,False,,"['None', 'Yes - Cancer History Relative', 'Not Reported', 'Unknown', '']",,FamilyHistory +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,FamilyHistory +Relationship Gender,Relationship Gender,RelationshipGender,The text term used to describe the gender of the patient's relative with a history of cancer.,False,True,"['Not Reported', 'unspecified', 'Unknown', 'female', 'male', '']"," If Relative with Cancer History is ""Yes - Cancer History Relative"" then ""Relationship Gender"" is required",FamilyHistory +Relationship Type,Relationship Type,RelationshipType,The subgroup that describes the state of connectedness between members of the unit of society organized around kinship ties.,False,True,"['Unrelated', 'Adoptive Father', 'Stepdaughter', 'Foster Father', 'Cousin', 'Identical Twin Sibling', 'Domestic Partner', 'Natural Father', 'Identical Twin Brother', 'Parent', 'Paternal Aunt', 'Paternal Half Sister', 'Maternal Great Aunt', 'Fraternal Twin Brother', 'Adopted Son', 'Identical Twin Sister', 'Not Reported', 'Child', 'Maternal Great Grandparent', 'Step Sibling', 'Maternal Aunt', 'Paternal Grandfather', 'Maternal First Cousin', 'Stepson', 'Son-in-law', 'Fraternal Twin Sibling', 'Other', 'Wife', 'Foster Sister', 'Nephew', 'Paternal Grandmother', 'Adoptive Mother', 'Maternal Uncle', 'Natural Sibling', 'Grandson', 'Grandfather', 'Half Sibling', 'Spouse', 'Paternal First Cousin', 'Stepbrother', 'Natural Grandparent', 'Paternal First Cousin Once Removed', 'Unknown', 'Paternal Grandparent', 'Sibling', 'Stepfather', 'Grandmother', 'Maternal Half Sibling', 'Paternal Half Brother', 'Grand Nephew', 'Half Brother', 'Stepsister', 'Stepmother', 'Full Brother', 'Refused', 'Foster Brother', 'Fraternal Twin Sister', 'Natural Grandchild', 'Grandchild', 'Male Cousin', 'Uncle', 'Niece', 'Foster Son', 'First Cousin', 'Brother-in-law', 'Natural Parent', 'Husband', 'Paternal Uncle', 'First Cousin Once Removed', 'Granddaughter', 'Mother', 'Natural Child', 'Sister', 'Adoptive Sister', 'Paternal Great Grandparent', 'Niece Second Degree Relative', 'Son', 'Maternal Grandfather', 'Daughter-in-law', 'Half Sister', 'Natural Daughter', 'Paternal Great Uncle', 'Maternal Grandparent', 'Natural Son', 'Aunt', 'Maternal First Cousin Once Removed', 'Maternal Half Sister', 'Grandparent', 'Step Child', 'Natural Grandmother', 'Full Sister', 'Legal Guardian', 'Adopted Daughter', 'Natural Sister', 'Twin Sibling', 'Paternal Half Sibling', 'Sister-in-law', 'Natural Brother', 'Ward', 'Paternal Great Aunt', 'Father-in-law', 'Adoptive Brother', 'Female Cousin', 'Father', 'Natural Mother', 'Natural Grandfather', 'Grand Niece', 'Great Grandchild', 'Daughter', 'Maternal Grandmother', 'Brother', 'Foster Daughter', 'Maternal Great Uncle', 'Foster Mother', 'Maternal Half Brother', 'Mother-in-law', '']"," If Relative with Cancer History is ""Yes - Cancer History Relative"" then ""Relationship Type"" is required",FamilyHistory +Relationship Age at Diagnosis,Relationship Age at Diagnosis,RelationshipAgeatDiagnosis,The age (in years) when the patient's relative was first diagnosed.,False,True,," If Relative with Cancer History is ""Yes - Cancer History Relative"" then ""Relationship Age at Diagnosis"" is required",FamilyHistory +Relatives with Cancer History Count,Relatives with Cancer History Count,RelativeswithCancerHistoryCount,The number of relatives the patient has with a known history of cancer.,False,True,," If Relative with Cancer History is ""Yes - Cancer History Relative"" then ""Relatives with Cancer History Count"" is required",FamilyHistory +Relationship Primary Diagnosis,Relationship Primary Diagnosis,RelationshipPrimaryDiagnosis,The text term used to describe the malignant diagnosis of the patient's relative with a history of cancer.,False,True,"['Sarcoma', 'Lymphoma', 'Bladder Cancer', 'Tonsillar Cancer', 'Chondrosarcoma', 'Kaposi Sarcoma', 'Esophageal Cancer', 'Gynecologic Cancer', 'Uterine Cancer', 'Leukemia', 'Wilms Tumor', 'Lung Cancer', 'Liver Cancer', 'Osteosarcoma', 'Throat Cancer', 'Mesothelioma', 'Bone Cancer', 'Ewing Sarcoma', 'Melanoma', 'Head and Neck Cancer', 'Unknown', 'Blood Cancer', 'Kidney Cancer', 'Brain Cancer', 'Adrenal Gland Cancer', 'Glioblastoma', 'Skin Cancer', 'Not Reported', 'Cervical Cancer', 'Basal Cell Cancer', 'Tongue Cancer', 'Hematologic Cancer', 'Multiple Myeloma', 'Ovarian Cancer', 'Laryngeal Cancer', 'Breast Cancer', 'Rectal Cancer', 'Spleen Cancer', 'Rhabdomyosarcoma', 'Prostate Cancer', 'Pancreas Cancer', 'Bile Duct Cancer', 'Gallbladder Cancer', 'Testicular Cancer', 'CNS Cancer', 'Neuroblastoma', 'Thyroid Cancer', 'Lymph Node Cancer', 'Colorectal Cancer', 'Cancer', 'Gastric Cancer', '']"," If Relative with Cancer History is ""Yes - Cancer History Relative"" then ""Relationship Primary Diagnosis"" is required",FamilyHistory +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,Exposure +Coal Dust Exposure,Coal Dust Exposure,CoalDustExposure,The yes/no/unknown indicator used to describe whether a patient was exposed to fine powder derived by the crushing of coal.,False,,"['No', 'Unknown', 'Yes', '']",,Exposure +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Exposure +Radon Exposure,Radon Exposure,RadonExposure,The yes/no/unknown indicator used to describe whether the patient was exposed to radon.,False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,Exposure +Respirable Crystalline Silica Exposure,Respirable Crystalline Silica Exposure,RespirableCrystallineSilicaExposure,"The yes/no/unknown indicator used to describe whether a patient was exposured to respirable crystalline silica, a widespread, naturally occurring, crystalline metal oxide that consists of different forms including quartz, cristobalite, tridymite, tripoli, ganister, chert and novaculite.",False,,"['No', 'Unknown', 'Yes', '']",,Exposure +Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,Exposure +Alcohol Exposure,Alcohol Exposure,AlcoholExposure,Indicate if individual has alcohol exposure,True,,"['Not Reported', 'No - Alcohol Exposure', 'Yes - Alcohol Exposure']",,Exposure +Environmental Tobacco Smoke Exposure,Environmental Tobacco Smoke Exposure,EnvironmentalTobaccoSmokeExposure,"The yes/no/unknown indicator used to describe whether a patient was exposed to smoke that is emitted from burning tobacco, including cigarettes, pipes, and cigars. This includes tobacco smoke exhaled by smokers.",False,,"['No', 'Unknown', 'Yes', '']",,Exposure +Smoking Exposure,Smoking Exposure,SmokingExposure,Indicate if individual has smoking exposure,True,,"['No - Smoking Exposure', 'Not Reported', 'Yes - Smoking Exposure']",,Exposure +Asbestos Exposure,Asbestos Exposure,AsbestosExposure,The yes/no/unknown indicator used to describe whether the patient was exposed to asbestos.,False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,Exposure +Alcohol Drinks Per Day,Alcohol Drinks Per Day,AlcoholDrinksPerDay,Numeric value used to describe the average number of alcoholic beverages a person consumes per day.,False,True,," If Alcohol Exposure is ""Yes - Alcohol Exposure"" then ""Alcohol Drinks Per Day"" is required",Exposure +Alcohol Days Per Week,Alcohol Days Per Week,AlcoholDaysPerWeek,Numeric value used to describe the average number of days each week that a person consumes an alcoholic beverage.,False,True,," If Alcohol Exposure is ""Yes - Alcohol Exposure"" then ""Alcohol Days Per Week"" is required",Exposure +Alcohol Intensity,Alcohol Intensity,AlcoholIntensity,Category to describe the patient's current level of alcohol use as self-reported by the patient.,False,True,"['Non-Drinker', 'Not Reported', 'Unknown', 'Lifelong Non-Drinker', 'Occasional Drinker', 'Drinker', 'Heavy Drinker', '']"," If Alcohol Exposure is ""Yes - Alcohol Exposure"" then ""Alcohol Intensity"" is required",Exposure +Alcohol Type,Alcohol Type,AlcoholType,Type of alcohol use,False,True,"['Beer', 'Wine', 'Not Reported', 'Other', 'Unknown', 'Liquor', '']"," If Alcohol Exposure is ""Yes - Alcohol Exposure"" then ""Alcohol Type"" is required",Exposure +Alcohol History,Alcohol History,AlcoholHistory,A response to a question that asks whether the participant has consumed at least 12 drinks of any kind of alcoholic beverage in their lifetime.,False,True,"['No', 'Unknown', 'Not Reported', 'Yes', '']"," If Alcohol Exposure is ""Yes - Alcohol Exposure"" then ""Alcohol History"" is required",Exposure +Tobacco Smoking Quit Year,Tobacco Smoking Quit Year,TobaccoSmokingQuitYear,The year in which the participant quit smoking.,False,True,," If Smoking Exposure is ""Yes - Smoking Exposure"" then ""Tobacco Smoking Quit Year"" is required",Exposure +Smoking Frequency,Smoking Frequency,SmokingFrequency,The text term used to generally decribe how often the patient smokes.,False,True,"['Unknown', 'Some days', 'Every day', '']"," If Smoking Exposure is ""Yes - Smoking Exposure"" then ""Smoking Frequency"" is required",Exposure +Tobacco Smoking Status,Tobacco Smoking Status,TobaccoSmokingStatus,Category describing current smoking status and smoking history as self-reported by a patient,False,True,"['Smoking history not documented', 'Not Reported', 'Current Reformed Smoker for > 15 yrs', 'Unknown', 'Current Reformed Smoker for < or = 15 yrs', 'Lifelong Non-Smoker', 'Current Smoker', 'Duration Not Specified', 'Current Reformed Smoker', '']"," If Smoking Exposure is ""Yes - Smoking Exposure"" then ""Tobacco Smoking Status"" is required",Exposure +Tobacco Use per Day,Tobacco Use per Day,TobaccoUseperDay,Numeric value that represents the number of times the patient uses tobacco each day.,False,True,," If Smoking Exposure is ""Yes - Smoking Exposure"" then ""Tobacco Use per Day"" is required",Exposure +Type of Smoke Exposure,Type of Smoke Exposure,TypeofSmokeExposure,The text term used to describe the patient's specific type of smoke exposure.,False,True,"['Workrelated smoke artificial smoke machines', 'Workrelated smoke fire fighting', 'No Smoke Exposure', 'Workrelated smoke foundry', 'Volcanic smoke', 'Factory smokestack smoke', 'Field burning smoke', 'Hashish smoke', 'Grilling smoke', 'Accidental building fire smoke', 'Indoor wood burning stove or fireplace smoke', 'Oil burning smoke Kerosene', 'Workrelated smoke generators', 'Workrelated smoke paint baking', 'Accidental fire smoke NOS', 'Indoor coal burning stove or fireplace smoke', 'Tobacco smoke cigarettes', 'Workrelated smoke military', 'Tobacco smoke cigar', 'Unknown', 'Fire smoke NOS', 'Smokehouse smoke', 'Wood burning smoke factory', 'Accidental vehicle fire smoke', 'Aircraft smoke', 'Waste burning smoke', 'Wood burning smoke NOS', 'Machine smoke', 'Oil burning smoke NOS', 'Workrelated smoke plumbing', 'Coal smoke NOS', 'Tobacco smoke pipe', 'Furnace or boiler smoke', 'Accidental forest fire smoke', 'Marijuana smoke', 'Workrelated smoke plastics factory', 'Smoke exposure NOS', 'Gas burning smoke propane', 'Cooking related smoke NOS', 'Electrical fire smoke', 'Burning tree smoke', 'Indoor stove or fireplace smoke NOS', 'Electronic cigarette smoke NOS', 'Environmental tobacco smoke', 'Accidental grass fire smoke', 'Workrelated smoke soldering/welding', 'Recreational fire smoke', 'Workrelated smoke NOS', 'Grease fire smoke', '']"," If Smoking Exposure is ""Yes - Smoking Exposure"" then ""Type of Smoke Exposure"" is required",Exposure +Time between Waking and First Smoke,Time between Waking and First Smoke,TimebetweenWakingandFirstSmoke,TBD,False,True,," If Smoking Exposure is ""Yes - Smoking Exposure"" then ""Time between Waking and First Smoke"" is required",Exposure +Tobacco Smoking Onset Year,Tobacco Smoking Onset Year,TobaccoSmokingOnsetYear,The year in which the participant began smoking.,False,True,," If Smoking Exposure is ""Yes - Smoking Exposure"" then ""Tobacco Smoking Onset Year"" is required",Exposure +Cigarettes per Day,Cigarettes per Day,CigarettesperDay,The average number of cigarettes smoked per day.,False,True,," If Smoking Exposure is ""Yes - Smoking Exposure"" then ""Cigarettes per Day"" is required",Exposure +Years Smoked,Years Smoked,YearsSmoked,Numeric value (or unknown) to represent the number of years a person has been smoking.,False,True,," If Smoking Exposure is ""Yes - Smoking Exposure"" then ""Years Smoked"" is required",Exposure +Smokeless Tobacco Quit Age,Smokeless Tobacco Quit Age,SmokelessTobaccoQuitAge,Smokeless tobacco quit age,False,True,," If Smoking Exposure is ""Yes - Smoking Exposure"" then ""Smokeless Tobacco Quit Age"" is required",Exposure +Smoke Exposure Duration,Smoke Exposure Duration,SmokeExposureDuration,Text term used to describe the length of time the patient was exposed to an environmental factor.,False,True,"['Unknown', 'Not Reported', 'Six Weeks or More', '']"," If Smoking Exposure is ""Yes - Smoking Exposure"" then ""Smoke Exposure Duration"" is required",Exposure +Secondhand Smoke as Child,Secondhand Smoke as Child,SecondhandSmokeasChild,The text term used to indicate whether the patient was exposed to secondhand smoke as a child.,False,True,"['No', 'Unknown', 'Not Reported', 'Yes', '']"," If Smoking Exposure is ""Yes - Smoking Exposure"" then ""Secondhand Smoke as Child"" is required",Exposure +Type of Tobacco Used,Type of Tobacco Used,TypeofTobaccoUsed,The text term used to describe the specific type of tobacco used by the patient.,False,True,"['Cigar', 'Marijuana', 'Other', 'Cigarettes', 'Pipe', 'Smokeless Tobacco', 'Electronic Cigarette', '']"," If Smoking Exposure is ""Yes - Smoking Exposure"" then ""Type of Tobacco Used"" is required",Exposure +Pack Years Smoked,Pack Years Smoked,PackYearsSmoked,Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes smoked per day x number of years smoked divided by 20.,False,True,," If Smoking Exposure is ""Yes - Smoking Exposure"" then ""Pack Years Smoked"" is required",Exposure +Marijuana Use Per Week,Marijuana Use Per Week,MarijuanaUsePerWeek,Numeric value that represents the number of times the patient uses marijuana each day.,False,True,," If Type is ""Marijuana smoke"" then ""Marijuana Use Per Week"" is required",Exposure +Karnofsky Performance Status,Karnofsky Performance Status,KarnofskyPerformanceStatus,Text term used to describe the classification used of the functional capabilities of a person.,False,,"['100', '40', '30', '70', '90', '50', '60', '10', '20', '80', '0', '']",,FollowUp +Barretts Esophagus Goblet Cells Present,Barretts Esophagus Goblet Cells Present,BarrettsEsophagusGobletCellsPresent,TBD,False,,,,FollowUp +Imaging Result,Imaging Result,ImagingResult,The text term used to describe the result of the imaging or scan performed on the patient.,False,,"['Not Reported', 'Not Performed', 'Positive', 'Unknown', 'Indeterminate', 'Negative', '']",,FollowUp +Pregnancy Outcome,Pregnancy Outcome,PregnancyOutcome,The text term used to describe the type of pregnancy the patient had,False,,"['Induced Abortion', 'Ectopic Pregnancy', 'Not Reported', 'Miscarriage', 'Unknown', 'Live Birth', 'Stillbirth', '']",,FollowUp +Days to Follow Up,Days to Follow Up,DaystoFollowUp,Number of days between the date used for index and the date of the patient's last follow-up appointment or contact.,True,,,,FollowUp +Hysterectomy Type,Hysterectomy Type,HysterectomyType,The text term used to describe the type of hysterectomy the patient had.,False,,"['Not Reported', 'Radical Hysterectomy', 'Unknown', 'Simple Hysterectomy', 'Hysterectomy NOS', 'Not performed', '']",,FollowUp +Immunosuppressive Treatment Type,Immunosuppressive Treatment Type,ImmunosuppressiveTreatmentType,The text term used to describe the type of immunosuppresive treatment the patient received.,False,,"['Anti-TNFTherapy', 'None', 'Methotrexate', 'Not Reported', 'Azathioprine', 'Other', 'Unknown', 'Cyclophosphamide', '']",,FollowUp +CDC HIV Risk Factors,CDC HIV Risk Factors,CDCHIVRiskFactors,"The text term used to describe a risk factor for human immunodeficiency virus, as described by the Center for Disease Control.",False,,"['None', 'Homosexual Contact', 'Not Reported', 'Hemophiliac', 'Intravenous Drug User', 'Unknown', 'Transfusion Recipient', 'Heterosexual Contact', '']",,FollowUp +Adverse Event,Adverse Event,AdverseEvent,Text that represents the Common Terminology Criteria for Adverse Events low level term name for an adverse event.,False,,"['Intraoperative Ear Injury', 'Depression', 'Hiccups', 'Tumor Lysis Syndrome', 'Paroxysmal Atrial Tachycardia', 'Stridor', 'Hypoxia', 'Intestinal Stoma Obstruction', 'Pancreatic Anastomotic Leak', 'Urostomy Stenosis', 'Colonic Stenosis', 'Soft Tissue Necrosis Upper Limb', 'Pneumothorax', 'Encephalomyelitis Infection', 'Ischemia Cerebrovascular', 'Bladder Perforation', 'Intraoperative Arterial Injury', 'Disseminated Intravascular Coagulation', 'Venous Injury', 'Tooth Development Disorder', 'Back Pain', 'Hip Fracture', 'Injury', 'Intestinal Stoma Site Bleeding', 'Nipple Deformity', 'Cytokine Release Syndrome', 'Pulmonary Hypertension', 'Ovulation Pain', 'Fibrosis Deep Connective Tissue', 'Peritoneal Necrosis', 'Hemolytic Uremic Syndrome', 'Alkalosis', 'Proctitis', 'Urinary Tract Infection', 'Psychiatric Disorders Other', 'Infective Myositis', 'Prolapse of Intestinal Stoma', 'Facial Pain', 'Esophageal Perforation', 'Laryngeal Stenosis', 'Joint Infection', 'Pulmonary Fistula', 'Infusion Site Extravasation', 'Ileal Ulcer', 'Perineal Pain', 'Gastric Stenosis', 'Muscle Weakness Left-Sided', 'Platelet Count Decreased', 'Duodenal Ulcer', 'Malignant and Unspecified (Incl Cysts and Polyps) Other', 'Infections and Infestations Other', 'Peritoneal Infection', 'Mitral Valve Disease', 'Intraoperative Cardiac Injury', 'Upper Gastrointestinal Hemorrhage', 'Lymph Gland Infection', 'Breast Pain', 'Precocious Puberty', 'Bone Infection', 'Rectal Perforation', 'Biliary Tract Infection', 'Hirsutism', 'Testicular Disorder', 'Gastroparesis', 'Anorexia', 'Atrial Fibrillation', 'Extraocular Muscle Paresis', 'Erythroderma', 'Tumor Pain', 'Pericardial Effusion', 'Supraventricular Tachycardia', 'Congenital', 'Pharyngeal Stenosis', 'Bladder Spasm', 'Osteonecrosis of Jaw', 'Transient Ischemic Attacks', 'Anal Fistula', 'Palmar-Plantar Erythrodysesthesia Syndrome', 'Spermatic Cord Hemorrhage', 'Splenic Infection', 'Nausea', 'Kidney Infection', 'Unintended Pregnancy', 'Dysarthria', 'Rectal Anastomotic Leak', 'Mediastinal Infection', 'Skin Hyperpigmentation', 'Intraoperative Ocular Injury', 'Lung Infection', 'Vaginal Discharge', 'Rectal Fistula', 'Hemorrhoidal Hemorrhage', 'Thromboembolic Event', 'Large Intestinal Anastomotic Leak', 'Pleuritic Pain', 'Pulmonary Valve Disease', 'Dehydration', 'Diarrhea', 'Laryngeal Obstruction', 'Salivary Gland Infection', 'Uterine Fistula', 'Intraoperative Hepatobiliary Injury', 'Uterine Hemorrhage', 'Scrotal Infection', 'General Disorders and Administration Site Conditions Other', 'Seizure', 'Trismus', 'Hyperthyroidism', 'Radiation Recall Reaction (Dermatologic)', 'Neck Pain', 'Endocarditis Infective', 'Pharyngeal Fistula', 'Oral Dysesthesia', 'Urinary Frequency', 'Facial Muscle Weakness', 'Perforation Bile Duct', 'Scrotal Pain', 'Myocarditis', 'Rectal Stenosis', 'Endocrine Disorders Other', 'Eye Pain', 'Pharyngitis', 'Genital Edema', 'Spleen Disorder', 'Puerperium and Perinatal Conditions Other', 'Sneezing', 'External Ear Inflammation', 'Ileal Perforation', 'Edema Limbs', 'Death NOS', 'Renal and Urinary Disorders Other', 'Proteinuria', 'Unequal Limb Length', 'Alkaline Phosphatase Increased', 'Testicular Hemorrhage', 'Tracheal Mucositis', 'Dizziness', 'Pleural Effusion', 'Laryngeal Inflammation', 'Electrocardiogram QT Corrected Interval Prolonged', 'Azoospermia', 'Dysphagia', 'Ejection Fraction Decreased', 'Atrial Flutter', 'Telangiectasia', 'Prostate Infection', 'Vasculitis', 'Bronchial Fistula', 'Aortic Valve Disease', 'Papulopustular Rash', 'Oral Hemorrhage', 'Allergic Reaction', 'Bronchopulmonary Hemorrhage', 'Wheezing', 'Neck Edema', 'Right Ventricular Dysfunction', 'Stoma Site Infection', 'Neuralgia', 'Bile Duct Stenosis', 'Esophageal Obstruction', 'Cholesterol High', 'Gastric Hemorrhage', 'Vomiting', 'Joint Range of Motion Decreased Lumbar Spine', 'Gallbladder Infection', 'Chills', 'Eye Infection', 'Typhlitis', 'Meningismus', 'Laryngeal Fistula', 'Intraoperative Skin Injury', 'Dry Eye', 'Intraoperative Breast Injury', 'Arteritis Infective', 'Uterine Perforation', 'Feminization Acquired', 'Lymphocyte Count Increased', 'Alcohol Intolerance', 'Esophageal Necrosis', 'CD4 Lymphocytes Decreased', 'Esophagitis', 'Hypercalcemia', 'Nystagmus', 'Activated Partial Thromboplastin Time Prolonged', 'Lipohypertrophy', 'Vaginismus', 'Prolapse of Urostomy', 'Vitreous Hemorrhage', 'Vulval Infection', 'Erectile Dysfunction', 'Fibrinogen Decreased', 'Oculomotor Nerve Disorder', 'Irritability', 'Rectal Ulcer', 'Gastric Ulcer', 'Stenosis of Gastrointestinal Stoma', 'Otitis Externa', 'Febrile Neutropenia', 'Recurrent Laryngeal Nerve Palsy', 'Generalized Muscle Weakness', 'Skin Hypopigmentation', 'Glucose Intolerance', 'Pleural Infection', 'Growth Suppression', 'Lordosis', 'Creatinine Increased', 'Tracheal Stenosis', 'Hematuria', 'Lethargy', 'Hepatitis Viral', 'Hemorrhoids', 'Superficial Thrombophlebitis', 'Penile Pain', 'Tracheal Hemorrhage', 'Ventricular Arrhythmia', 'Hypertriglyceridemia', 'Cerebrospinal Fluid Leakage', 'Olfactory Nerve Disorder', 'Enterocolitis', 'Lactation Disorder', 'Mucosal Infection', 'Serum Amylase Increased', 'Growth Accelerated', 'Injection Site Reaction', 'Flatulence', 'Pancreatic Fistula', 'Optic Nerve Disorder', 'Rectal Mucositis', 'Phantom Pain', 'Urethral Infection', 'Skin Induration', 'Gallbladder Pain', 'Non-Cardiac Chest Pain', 'Movements Involuntary', 'Joint Range of Motion Decreased Cervical Spine', 'Enterovesical Fistula', 'Hepatobiliary Disorders Other', 'Purpura', 'Paresthesia', 'Cough', 'Wound Complication', 'Penile Infection', 'Palpitations', 'Libido Increased', 'Menorrhagia', 'IVth Nerve Disorder', 'Delirium', 'Uterine Pain', 'Obstruction Gastric', 'Floaters', 'Small Intestine Ulcer', 'Wrist Fracture', 'Gum Infection', 'Injury to Carotid Artery', 'Injury to Jugular Vein', 'Duodenal Perforation', 'Pruritus', 'Intraoperative Gastrointestinal Injury', 'Gait Disturbance', 'Bruising', 'Pancreatic Enzymes Decreased', 'Conjunctivitis', 'Injury to Inferior Vena Cava', 'Ventricular Tachycardia', 'Pain in Extremity', 'Mobitz (Type) II Atrioventricular Block', 'Salivary Duct Inflammation', 'Corneal Infection', 'Small Intestinal Mucositis', 'Rectal Necrosis', 'Suicide Attempt', 'Hyperparathyroidism', 'Psychosis', 'Sore Throat', 'Dysmenorrhea', 'Vaginal Perforation', 'Infusion Related Reaction', 'Gastrointestinal Disorders Other', 'Pulmonary Fibrosis', 'Blood Antidiuretic Hormone Abnormal', 'Lip Pain', 'Toxic Epidermal Necrolysis', 'Pneumonitis', 'Fecal Incontinence', 'Urostomy Obstruction', 'Premature Menopause', 'Agitation', 'Fatigue', 'Keratitis', 'Gastrointestinal Stoma Necrosis', 'Abdominal Soft Tissue Necrosis', 'Intraoperative Endocrine Injury', 'Leukocytosis', 'Gynecomastia', 'Ileal Fistula', 'Otitis Media', 'Poisoning and Procedural Complications Other', 'Small Intestinal Anastomotic Leak', 'Leukemia Secondary to Oncology Chemotherapy', 'Immune System Disorders Other', 'Vertigo', 'Neck Soft Tissue Necrosis', 'Acute Kidney Injury', 'Gallbladder Fistula', 'Jejunal Perforation', 'Breast Atrophy', 'Gallbladder Obstruction', 'Hypothermia', 'Intestinal Stoma Leak', 'Spermatic Cord Obstruction', 'Vaginal Infection', 'Vas Deferens Anastomotic Leak', 'Anxiety', 'Radiculitis', 'Vital Capacity Abnormal', 'Cecal Hemorrhage', 'Gastrointestinal Fistula', 'Pregnancy', 'Mediastinal Hemorrhage', 'Bladder Anastomotic Leak', 'Intraoperative Neurological Injury', 'Rectal Hemorrhage', 'Pelvic Infection', 'Confusion', 'Hearing Impaired', 'Hypoalbuminemia', 'Leukoencephalopathy', 'Carbon Monoxide Diffusing Capacity Decreased', 'Pharyngolaryngeal Pain', 'Chest Pain Cardiac', 'Osteoporosis', 'Accessory Nerve Disorder', 'Laryngitis', 'Gastric Anastomotic Leak', 'Gastritis', 'Hypotension', 'Ovarian Hemorrhage', 'Flu Like Symptoms', 'Autoimmune Disorder', 'Small Intestine Infection', 'Sinusitis', 'Tricuspid Valve Disease', 'Restlessness', 'Fallopian Tube Stenosis', 'Hypermagnesemia', 'Hypocalcemia', 'Respiratory Failure', 'Ovarian Rupture', 'Pelvic Pain', 'Weight Loss', 'Esophageal Hemorrhage', 'Peripheral Motor Neuropathy', 'Arthritis', 'Euphoria', 'Lymphocyte Count Decreased', 'Laryngospasm', 'Small Intestinal Perforation', 'Urticaria', 'Dyspepsia', 'GGT Increased', 'Ankle Fracture', 'Gallbladder Necrosis', 'Anorgasmia', 'Hyponatremia', 'Hyperhidrosis', 'Pericarditis', 'Dyspareunia', 'Laryngeal Edema', 'Ear Pain', 'Fat Atrophy', 'Heart Failure', 'Cardiac Disorders Other', 'Jejunal Obstruction', 'Abdominal Infection', 'Myelodysplastic Syndrome', 'Renal Calculi', 'Urinary Urgency', 'Joint Range of Motion Decreased', 'Gingival Pain', 'Hemolysis', 'Cervicitis Infection', 'Personality Change', 'Allergic Rhinitis', 'Hematosalpinx', 'Oral Cavity Fistula', 'Flank Pain', 'Pyramidal Tract Syndrome', 'Cataract', 'Hypoparathyroidism', 'Delayed Puberty', 'Appendicitis Perforated', 'Lymphedema', 'Pleural Hemorrhage', 'Trigeminal Nerve Disorder', 'Encephalopathy', 'Hypohidrosis', 'Vaginal Dryness', 'Hemoglobinuria', 'Apnea', 'Multi-Organ Failure', 'Presyncope', 'Intraoperative Renal Injury', 'Duodenal Obstruction', 'Ataxia', 'Thrombotic Thrombocytopenic Purpura', 'Nasal Congestion', 'Sinus Pain', 'Erythema Multiforme', 'Sudden Death NOS', 'Myalgia', 'Cystitis Noninfective', 'Toothache', 'Brachial Plexopathy', 'Urostomy Leak', 'Treatment Related Secondary Malignancy', 'Gastric Perforation', 'Flushing', 'Papilledema', 'Pancreatic Hemorrhage', 'Esophageal Ulcer', 'Hypertrichosis', 'Retinal Tear', 'Vaginal Inflammation', 'Cardiac Troponin T Increased', 'Pericardial Tamponade', 'Aphonia', 'Uterine Anastomotic Leak', 'Joint Effusion', 'Reproductive System and Breast Disorders Other', 'Lower Gastrointestinal Hemorrhage', 'Tracheostomy Site Bleeding', 'Cardiac Arrest', 'Localized Edema', 'Nervous System Disorders Other', 'Fracture', 'Neutrophil Count Decreased', 'Prostatic Obstruction', 'Device Related Infection', 'Oral Pain', 'Tracheitis', 'Libido Decreased', 'Colonic Obstruction', 'Forced Expiratory Volume Decreased', 'Acidosis', 'Bone Marrow Hypocellular', 'Breast Infection', 'Encephalitis Infection', 'Hepatic Infection', 'Urinary Retention', 'Bronchial Infection', 'Urine Output Decreased', 'Amnesia', 'Flashing Lights', 'Vaginal Hemorrhage', 'Vestibular Disorder', 'Arterial Injury', 'Hypophosphatemia', 'Dermatitis Radiation', 'Productive Cough', 'Dysphasia', 'Kyphosis', 'White Blood Cell Decreased', 'INR Increased', 'Wound Dehiscence', 'Sleep Apnea', 'Fetal Growth Retardation', 'Pharyngeal Anastomotic Leak', 'Cushingoid', 'Nail Ridging', 'Scoliosis', 'Akathisia', 'Malabsorption', 'Phlebitis', 'Concentration Impairment', 'Pancreas Infection', 'Vaginal Stricture', 'Glossopharyngeal Nerve Disorder', 'Intra-Abdominal Hemorrhage', 'Hot Flashes', 'Cognitive Disturbance', 'Stomal Ulcer', 'Dry Mouth', 'Esophageal Varices Hemorrhage', 'Renal Colic', 'Esophageal Stenosis', 'Pulmonary Edema', 'Bone Pain', 'Vasovagal Reaction', 'Duodenal Fistula', 'Dyspnea', 'Intraoperative Urinary Injury', 'Metabolism and Nutrition Disorders Other', 'Hypernatremia', 'Gastrointestinal Anastomotic Leak', 'Ileal Obstruction', 'Abducens Nerve Disorder', 'Night Blindness', 'Fallopian Tube Obstruction', 'Watering Eyes', 'Peripheral Nerve Infection', 'Photosensitivity', 'Rhinitis Infective', 'Hepatic Pain', 'Respiratory', 'Acute Coronary Syndrome', 'Constipation', 'Hypoglycemia', 'Muscle Weakness Lower Limb', 'Bronchial Stricture', 'Chylothorax', 'Vascular Access Complication', 'Syncope', 'Memory Impairment', 'Tracheal Obstruction', 'Hyperuricemia', 'Esophageal Anastomotic Leak', 'Periorbital Infection', 'Neoplasms Benign', 'Rash Pustular', 'Social Circumstances Other', 'Phlebitis Infective', 'Uveitis', 'Virilization', 'Enterocolitis Infectious', 'Postnasal Drip', 'Gastrointestinal Pain', 'Conduction Disorder', 'Mania', 'Malaise', 'Burn', 'Kidney Anastomotic Leak', 'Retinal Detachment', 'Visceral Arterial Ischemia', 'Blood Corticotrophin Decreased', 'Hemoglobin Increased', 'Colonic Perforation', 'Pancreatic Necrosis', 'Hypersomnia', 'Adult Respiratory Distress Syndrome', 'Duodenal Stenosis', 'Lymph Leakage', 'Stomach Pain', 'Aspartate Aminotransferase Increased', 'Aspiration', 'Depressed Level of Consciousness', 'Surgical and Medical Procedures Other', 'Soft Tissue Necrosis Lower Limb', 'Epistaxis', 'Vaginal Fistula', 'Intraoperative Musculoskeletal Injury', 'Pancreatitis', 'Sepsis', 'Fetal Death', 'Pancreatic Duct Stenosis', 'Female Genital Tract Fistula', 'Retinopathy', 'Jejunal Hemorrhage', 'Skin Ulceration', 'Atelectasis', 'Facial Nerve Disorder', 'Premature Delivery', 'Eye Disorders Other', 'Somnolence', 'Edema Trunk', 'Small Intestinal Obstruction', 'Injury to Superior Vena Cava', 'Voice Alteration', 'Peripheral Ischemia', 'Rash Acneiform', 'Scalp Pain', 'Periodontal Disease', 'Intraoperative Head and Neck Injury', 'Skin and Subcutaneous Tissue Disorders Other', 'Blood Bilirubin Increased', 'Hematoma', 'Esophageal Fistula', 'Vaginal Anastomotic Leak', 'CPK Increased', 'Colitis', 'Retinoic Acid Syndrome', 'Abdominal Distension', 'Buttock Pain', 'Dental Caries', 'Muscle Weakness Upper Limb', 'Head Soft Tissue Necrosis', 'Cardiac Troponin I Increased', 'Pharyngeal Necrosis', 'Skin Infection', 'Sick Sinus Syndrome', 'Adrenal Insufficiency', 'Delusions', 'Hypokalemia', 'Ileus', 'Uterine Infection', 'Growth Hormone Abnormal', 'Hypoglossal Nerve Disorder', 'Investigations Other', 'Blood Gonadotrophin Abnormal', 'Edema Cerebral', 'Pharyngeal Mucositis', 'Stevens-Johnson Syndrome', 'Ear and Labyrinth Disorders Other', 'Atrioventricular Block First Degree', 'Nail Infection', 'Prostatic Hemorrhage', 'Cheilitis', 'Colonic Ulcer', 'Menopause', 'Periorbital Edema', 'Ejaculation Disorder', 'Rectal Pain', 'Acoustic Nerve Disorder NOS', 'Familial and Genetic Disorders Other', 'Anal Hemorrhage', 'Haptoglobin Decreased', 'Intraoperative Hemorrhage', 'Intraoperative Splenic Injury', 'Iron Overload', 'Pelvic Soft Tissue Necrosis', 'Urine Discoloration', 'Obesity', 'Duodenal Infection', 'Ileal Stenosis', 'Chest Wall Pain', 'Lipase Increased', 'Laryngopharyngeal Dysesthesia', 'Ovarian Infection', 'Urinary Incontinence', 'Blood Prolactin Abnormal', 'Hoarseness', 'Capillary Leak Syndrome', 'Portal Hypertension', 'Hydrocephalus', 'Fallopian Tube Perforation', 'Intraoperative Venous Injury', 'External Ear Pain', 'Prostatic Pain', 'Spasticity', 'Hepatic Necrosis', 'Bronchopleural Fistula', 'Bronchial Obstruction', 'Esophageal Infection', 'Soft Tissue Infection', 'Anal Stenosis', 'Anaphylaxis', 'Urethral Anastomotic Leak', 'Mucositis Oral', 'Peripheral Sensory Neuropathy', 'Nail Loss', 'Spermatic Cord Anastomotic Leak', 'Hypothyroidism', 'Anal Necrosis', 'Postoperative Hemorrhage', 'Renal Hemorrhage', 'Sinus Bradycardia', 'Uterine Obstruction', 'Serum Sickness', 'Superficial Soft Tissue Fibrosis', 'Glaucoma', 'Intraoperative Reproductive Tract Injury', 'Myocardial Infarction', 'Laryngeal Mucositis', 'Blurred Vision', 'Thoracic and Mediastinal Disorders Other', 'Urinary Tract Pain', 'Bloating', 'Musculoskeletal and Connective Tissue Disorders Other', 'Paronychia', 'Left Ventricular Systolic Dysfunction', 'Aortic Injury', 'Salivary Gland Fistula', 'Tooth Discoloration', 'Exostosis', 'Dry Skin', 'Hyperkalemia', 'Tremor', 'Myositis', 'Muscle Weakness Right-Sided', 'Irregular Menstruation', 'Ileal Hemorrhage', 'Anal Ulcer', 'Testicular Pain', 'Abdominal Pain', 'Gallbladder Perforation', 'Urostomy Site Bleeding', 'Colonic Hemorrhage', 'Insomnia', 'Dysgeusia', 'Mobitz Type I', 'Body Odor', 'Avascular Necrosis', 'Colonic Fistula', 'Pain', 'Constrictive Pericarditis', 'Lymph Node Pain', 'Biliary Fistula', 'Anorectal Infection', 'Asystole', 'Lip Infection', 'Vaginal Obstruction', 'Skin Atrophy', 'Delayed Orgasm', 'Gastric Fistula', 'Central Nervous System Necrosis', 'Arthralgia', 'Oligospermia', 'Arachnoiditis', 'Duodenal Hemorrhage', 'Musculoskeletal Deformity', 'Scleral Disorder', 'Fall', 'Rash Maculo-Papular', 'Death Neonatal', 'Headache', 'Reversible Posterior Leukoencephalopathy Syndrome', 'Middle Ear Inflammation', 'Appendicitis', 'Hallucinations', 'Hyperglycemia', 'Ascites', 'Rectal Obstruction', 'Vascular Disorders Other', 'Chronic Kidney Disease', 'Anal Pain', 'Pharyngeal Hemorrhage', 'Cholecystitis', 'Endophthalmitis', 'Esophageal Pain', 'Wound Infection', 'Anal Mucositis', 'Biliary Anastomotic Leak', 'Bladder Infection', 'Nail Discoloration', 'Extrapyramidal Disorder', 'Atrioventricular Block Complete', 'Intraoperative Respiratory Injury', 'Portal Vein Thrombosis', 'Retinal Vascular Disorder', 'Suicidal Ideation', 'Sinus Tachycardia', 'Intracranial Hemorrhage', 'Restrictive Cardiomyopathy', 'Upper Respiratory Infection', 'Anemia', 'Myelitis', 'Pelvic Floor Muscle Weakness', 'Ventricular Fibrillation', 'Lymphocele', 'Wolff-Parkinson-White Syndrome', 'Cecal Infection', 'Hepatic Failure', 'Jejunal Fistula', 'Laryngeal Hemorrhage', 'Sinus Disorder', 'Jejunal Ulcer', 'Postoperative Thoracic Procedure Complication', 'Conjunctivitis Infective', 'Fever', 'Meningitis', 'Tooth Infection', 'Weight Gain', 'Urinary Fistula', 'Cranial Nerve Infection', 'Jejunal Stenosis', 'Superior Vena Cava Syndrome', 'Retroperitoneal Hemorrhage', 'Hypomagnesemia', 'Ureteric Anastomotic Leak', 'Muscle Weakness Trunk', 'Vaginal Pain', 'Stroke', 'Fallopian Tube Anastomotic Leak', 'Photophobia', 'Bronchospasm', 'Alopecia', 'Tinnitus', 'Gastroesophageal Reflux Disease', 'Hypertension', 'Seroma', 'Small Intestinal Stenosis', 'Gastric Necrosis', 'Spinal Fracture', 'Hepatic Hemorrhage', 'Corneal Ulcer', 'Alanine Aminotransferase Increased', 'Blood and Lymphatic System Disorders Other', 'Pain of Skin', 'Edema Face', 'Vagus Nerve Disorder', 'Catheter Related Infection', 'Tracheal Fistula', 'Urinary Tract Obstruction', 'Dysesthesia', 'Bullous Dermatitis', 'Eyelid Function Disorder', '']",,FollowUp +Recist Targeted Regions Number,Recist Targeted Regions Number,RecistTargetedRegionsNumber,"Numeric value that represents the number of baseline target lesions, as described by the Response Evaluation Criteria in Solid Tumours (RECIST) criteria",False,,,,FollowUp +Comorbidity,Comorbidity,Comorbidity,"The text term used to describe a comorbidity disease, which coexists with the patient's malignant disease.",False,,"['Depression', 'Adrenocortical Insufficiency', 'Familial Adenomatous Polyposis', 'Human Papillomavirus Infection', 'Adenomatous Polyposis Coli', 'Ischemic Heart Disease', 'Other Cancer Within 5 Years', 'Denys-Drash Syndrome', 'Glycogen Storage Disease', 'Epstein-Barr Virus', 'Sleep apnea', 'Diet Controlled Diabetes', ""Hashimoto's Thyroiditis"", 'Coronary Artery Disease', 'Iron Overload', 'Wagr Syndrome', 'Obesity', 'Insulin Controlled Diabetes', 'Congestive Heart Failure (CHF)', 'Osteoporosis or Osteopenia', 'Not Reported', 'Renal Dialysis', 'Rheumatologic Disease', 'Blood Clots', 'Chronic Hepatitis', 'Rubinstein-Taybi Syndrome', 'Diverticulitis', 'Transient Ischemic Attack', 'HIV / AIDS', 'Other', 'Psoriasis', 'H. pylori Infection', ""Crohn's Disease"", 'Tyrosinemia', 'Peutz-Jeghers Disease', 'Asthma', 'Hemihypertrophy', 'Hypothyroidism', 'Gout', 'COPD', 'Atrial Fibrillation', 'Myasthenia Gravis', 'Unknown', 'Glaucoma', 'Cholelithiasis', 'Myocardial Infarction', 'Deep Vein Thrombosis / Thromboembolism', 'Tuberculosis', 'Gorlin Syndrome', 'Arrhythmia', 'Sarcoidosis', 'MAI', 'Steatosis', 'Renal Failure (Requiring Dialysis)', 'Hyperlipidemia', 'Common Variable Immunodeficiency', 'Pulmonary Fibrosis', 'Liver Cirrhosis (Liver Disease)', 'Cryptogenic Organizing Pneumonia', 'Avascular Necrosis', 'unknown Etiology', 'Cerebrovascular Disease', 'Heart Disease', 'Kidney Disease', 'Fanconi Anemia', 'Peptic Ulcer (Ulcer)', 'Chronic Renal Failure', 'Basal Cell Carcinoma', ""Behcet's Disease"", 'Seizure', 'Hypospadias', 'Rheumatoid Arthritis', 'Diabetes', 'Renal Insufficiency', 'Osteoarthritis', 'Beckwith-Wiedemann', 'Colon Polyps', 'Hepatitis', 'High Grade Liver Dysplastic Nodule', 'Adenocarcinoma', 'Biliary Disorder', 'DVT/PE', 'Eczema', 'Hepatitis B Infection', 'Liver Toxicity (Non-Infectious)', 'Connective Tissue Disorder', 'Headache', 'Interstitial Pneumontis or ARDS', 'Li-Fraumeni Syndrome', 'Anxiety', 'Nonalcoholic Steatohepatitis', 'Joint Replacement', 'Low Grade Liver Dysplastic Nodule', 'Hyperglycemia', 'Other Nonmalignant Systemic Disease', 'Lupus', 'Intraductal Papillary Mucinous Neoplasm', 'Pregnancy in Patient or Partner', 'Cirrhosis', 'Bronchitis', 'Calcium Channel Blockers', 'Fibrosis', 'Peripheral Vascular Disease', 'Diabetic Neuropathy', 'Acute Renal Failure', 'Other Pulmonary Complications', 'Alpha-1 Antitrypsin', 'ITP', 'Gonadal Dysfunction', 'Cancer', 'Herpes', 'Bone Fracture(s)', 'Epilepsy', 'Anemia', 'Hereditary Non-polyposis Colon Cancer', 'Pancreatitis', 'Hepatitis C Infection', 'Arthritis', 'Organ transplant (site)', 'Hemorrhagic Cystitis', 'Pain (Various)', 'Cataracts', 'Lynch Syndrome', 'Type II', 'Pulmonary Hemorrhage', 'Peripheral Neuropathy', 'Stroke', 'Neuroendocrine Tumor', 'Smoking', 'Hypercholesterolemia', 'GERD', 'Ulcerative Colitis', ""Barrett's Esophagus"", 'Dyslipidemia', 'Turcot Syndrome', 'Allergies', 'Celiac Disease', 'Hepatitis A Infection', 'Gastroesophageal Reflux Disease', 'Hypertension', 'Hypercalcemia', 'HUS/TTP', 'Primary Sclerosing Cholangitis', 'Inflammatory Bowel Disease', '']",,FollowUp +AIDS Risk Factors,AIDS Risk Factors,AIDSRiskFactors,The text term used to describe a risk factor of the acquired immunodeficiency syndrome (AIDS) that the patient either had at time time of the study or experienced in the past.,False,,"['Mycobacterium tuberculosis', 'Cytomegalovirus', 'Mycobacterium avium Complex', 'Pneumonia', 'Mycobacterium', 'Herpes Simplex Virus', 'Candidiasis', 'Histoplasmosis', 'Wasting Syndrome', 'Cryptococcosis', 'Isosporiasis', 'Salmonella Septicemia', 'NOS', 'Coccidioidomycosis', 'Pneumocystis Pneumonia', 'Toxoplasmosis', 'Encephalopathy', 'Nocardiosis', 'Progressive Multifocal Leukoencephalopathy', '']",,FollowUp +Weight,Weight,Weight,The weight of the patient measured in kilograms.,False,,,,FollowUp +Pancreatitis Onset Year,Pancreatitis Onset Year,PancreatitisOnsetYear,TBD,False,,,,FollowUp +Reflux Treatment Type,Reflux Treatment Type,RefluxTreatmentType,Text term used to describe the types of treatment used to manage gastroesophageal reflux disease (GERD).,False,,"['Not Reported', 'Proton Pump Inhibitors', 'Not Applicable', 'Medically Treated', 'Surgically Treated', 'Antacids', 'Unknown', 'No Treatment', 'H2 Blockers', '']",,FollowUp +Adverse Event Grade,Adverse Event Grade,AdverseEventGrade,"The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.",False,,"['Grade 3', 'Grade 5', 'Grade 2', 'Grade 1', 'Grade 4', '']",,FollowUp +DLCO Ref Predictive Percent,DLCO Ref Predictive Percent,DLCORefPredictivePercent,"The value, as a percentage of predicted lung volume, measuring the amount of carbon monoxide detected in a patient's lungs.",False,,,,FollowUp +Days to Imaging,Days to Imaging,DaystoImaging,Number of days between the date used for index and the date the imaging or scan was performed on the patient.,False,,,,FollowUp +Menopause Status,Menopause Status,MenopauseStatus,Text term used to describe the patient's menopause status.,False,,"['Not Reported', 'Perimenopausal', 'Postmenopausal', 'Unknown', 'Premenopausal', '']",,FollowUp +Scan Tracer Used,Scan Tracer Used,ScanTracerUsed,The text term used to describe the type of tracer used during the imaging or scan of the patient.,False,,"['Sodium Fluoride', 'Axumin', 'PSMA', 'Acetate', 'Choline', '']",,FollowUp +Disease Response,Disease Response,DiseaseResponse,Code assigned to describe the patient's response or outcome to the disease.,False,,"['DU-Disease Unchanged', 'PDM-Persistent Distant Metastasis', 'MX-Mixed Response', 'PSR-Pseudoresponse', 'CRU-Complete Response Unconfirmed', 'PPD-Pseudoprogression', 'CPD-Clinical Progression', 'IMR-Immunoresponse', 'BED-Biochemical Evidence of Disease', 'SD-Stable Disease', 'SPD-Surgical Progression', 'PB-Palliative Benefit', 'WT-With Tumor', 'PA-Palliative Therapy', 'VGPR-Very Good Partial Response', 'Unknown', 'CR-Complete Response', 'NR-No Response', 'RPD-Radiographic Progressive Disease', 'sCR-Stringent Complete Response', 'MR-Minimal/Marginal response', 'NPB-No Palliative Benefit', 'Not Reported', 'RP-Response', 'TE-Too Early', 'PLD-Persistent Locoregional Disease', 'TF-Tumor Free', 'PR-Partial Response', 'AJ-Adjuvant Therapy', 'Non-CR/Non-PD-Non-CR/Non-PD', 'PD-Progressive Disease', 'RD-Responsive Disease', 'IPD-Immunoprogression', '']",,FollowUp +Viral Hepatitis Serologies,Viral Hepatitis Serologies,ViralHepatitisSerologies,Text term that describes the kind of serological laboratory test used to determine the patient's hepatitus status.,False,,"['Hepatitis C Antibody', 'Not Reported', 'HBV Surface Antibody', 'HBV Core Antibody', 'Hepatitis C Virus RNA', 'HCV Genotype', 'Unknown', 'HBV Genotype', 'HBV DNA', 'Hepatitis B Surface Antigen', '']",,FollowUp +Body Surface Area,Body Surface Area,BodySurfaceArea,Numeric value used to represent the 2-dimensional extent of the body surface relating height to weight.,False,,,,FollowUp +HIV Viral Load,HIV Viral Load,HIVViralLoad,"Numeric value that represents the concentration of an analyte or aliquot extracted from the sample or sample portion, measured in milligrams per milliliter.",False,,,,FollowUp +Risk Factor,Risk Factor,RiskFactor,The text term used to describe a risk factor the patient had at the time of or prior to their diagnosis.,False,,"['Diet', 'HIV', 'Familial Adenomatous Polyposis', 'Common variable immune deficiency (CVID)', 'Human Papillomavirus Infection', 'Gastric Polyp(s)', 'Denys-Drash Syndrome', 'Epstein-Barr Virus', 'Allergy Mold or Dust', ""Hashimoto's Thyroiditis"", 'Iron Overload', 'Thyroid Nodular Hyperplasia', 'Wagr Syndrome', 'Obesity', 'Not Reported', 'Helicobacter Pylori-Associated Gastritis', ""Gilbert's Syndrome"", 'Rubinstein-Taybi Syndrome', 'Chronic Hepatitis', 'Diverticulitis', 'Endometriosis', 'Parasitic Disease of Biliary Tract', 'Endosalpingiosis', 'Lymphocytic Thyroiditis', 'Autoimmune Atrophic Chronic Gastritis', 'Allergy Dog', 'Hemihypertrophy', 'Nonalcoholic Fatty Liver Disease', 'Tobacco Smokeless', 'Tattoo', 'Allergy Meat', 'Allergy Bee', 'Diabetes Type II', 'Myasthenia Gravis', 'Serous tubal intraepithelial carcinoma (STIC)', 'Unknown', 'Allergy Eggs', 'Intestinal Metaplasia', 'Cholelithiasis', 'Tobacco Smoking', 'Gorlin Syndrome', 'Sarcoidosis', 'Alcohol Consumption', 'Oral Contraceptives', 'Steatosis', 'Tobacco NOS', 'Allergy Cat', 'Low Grade Dysplasia', 'High Grade Dysplasia', 'Allergy Animal NOS', 'Allergy Nuts', 'Fanconi Anemia', 'Alcoholic Liver Disease', 'Diabetes NOS', ""Behcet's Disease"", 'Seizure', 'Hypospadias', 'Rheumatoid Arthritis', 'Beckwith-Wiedemann', 'Colon Polyps', 'Eczema', 'Hepatitis B Infection', 'Hepatic Encephalopathy', 'Allergy Wasp', 'Headache', 'Li-Fraumeni Syndrome', 'Vision Changes', 'Nonalcoholic Steatohepatitis', 'Hemochromatosis', 'Allergy Dairy or Lactose', 'Sensory Changes', 'Hay Fever', 'Reflux Disease', 'Cirrhosis', 'Allergy Fruit', 'Fibrosis', 'Hematologic Disorder NOS', 'Allergy Ant', 'Allergy Processed Foods', 'Cancer', 'Diabetes Type I', 'Pancreatitis', 'Hepatitis C Infection', 'Allergy Seafood', 'Lynch Syndrome', 'Allergy Food NOS', ""Barrett's Esophagus"", 'Turcot Syndrome', 'Undescended Testis', 'Hepatitis NOS', 'Alpha-1 Antitrypsin Deficiency', 'Primary Sclerosing Cholangitis', 'Recurrent Pyogenic Cholangitis', '']",,FollowUp +FEV1 Ref Post Bronch Percent,FEV1 Ref Post Bronch Percent,FEV1RefPostBronchPercent,The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second post-bronchodilator.,False,,,,FollowUp +ECOG Performance Status,ECOG Performance Status,ECOGPerformanceStatus,The ECOG functional performance status of the patient/participant.,False,,"['3.0', '4', '4.0', '1', '1.0', '5', '5.0', '0.0', '2.0', '2', '3', '0', '']",,FollowUp +HAART Treatment Indicator,HAART Treatment Indicator,HAARTTreatmentIndicator,The text term used to indicate whether the patient received Highly Active Antiretroviral Therapy (HAART).,False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,FollowUp +Days to Adverse Event,Days to Adverse Event,DaystoAdverseEvent,Number of days between the date used for index and the date of the patient's adverse event.,False,,,,FollowUp +FEV1 Ref Pre Bronch Percent,FEV1 Ref Pre Bronch Percent,FEV1RefPreBronchPercent,The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second pre-bronchodilator.,False,,,,FollowUp +Cause of Response,Cause of Response,CauseofResponse,The text term used to describe the suspected cause or reason for the patient disease response.,False,,,,FollowUp +FEV 1 FVC Pre Bronch Percent,FEV 1 FVC Pre Bronch Percent,FEV1FVCPreBronchPercent,Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) pre-bronchodilator.,False,,,,FollowUp +Risk Factor Treatment,Risk Factor Treatment,RiskFactorTreatment,The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.,False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,FollowUp +Progression or Recurrence,Progression or Recurrence,ProgressionorRecurrence,Yes/No/unknown indicator to identify whether a patient has had a new tumor event after initial treatment.,True,,"['No', 'Yes - Progression or Recurrence', 'Unknown', 'Not Reported']",,FollowUp +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,FollowUp +CD4 Count,CD4 Count,CD4Count,The text term used to describe the outcome of the procedure to determine the amount of the CD4 expressing cells in a sample.,False,,,,FollowUp +Diabetes Treatment Type,Diabetes Treatment Type,DiabetesTreatmentType,Text term used to describe the types of treatment used to manage diabetes.,False,,"['Alpha-Glucosidase Inhibitor', 'Diet', 'Sulfonylurea', 'Oral Hypoglycemic', 'Not Reported', 'Injected Insulin', 'Thiazolidinedione', 'Other', 'Unknown', 'Biguanide', 'Insulin', '']",,FollowUp +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,FollowUp +FEV1 FVC Post Bronch Percent,FEV1 FVC Post Bronch Percent,FEV1FVCPostBronchPercent,Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) post-bronchodilator.,False,,,,FollowUp +Nadir CD4 Count,Nadir CD4 Count,NadirCD4Count,Numeric value that represents the lowest point to which the CD4 count has dropped (nadir).,False,,,,FollowUp +Recist Targeted Regions Sum,Recist Targeted Regions Sum,RecistTargetedRegionsSum,"Numeric value that represents the sum of baseline target lesions, as described by the Response Evaluation Criteria in Solid Tumours (RECIST) criteria.",False,,,,FollowUp +Evidence of Recurrence Type,Evidence of Recurrence Type,EvidenceofRecurrenceType,The text term used to describe the type of evidence used to determine whether the patient's disease recurred,False,,"['Biopsy with Histologic Confirmation', 'Positive Biomarkers', 'Convincing Image Source', '']",,FollowUp +Comorbidity Method of Diagnosis,Comorbidity Method of Diagnosis,ComorbidityMethodofDiagnosis,The text term used to describe the method used to diagnose the patient's comorbidity disease.,False,,"['Radiology', 'Not Reported', 'Pathology', 'Histology', 'Unknown', '']",,FollowUp +Imaging Type,Imaging Type,ImagingType,The text term used to describe the type of imaging or scan performed on the patient.,False,,"['99mTc Bone Scintigraphy', 'MRI', 'CT Scan', 'PET', '']",,FollowUp +Hysterectomy Margins Involved,Hysterectomy Margins Involved,HysterectomyMarginsInvolved,The text term used to indicate whether the patient's disease was determined to be involved based on the surgical margins of the hysterectomy.,False,,"['None', 'Not Reported', 'Macroscopic Parametrium', 'Microscopic Parametrium', 'Unknown', 'Bladder', 'Vagina', '']",,FollowUp +HPV Positive Type,HPV Positive Type,HPVPositiveType,Text classification to represent the strain or type of human papillomavirus identified in an individual.,False,,"['58', '26', '51', '82', '59', '73', '33', '18', '53', '63', '66', '31', '39', '16', '45', '52', '70', '56', '35', '68', '']",,FollowUp +Hepatitis Sustained Virological Response,Hepatitis Sustained Virological Response,HepatitisSustainedVirologicalResponse,The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.,False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,FollowUp +BMI,BMI,BMI,A calculated numerical quantity that represents an individual's weight to height ratio.,False,,,,FollowUp +Days to Comorbidity,Days to Comorbidity,DaystoComorbidity,Number of days between the date used for index and the date the patient was diagnosed with a comorbidity.,False,,,,FollowUp +Height,Height,Height,The height of the patient in centimeters.,False,,,,FollowUp +Hormonal Contraceptive Use,Hormonal Contraceptive Use,HormonalContraceptiveUse,The text term used to indicate whether the patient used hormonal contraceptives.,False,,"['Current User', 'Not Reported', 'Former User', 'Unknown', 'Never Used', '']",,FollowUp +Days to Recurrence,Days to Recurrence,DaystoRecurrence,Number of days between the date used for index and the date the patient's disease recurred.,False,True,," If Progression or Recurrence is ""Yes - Progression or Recurrence"" then ""Days to Recurrence"" is required",FollowUp +Days to Progression,Days to Progression,DaystoProgression,Number of days between the date used for index and the date the patient's disease progressed.,False,True,," If Progression or Recurrence is ""Yes - Progression or Recurrence"" then ""Days to Progression"" is required",FollowUp +Progression or Recurrence Type,Progression or Recurrence Type,ProgressionorRecurrenceType,The text term used to describe the type of progressive or recurrent disease or relapsed disease.,False,True,"['Distant', 'Not Reported', 'Unknown', 'Biochemical', 'Regional', 'Local', '']"," If Progression or Recurrence is ""Yes - Progression or Recurrence"" then ""Progression or Recurrence Type"" is required",FollowUp +Progression or Recurrence Anatomic Site,Progression or Recurrence Anatomic Site,ProgressionorRecurrenceAnatomicSite,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,False,True,"['Paraurethral gland', 'Colon NOS', 'Frontal sinus', 'Overlapping lesion of tongue', 'Overlapping lesion of palate', 'Scrotum NOS', 'Bone marrow', 'Axillary tail of breast', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'unknown primary site', 'Broad ligament', 'Lateral floor of mouth', 'Overlapping lesion of vulva', 'Trigone of bladder', 'Lacrimal gland', 'Thorax NOS', 'Ampulla of Vater', 'Myometrium', 'Penis NOS', 'Female genital tract NOS', 'Submandibular gland', 'Anterior 2/3 of tongue NOS', 'Posterior wall of bladder', 'Thymus', 'Endocrine gland NOS', 'Stomach NOS', 'Unknown', 'Cerebrum', 'Splenic flexure of colon', 'Urachus', 'Skin of lip NOS', 'Mucosa of lip NOS', 'Accessory sinus NOS', 'Cortex of adrenal gland', 'Other ill-defined sites', 'Middle lobe lung', 'Pelvis NOS', 'Anus NOS', 'Upper-inner quadrant of breast', 'Posterior mediastinum', 'Esophagus NOS', 'Duodenum', 'Cervical esophagus', 'Optic nerve', 'Long bones of lower limb and associated joints', 'Middle ear', 'Breast NOS', 'Dorsal surface of tongue NOS', 'Lesser curvature of stomach NOS', 'Overlapping lesion of floor of mouth', 'Overlapping lesion of heart mediastinum and pleura', 'Eye NOS', 'Overlapping lesion of esophagus', 'Ciliary body', 'Ureteric orifice', 'Postcricoid region', 'External ear', 'Base of tongue NOS', 'Liver', 'Commissure of lip', 'Cloacogenic zone', 'Lower lobe lung', 'Transverse colon', 'Acoustic nerve', 'Supraglottis', 'Fallopian tube', 'Upper third of esophagus', 'Skin of scalp and neck', 'Choroid', 'Long bones of upper limb scapula and associated joints', 'Overlapping lesion of brain', 'Upper gum', 'Skin NOS', 'Hard palate', 'Ileum', 'Overlapping lesion of colon', 'Ascending colon', 'Lower gum', 'Pelvic bones sacrum coccyx and associated joints', 'Hepatic flexure of colon', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Vestibule of mouth', 'Cervix uteri', 'Bones of skull and face and associated joints', 'Overlapping lesion of lip oral cavity and pharynx', 'Endometrium', 'Sphenoid sinus', 'Overlapping lesion of ill-defined sites', 'Sigmoid colon', 'Peritoneum NOS', 'Specified parts of peritoneum', 'Meckel diverticulum', 'Rectosigmoid junction', 'Kidney NOS', 'Reticuloendothelial system NOS', 'Rectum NOS', 'Pylorus', 'Overlapping lesion of tonsil', 'Pleura NOS', 'Jejunum', 'Vallecula', 'Skin of lower limb and hip', 'Pelvic lymph nodes', 'External lower lip', 'Overlapping lesion of skin', 'Mucosa of upper lip', 'Ovary', 'Cauda equina', 'Lower limb NOS', 'Body of stomach', 'Overlapping lesion of larynx', 'Pancreas NOS', 'Overlapping lesion of lung', 'Overlapping lesion of major salivary glands', 'Uvula', 'Overlapping lesion of hypopharynx', 'Round ligament', 'Corpus uteri', 'Biliary tract NOS', 'Male genital organs NOS', 'Parametrium', 'External lip NOS', 'Overlapping lesion of accessory sinuses', 'Cardia NOS', 'Islets of Langerhans', 'Carotid body', 'Ventral surface of tongue NOS', 'Autonomic nervous system NOS', 'Overlapping lesion of corpus uteri', 'Spinal meninges', 'Posterior wall of nasopharynx', 'Placenta', 'Intrahepatic bile duct', 'Overlapping lesion of digestive system', 'Mediastinum NOS', 'Hematopoietic system NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Major salivary gland NOS', 'Cerebellum NOS', 'Overlapping lesion of stomach', 'Vulva NOS', 'Craniopharyngeal duct', 'Lung NOS', 'Greater curvature of stomach NOS', 'Upper-outer quadrant of breast', 'Gallbladder', 'Thoracic esophagus', 'Lymph nodes of axilla or arm', 'Ventricle NOS', 'Overlapping lesion of biliary tract', 'Hypopharynx NOS', 'Clitoris', 'Exocervix', 'Parietal lobe', 'Waldeyer ring', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Head face or neck NOS', 'Anterior wall of nasopharynx', 'Urethra', 'Overlapping lesion of nasopharynx', 'Maxillary sinus', 'Lymph nodes of inguinal region or leg', 'Ureter', 'Tonsillar pillar', 'Sublingual gland', 'Pituitary gland', 'Gastrointestinal tract NOS', 'Pineal gland', 'Meninges NOS', 'Lingual tonsil', 'Trachea', 'Pyriform sinus', 'Mucosa of lower lip', 'Not Reported', 'Posterior wall of hypopharynx', 'Urinary system NOS', 'Orbit NOS', 'Short bones of lower limb and associated joints', 'Connective subcutaneous and other soft tissues of thorax', 'Upper limb NOS', 'Gastric antrum', 'Lymph node NOS', 'Peripheral nerves and autonomic nervous system of thorax', 'Ill-defined sites within respiratory system', 'Other specified parts of male genital organs', 'Rib sternum clavicle and associated joints', 'Overlapping lesion of bladder', 'Appendix', 'Prostate gland', 'Lymph nodes of multiple regions', 'Lateral wall of nasopharynx', 'Branchial cleft', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Floor of mouth NOS', 'Connective subcutaneous and other soft tissues NOS', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Bladder neck', 'Border of tongue', 'Connective subcutaneous and other soft tissues of abdomen', 'Overlapping lesion of small intestine', 'Lateral wall of bladder', 'Soft palate NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Isthmus uteri', 'Nasal cavity', 'Endocervix', 'Tonsil NOS', 'Glottis', 'Retroperitoneum', 'Peripheral nerves and autonomic nervous system of pelvis', 'Frontal lobe', 'Vagina NOS', 'Undescended testis', 'Laryngeal cartilage', 'Eyelid', 'Hypopharyngeal aspect of aryepiglottic fold', 'Overlapping lesion of other and unspecified parts of mouth', 'Upper lobe lung', 'Lip NOS', 'Lymph nodes of head face and neck', 'Overlapping lesion of brain and central nervous system', 'Overlapping lesion of penis', 'Overlapping lesion of retroperitoneum and peritoneum', 'Parotid gland', 'Dome of bladder', 'Bone of limb NOS', 'Descended testis', 'Vertebral column', 'Fundus uteri', 'Connective subcutaneous and other soft tissues of pelvis', 'Epididymis', 'Intra-abdominal lymph nodes', 'Prepuce', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Pharynx NOS', 'Overlapping lesion of endocrine glands and related structures', 'Gum NOS', 'Spinal cord', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Skin of upper limb and shoulder', 'Nasopharynx NOS', 'Parathyroid gland', 'Bone NOS', 'Mouth NOS', 'Abdomen NOS', 'Conjunctiva', 'Spermatic cord', 'External upper lip', 'Labium minus', 'Renal pelvis', 'Overlapping lesion of lip', 'Short bones of upper limb and associated joints', 'Main bronchus', 'Upper respiratory tract NOS', 'Body of penis', 'Small intestine NOS', 'Central portion of breast', 'Lower-inner quadrant of breast', 'Labium majus', 'Tonsillar fossa', 'Cecum', 'Glans penis', 'Tail of pancreas', 'Lower third of esophagus', 'Body of pancreas', 'Intestinal tract NOS', 'Brain stem', 'Overlapping lesion of rectum anus and anal canal', 'Posterior wall of oropharynx', 'Pancreatic duct', 'Blood', 'Temporal lobe', 'Anterior floor of mouth', 'Nervous system NOS', 'Cornea NOS', 'Palate NOS', 'Occipital lobe', 'Abdominal esophagus', 'Overlapping lesion of pancreas', 'Overlapping lesion of female genital organs', 'Cheek mucosa', 'Retina', 'Overlapping lesion of male genital organs', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Larynx NOS', 'Skin of other and unspecified parts of face', 'Spleen', 'Oropharynx NOS', 'Anal canal', 'Subglottis', 'Cerebral meninges', 'Lateral wall of oropharynx', 'Middle third of esophagus', 'Nipple', 'Medulla of adrenal gland', 'Overlapping lesion of eye and adnexa', 'Olfactory nerve', 'Ethmoid sinus', 'Overlapping lesion of cervix uteri', 'Descending colon', 'Brain NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Anterior wall of bladder', 'Mandible', 'Other specified parts of pancreas', 'Skin of trunk', 'Other specified parts of female genital organs', 'Uterus NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Intrathoracic lymph nodes', 'Heart', 'Adrenal gland NOS', 'Aortic body and other paraganglia', 'Extrahepatic bile duct', 'Overlapping lesion of breast', 'Superior wall of nasopharynx', 'Fundus of stomach', 'Anterior mediastinum', 'Tongue NOS', 'Cranial nerve NOS', 'Head of pancreas', 'Overlapping lesions of oropharynx', 'Overlapping lesion of bones joints and articular cartilage', 'Retromolar area', 'Testis NOS', 'Connective subcutaneous and other soft tissues of head face and neck', 'Bladder NOS', 'Overlapping lesion of urinary organs', 'Lower-outer quadrant of breast', 'Thyroid gland', 'Anterior surface of epiglottis', 'Uterine adnexa', '']"," If Progression or Recurrence is ""Yes - Progression or Recurrence"" then ""Progression or Recurrence Anatomic Site"" is required",FollowUp +Days to Progression Free,Days to Progression Free,DaystoProgressionFree,Number of days between the date used for index and the date the patient's disease was formally confirmed as progression-free.,False,True,," If Progression or Recurrence is ""Yes - Progression or Recurrence"" then ""Days to Progression Free"" is required",FollowUp +Anaplasia Present,Anaplasia Present,AnaplasiaPresent,Yes/no/unknown/Not Reported indicator used to describe whether anaplasia was present at the time of diagnosis.,False,,"['No', 'Yes - Anaplasia Present', 'Unknown', 'Not Reported', '']",,Diagnosis +Cog Neuroblastoma Risk Group,Cog Neuroblastoma Risk Group,CogNeuroblastomaRiskGroup,Text term that represents the categorization of patients on the basis of prognostic factors per a system developed by Children's Oncology Group (COG). Risk level is used to assign treatment intensity.,False,,"['Not Reported', 'High Risk', 'Intermediate Risk', 'Unknown', 'Low Risk', '']",,Diagnosis +Days to Last Known Disease Status,Days to Last Known Disease Status,DaystoLastKnownDiseaseStatus,"Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days.",True,,,,Diagnosis +Tissue or Organ of Origin,Tissue or Organ of Origin,TissueorOrganofOrigin,"The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",True,,"['Paraurethral gland', 'Colon NOS', 'Frontal sinus', 'Overlapping lesion of tongue', 'Overlapping lesion of palate', 'Scrotum NOS', 'Bone marrow', 'Axillary tail of breast', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'unknown primary site', 'Broad ligament', 'Lateral floor of mouth', 'Overlapping lesion of vulva', 'Trigone of bladder', 'Lacrimal gland', 'Thorax NOS', 'Ampulla of Vater', 'Myometrium', 'Penis NOS', 'Female genital tract NOS', 'Submandibular gland', 'Anterior 2/3 of tongue NOS', 'Posterior wall of bladder', 'Thymus', 'Endocrine gland NOS', 'Stomach NOS', 'Unknown', 'Cerebrum', 'Splenic flexure of colon', 'Urachus', 'Skin of lip NOS', 'Mucosa of lip NOS', 'Accessory sinus NOS', 'Cortex of adrenal gland', 'Other ill-defined sites', 'Middle lobe lung', 'Pelvis NOS', 'Anus NOS', 'Upper-inner quadrant of breast', 'Posterior mediastinum', 'Esophagus NOS', 'Duodenum', 'Cervical esophagus', 'Optic nerve', 'Long bones of lower limb and associated joints', 'Middle ear', 'Breast NOS', 'Dorsal surface of tongue NOS', 'Lesser curvature of stomach NOS', 'Overlapping lesion of floor of mouth', 'Overlapping lesion of heart mediastinum and pleura', 'Eye NOS', 'Overlapping lesion of esophagus', 'Ciliary body', 'Ureteric orifice', 'Postcricoid region', 'External ear', 'Base of tongue NOS', 'Liver', 'Commissure of lip', 'Cloacogenic zone', 'Lower lobe lung', 'Transverse colon', 'Acoustic nerve', 'Supraglottis', 'Fallopian tube', 'Upper third of esophagus', 'Skin of scalp and neck', 'Choroid', 'Long bones of upper limb scapula and associated joints', 'Overlapping lesion of brain', 'Upper gum', 'Skin NOS', 'Hard palate', 'Ileum', 'Overlapping lesion of colon', 'Ascending colon', 'Lower gum', 'Pelvic bones sacrum coccyx and associated joints', 'Hepatic flexure of colon', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Vestibule of mouth', 'Cervix uteri', 'Bones of skull and face and associated joints', 'Overlapping lesion of lip oral cavity and pharynx', 'Endometrium', 'Sphenoid sinus', 'Overlapping lesion of ill-defined sites', 'Sigmoid colon', 'Peritoneum NOS', 'Specified parts of peritoneum', 'Meckel diverticulum', 'Rectosigmoid junction', 'Kidney NOS', 'Reticuloendothelial system NOS', 'Rectum NOS', 'Pylorus', 'Overlapping lesion of tonsil', 'Pleura NOS', 'Jejunum', 'Vallecula', 'Skin of lower limb and hip', 'Pelvic lymph nodes', 'External lower lip', 'Overlapping lesion of skin', 'Mucosa of upper lip', 'Ovary', 'Cauda equina', 'Lower limb NOS', 'Body of stomach', 'Overlapping lesion of larynx', 'Pancreas NOS', 'Overlapping lesion of lung', 'Overlapping lesion of major salivary glands', 'Uvula', 'Overlapping lesion of hypopharynx', 'Round ligament', 'Corpus uteri', 'Biliary tract NOS', 'Male genital organs NOS', 'Parametrium', 'External lip NOS', 'Overlapping lesion of accessory sinuses', 'Cardia NOS', 'Islets of Langerhans', 'Carotid body', 'Ventral surface of tongue NOS', 'Autonomic nervous system NOS', 'Overlapping lesion of corpus uteri', 'Spinal meninges', 'Posterior wall of nasopharynx', 'Placenta', 'Intrahepatic bile duct', 'Overlapping lesion of digestive system', 'Mediastinum NOS', 'Hematopoietic system NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Major salivary gland NOS', 'Cerebellum NOS', 'Overlapping lesion of stomach', 'Vulva NOS', 'Craniopharyngeal duct', 'Lung NOS', 'Greater curvature of stomach NOS', 'Upper-outer quadrant of breast', 'Gallbladder', 'Thoracic esophagus', 'Lymph nodes of axilla or arm', 'Ventricle NOS', 'Overlapping lesion of biliary tract', 'Hypopharynx NOS', 'Clitoris', 'Exocervix', 'Parietal lobe', 'Waldeyer ring', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Head face or neck NOS', 'Anterior wall of nasopharynx', 'Urethra', 'Overlapping lesion of nasopharynx', 'Maxillary sinus', 'Lymph nodes of inguinal region or leg', 'Ureter', 'Tonsillar pillar', 'Sublingual gland', 'Pituitary gland', 'Gastrointestinal tract NOS', 'Pineal gland', 'Meninges NOS', 'Lingual tonsil', 'Trachea', 'Pyriform sinus', 'Mucosa of lower lip', 'Not Reported', 'Posterior wall of hypopharynx', 'Urinary system NOS', 'Orbit NOS', 'Short bones of lower limb and associated joints', 'Connective subcutaneous and other soft tissues of thorax', 'Upper limb NOS', 'Gastric antrum', 'Lymph node NOS', 'Peripheral nerves and autonomic nervous system of thorax', 'Ill-defined sites within respiratory system', 'Other specified parts of male genital organs', 'Rib sternum clavicle and associated joints', 'Overlapping lesion of bladder', 'Appendix', 'Prostate gland', 'Lymph nodes of multiple regions', 'Lateral wall of nasopharynx', 'Branchial cleft', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Floor of mouth NOS', 'Connective subcutaneous and other soft tissues NOS', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Bladder neck', 'Border of tongue', 'Connective subcutaneous and other soft tissues of abdomen', 'Overlapping lesion of small intestine', 'Lateral wall of bladder', 'Soft palate NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Isthmus uteri', 'Nasal cavity', 'Endocervix', 'Tonsil NOS', 'Glottis', 'Retroperitoneum', 'Peripheral nerves and autonomic nervous system of pelvis', 'Frontal lobe', 'Vagina NOS', 'Undescended testis', 'Laryngeal cartilage', 'Eyelid', 'Hypopharyngeal aspect of aryepiglottic fold', 'Overlapping lesion of other and unspecified parts of mouth', 'Upper lobe lung', 'Lip NOS', 'Lymph nodes of head face and neck', 'Overlapping lesion of brain and central nervous system', 'Overlapping lesion of penis', 'Overlapping lesion of retroperitoneum and peritoneum', 'Parotid gland', 'Dome of bladder', 'Bone of limb NOS', 'Descended testis', 'Vertebral column', 'Fundus uteri', 'Connective subcutaneous and other soft tissues of pelvis', 'Epididymis', 'Intra-abdominal lymph nodes', 'Paraspinal', 'Prepuce', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Pharynx NOS', 'Overlapping lesion of endocrine glands and related structures', 'Gum NOS', 'Spinal cord', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Skin of upper limb and shoulder', 'Nasopharynx NOS', 'Parathyroid gland', 'Bone NOS', 'Mouth NOS', 'Abdomen NOS', 'Conjunctiva', 'Spermatic cord', 'External upper lip', 'Labium minus', 'Renal pelvis', 'Overlapping lesion of lip', 'Short bones of upper limb and associated joints', 'Main bronchus', 'Upper respiratory tract NOS', 'Body of penis', 'Small intestine NOS', 'Central portion of breast', 'Lower-inner quadrant of breast', 'Labium majus', 'Tonsillar fossa', 'Cecum', 'Glans penis', 'Tail of pancreas', 'Lower third of esophagus', 'Body of pancreas', 'Intestinal tract NOS', 'Brain stem', 'Overlapping lesion of rectum anus and anal canal', 'Posterior wall of oropharynx', 'Pancreatic duct', 'Blood', 'Temporal lobe', 'Anterior floor of mouth', 'Nervous system NOS', 'Cornea NOS', 'Palate NOS', 'Occipital lobe', 'Abdominal esophagus', 'Overlapping lesion of pancreas', 'Overlapping lesion of female genital organs', 'Cheek mucosa', 'Retina', 'Overlapping lesion of male genital organs', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Larynx NOS', 'Skin of other and unspecified parts of face', 'Spleen', 'Oropharynx NOS', 'Anal canal', 'Subglottis', 'Cerebral meninges', 'Lateral wall of oropharynx', 'Middle third of esophagus', 'Nipple', 'Medulla of adrenal gland', 'Overlapping lesion of eye and adnexa', 'Olfactory nerve', 'Ethmoid sinus', 'Overlapping lesion of cervix uteri', 'Descending colon', 'Brain NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Anterior wall of bladder', 'Mandible', 'Other specified parts of pancreas', 'Skin of trunk', 'Other specified parts of female genital organs', 'Uterus NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Intrathoracic lymph nodes', 'Heart', 'Adrenal gland NOS', 'Aortic body and other paraganglia', 'Extrahepatic bile duct', 'Overlapping lesion of breast', 'Superior wall of nasopharynx', 'Fundus of stomach', 'Anterior mediastinum', 'Tongue NOS', 'Cranial nerve NOS', 'Head of pancreas', 'Overlapping lesions of oropharynx', 'Overlapping lesion of bones joints and articular cartilage', 'Retromolar area', 'Testis NOS', 'Connective subcutaneous and other soft tissues of head face and neck', 'Bladder NOS', 'Overlapping lesion of urinary organs', 'Lower-outer quadrant of breast', 'Thyroid gland', 'Anterior surface of epiglottis', 'Uterine adnexa']",,Diagnosis +Primary Gleason Grade,Primary Gleason Grade,PrimaryGleasonGrade,"The text term used to describe the primary Gleason score, which describes the pattern of cells making up the largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.",False,,"['Pattern 2', 'Pattern 3', 'Pattern 5', 'Pattern 1', 'Pattern 4', '']",,Diagnosis +Mitosis Karyorrhexis Index,Mitosis Karyorrhexis Index,MitosisKaryorrhexisIndex,Text term that represents the component of the International Neuroblastoma Pathology Classification (INPC) for mitosis-karyorrhexis index (MKI).,False,,"['Not Reported', 'Low', 'Intermediate', 'Unknown', 'High', '']",,Diagnosis +IRS Stage,IRS Stage,IRSStage,"The text term used to describe the classification of rhabdomyosarcoma tumors, as defined by the Intergroup Rhabdomyosarcoma Study (IRS).",False,,"['4', '1', 'Not Reported', 'Unknown', '2', '3', '']",,Diagnosis +Anaplasia Present Type,Anaplasia Present Type,AnaplasiaPresentType,"The text term used to describe the morphologic findings indicating the presence of a malignant cellular infiltrate characterized by the presence of large pleomorphic cells, necrosis, and high mitotic activity in a tissue sample.",False,,"['Equivocal', 'Not Reported', 'Absent', 'Unknown', 'Focal', 'Sclerosis', 'Diffuse', 'Present', '']",,Diagnosis +International Prognostic Index,International Prognostic Index,InternationalPrognosticIndex,"The text term used to describe the International Prognostic Index, which classifies the prognosis of patients with aggressive non-Hodgkin's lymphoma.",False,,"['High Risk', 'High-Intermediate Risk', 'Low-Intermediate Risk', 'Low Risk', '']",,Diagnosis +Days to Last Follow up,Days to Last Follow up,DaystoLastFollowup,"Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days.",True,,,,Diagnosis +AJCC Pathologic M,AJCC Pathologic M,AJCCPathologicM,"Code to represent the defined absence or presence of distant spread or metastases (M) to locations via vascular channels or lymphatics beyond the regional lymph nodes, using criteria established by the American Joint Committee on Cancer (AJCC).",False,,"['M1c', 'M1', 'Not Reported', 'Unknown', 'M1b', 'M0', 'M1a', 'cM0 (i+)', 'MX', '']",,Diagnosis +Ovarian Specimen Status,Ovarian Specimen Status,OvarianSpecimenStatus,The text term used to describe the physical condition of the involved ovary.,False,,"['Ovarian Capsule Ruptured', 'Not Reported', 'Ovarian Capsule Intact', 'Unknown', 'Ovarian Capsule Fragmented', '']",,Diagnosis +AJCC Pathologic Stage,AJCC Pathologic Stage,AJCCPathologicStage,"The extent of a cancer, especially whether the disease has spread from the original site to other parts of the body based on AJCC staging criteria.",False,,"['Stage IC', 'Stage IIA', 'Stage IIC', 'Stage IVB', 'Stage IIIA', 'Stage IB', 'Stage IIIC2', 'Stage IS', 'Stage I', 'Stage IVC', 'Stage 0', 'Stage IB2', 'Stage IIC1', 'Unknown', 'Stage 0is', 'Stage IVA', 'Stage IA', 'Not Reported', 'Stage 0a', 'Stage Tis', 'Stage X', 'Stage IB1', 'Stage IIB', 'Stage II', 'Stage IA2', 'Stage III', 'Stage IIIC1', 'Stage IV', 'Stage IIIB', 'Stage IIA1', 'Stage IA1', 'Stage IIIC', 'Stage IIA2', '']",,Diagnosis +Gleason Grade Tertiary,Gleason Grade Tertiary,GleasonGradeTertiary,The text term used to describe the tertiary pattern as described by the Gleason Grading System.,False,,"['Pattern 5', 'Pattern 4', '']",,Diagnosis +Lymph Nodes Positive,Lymph Nodes Positive,LymphNodesPositive,The number of lymph nodes involved with disease as determined by pathologic examination.,False,,,,Diagnosis +Micropapillary Features,Micropapillary Features,MicropapillaryFeatures,The yes/no/unknown indicator used to describe whether micropapillary features were determined to be present.,False,,"['Absent', 'Unknown', 'Not Reported', 'Present', '']",,Diagnosis +AJCC Clinical N,AJCC Clinical N,AJCCClinicalN,Extent of the regional lymph node involvement for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.,False,,"['N3', 'N0 (i-)', 'N3c', 'N1b', 'N1a', 'N2c', 'N4', 'N0 (mol+)', 'N1bII', 'N1bIV', 'Unknown', 'N2b', 'N1c', 'Not Reported', 'N3a', 'N1', 'N1bI', 'N3b', 'N0', 'N1mi', 'N0 (i+)', 'N2a', 'N0 (mol-)', 'N1bIII', 'N2', 'NX', '']",,Diagnosis +Tumor Largest Dimension Diameter,Tumor Largest Dimension Diameter,TumorLargestDimensionDiameter,"Numeric value used to describe the maximum diameter or dimension of the primary tumor, measured in centimeters.",False,,,,Diagnosis +WHO NTE Grade,WHO NTE Grade,WHONTEGrade,WHO NTE Grade,False,,"['Not Reported', 'GX', 'G2', 'Unknown', 'G3', 'G1', '']",,Diagnosis +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Diagnosis +Year of Diagnosis,Year of Diagnosis,YearofDiagnosis,Numeric value to represent the year of an individual's initial pathologic diagnosis of cancer.,False,,,,Diagnosis +Last Known Disease Status,Last Known Disease Status,LastKnownDiseaseStatus,Text term that describes the last known state or condition of an individual's neoplasm.,True,,"['With tumor', 'Not Reported', 'Not Applicable', 'unknown tumor status', 'Distant met recurrence/progression', 'Loco-regional recurrence/progression', 'Tumor free', 'Biochemical evidence of disease without structural correlate', 'Not Allowed To Collect']",,Diagnosis +IGCCCG Stage,IGCCCG Stage,IGCCCGStage,"The text term used to describe the International Germ Cell Cancer Collaborative Group (IGCCCG), a grouping used to further classify metastatic testicular tumors.",False,,"['Good Prognosis', 'Intermediate Prognosis', 'Not Reported', 'Poor Prognosis', 'Unknown', '']",,Diagnosis +Residual Disease,Residual Disease,ResidualDisease,Text terms to describe the status of a tissue margin following surgical resection.,False,,"['Not Reported', 'R1', 'RX', 'R0', 'Unknown', 'R2', '']",,Diagnosis +Best Overall Response,Best Overall Response,BestOverallResponse,The best improvement achieved throughout the entire course of protocol treatment.,False,,"['DU-Disease Unchanged', 'MX-Mixed Response', 'PSR-Pseudoresponse', 'CRU-Complete Response Unconfirmed', 'PPD-Pseudoprogression', 'CPD-Clinical Progression', 'IMR-Immunoresponse', 'SD-Stable Disease', 'SPD-Surgical Progression', 'PB-Palliative Benefit', 'PA-Palliative Therapy', 'VGPR-Very Good Partial Response', 'CR-Complete Response', 'NR-No Response', 'RPD-Radiographic Progressive Disease', 'sCR-Stringent Complete Response', 'NPB-No Palliative Benefit', 'MR-Minimal/Marginal Response', 'RP-Response', 'TE-Too Early', 'PR-Partial Response', 'AJ-Adjuvant Therapy', 'Non-CR/Non-PD-Non-CR/Non-PD', 'PD-Progressive Disease', 'RD-Responsive Disease', 'IPD-Immunoprogression', '']",,Diagnosis +AJCC Clinical Stage,AJCC Clinical Stage,AJCCClinicalStage,"Stage group determined from clinical information on the tumor (T), regional node (N) and metastases (M) and by grouping cases with similar prognosis for cancer.",False,,"['Stage IC', 'Stage IIA', 'Stage IIC', 'Stage IVB', 'Stage IIIA', 'Stage IB', 'Stage IIIC2', 'Stage IS', 'Stage I', 'Stage IVC', 'Stage 0', 'Stage IB2', 'Stage IIC1', 'Unknown', 'Stage 0is', 'Stage IVA', 'Stage IA', 'Not Reported', 'Stage 0a', 'Stage Tis', 'Stage X', 'Stage IB1', 'Stage IIB', 'Stage II', 'Stage IA2', 'Stage III', 'Stage IIIC1', 'Stage IV', 'Stage IIIB', 'Stage IIA1', 'Stage IA1', 'Stage IIIC', 'Stage IIA2', '']",,Diagnosis +Synchronous Malignancy,Synchronous Malignancy,SynchronousMalignancy,"A yes/no/unknown indicator used to describe whether the patient had an additional malignant diagnosis at the same time the tumor used for sequencing was diagnosed. If both tumors were sequenced, both tumors would have synchronous malignancies.",False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,Diagnosis +Classification of Tumor,Classification of Tumor,ClassificationofTumor,Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint.,False,,"['Not Reported', 'primary', 'Other', 'Unknown', 'Metastasis', 'Recurrence', 'Not Allowed To Collect', '']",,Diagnosis +Medulloblastoma Molecular Classification,Medulloblastoma Molecular Classification,MedulloblastomaMolecularClassification,The text term used to describe the classification of medulloblastoma tumors based on molecular features.,False,,"['SHH-Activated', 'Not Reported', 'Not Determined', 'WNT-Activated', 'Non-WNT/non-SHH Activated', 'Unknown', '']",,Diagnosis +Supratentorial Localization,Supratentorial Localization,SupratentorialLocalization,Text term to specify the location of the supratentorial tumor.,False,,"['Not Reported', 'Spinal Cord', 'Unknown', 'Cerebral Cortex', 'White Matter', 'Deep Gray', '']",,Diagnosis +Non Nodal Regional Disease,Non Nodal Regional Disease,NonNodalRegionalDisease,The text term used to describe whether the patient had non-nodal regional disease.,False,,"['Not Reported', 'Absent', 'Unknown', 'Indeterminate', 'Present', '']",,Diagnosis +Tumor Focality,Tumor Focality,TumorFocality,The text term used to describe whether the patient's disease originated in a single location or multiple locations.,False,,"['Unknown', 'Unifocal', 'Not Reported', 'Multifocal', '']",,Diagnosis +AJCC Clinical M,AJCC Clinical M,AJCCClinicalM,Extent of the distant metastasis for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.,False,,"['M1c', 'M1', 'Not Reported', 'Unknown', 'M1b', 'M0', 'M1a', 'cM0 (i+)', 'MX', '']",,Diagnosis +First Symptom Prior to Diagnosis,First Symptom Prior to Diagnosis,FirstSymptomPriortoDiagnosis,Text term used to describe the patient's first symptom experienced prior to diagnosis and thought to be related to the disease.,False,,"['Visual Changes', 'Not Reported', 'Altered Mental Status', 'Headaches', 'Motor or Movement Changes', 'Unknown', 'Sensory Changes', 'Seizures', '']",,Diagnosis +Greatest Tumor Dimension,Greatest Tumor Dimension,GreatestTumorDimension,Numeric value that represents the measurement of the widest portion of the tumor in centimeters.,False,,,,Diagnosis +AJCC Pathologic N,AJCC Pathologic N,AJCCPathologicN,The codes that represent the stage of cancer based on the nodes present (N stage) according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.,False,,"['N3', 'N0 (i-)', 'N3c', 'N1b', 'N1a', 'N2c', 'N4', 'N0 (mol+)', 'N1bII', 'N1bIV', 'Unknown', 'N2b', 'N1c', 'Not Reported', 'N3a', 'N1', 'N1bI', 'N3b', 'N0', 'N1mi', 'N0 (i+)', 'N2a', 'N0 (mol-)', 'N1bIII', 'N2', 'NX', '']",,Diagnosis +Metastasis at Diagnosis,Metastasis at Diagnosis,MetastasisatDiagnosis,The text term used to describe the extent of metastatic disease present at diagnosis.,False,,"['Not Reported', 'Regional Metastasis', 'Distant Metastasis', 'Metastasis NOS', 'Unknown', 'No Metastasis', '']",,Diagnosis +Gross Tumor Weight,Gross Tumor Weight,GrossTumorWeight,"Numeric value used to describe the gross pathologic tumor weight, measured in grams.",False,,,,Diagnosis +Breslow Thickness,Breslow Thickness,BreslowThickness,"The number that describes the distance, in millimeters, between the upper layer of the epidermis and the deepest point of tumor penetration.",False,,,,Diagnosis +Lymph Node Involved Site,Lymph Node Involved Site,LymphNodeInvolvedSite,The text term used to describe the anatomic site of lymph node involvement.,False,,"['Epitrochlear', 'Splenic', 'Retroperitoneal', 'Iliac-external', 'Femoral', 'Axillary', 'None', 'Cervical', 'Unknown', 'Paraaortic', 'Mesenteric', 'Not Reported', 'Popliteal', 'Hilar', 'Supraclavicular', 'Inguinal', 'Iliac-common', 'Occipital', 'Iliac', 'Submandibular', 'NOS', 'Parotid', 'Mediastinal', '']",,Diagnosis +Progression or Recurrence,Progression or Recurrence,ProgressionorRecurrence,Yes/No/unknown indicator to identify whether a patient has had a new tumor event after initial treatment.,True,,"['No', 'Yes - Progression or Recurrence', 'Unknown', 'Not Reported']",,Diagnosis +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,Diagnosis +Gleason Patterns Percent,Gleason Patterns Percent,GleasonPatternsPercent,"Numeric value that represents the percentage of Patterns 4 and 5, which is used when the Gleason score is greater than 7 to predict prognosis.",False,,,,Diagnosis +Vascular Invasion Present,Vascular Invasion Present,VascularInvasionPresent,The yes/no indicator to ask if large vessel or venous invasion was detected by surgery or presence in a tumor specimen.,False,,"['Yes - Vascular Invasion Present', 'Not Reported', 'No', 'Unknown', 'Not Allowed To Collect', '']",,Diagnosis +Mitotic Count,Mitotic Count,MitoticCount,"The number of mitoses identified under the microscope in tumors. The method of counting varies, according to the specific tumor examined. Usually, the mitotic count is determined based on the number of mitoses per high power field (40X) or 10 high power fields.",False,,,,Diagnosis +Perineural Invasion Present,Perineural Invasion Present,PerineuralInvasionPresent,A yes/no indicator to ask if perineural invasion or infiltration of tumor or cancer is present.,False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,Diagnosis +Secondary Gleason Grade,Secondary Gleason Grade,SecondaryGleasonGrade,"The text term used to describe the secondary Gleason score, which describes the pattern of cells making up the second largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.",False,,"['Pattern 2', 'Pattern 3', 'Pattern 5', 'Pattern 1', 'Pattern 4', '']",,Diagnosis +ISS Stage,ISS Stage,ISSStage,The multiple myeloma disease stage at diagnosis.,False,,"['Not Reported', 'III', 'Unknown', 'I', 'II', '']",,Diagnosis +Margins Involved Site,Margins Involved Site,MarginsInvolvedSite,The text term used to describe the anatomic sites that were involved in the survival margins.,False,,"['Renal Sinus', 'Gerota Fascia', 'Renal Vein', 'Ureter', 'Renal', 'Parenchyma', 'Perinephric Fat', 'Renal Capsule', '']",,Diagnosis +INPC Grade,INPC Grade,INPCGrade,"Text term used to describe the classification of neuroblastic differentiation within neuroblastoma tumors, as defined by the International Neuroblastoma Pathology Classification (INPC).",False,,"['Differentiating', 'Poorly Differentiated', 'Not Reported', 'Unknown', 'Undifferentiated', '']",,Diagnosis +Morphology,Morphology,Morphology,"The third edition of the International Classification of Diseases for Oncology, published in 2000 used principally in tumor and cancer registries for coding the site (topography) and the histology (morphology) of neoplasms. The study of the structure of the cells and their arrangement to constitute tissues and, finally, the association among these to form organs. In pathology, the microscopic process of identifying normal and abnormal morphologic characteristics in tissues, by employing various cytochemical and immunocytochemical stains. A system of numbered categories for representation of data.",True,,,,Diagnosis +Tumor Grade,Tumor Grade,TumorGrade,"Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.",True,,"['Low Grade', 'Not Reported', 'High Grade', 'Intermediate Grade', 'Not Applicable', 'GX', 'G2', 'Unknown', 'GB', 'G3', 'G4', 'G1']",,Diagnosis +Ovarian Surface Involvement,Ovarian Surface Involvement,OvarianSurfaceInvolvement,The text term that describes whether the surface tissue (outer boundary) of the ovary shows evidence of involvement or presence of cancer.,False,,"['Not Reported', 'Absent', 'Unknown', 'Indeterminate', 'Present', '']",,Diagnosis +AJCC Staging System Edition,AJCC Staging System Edition,AJCCStagingSystemEdition,"The text term used to describe the version or edition of the American Joint Committee on Cancer Staging Handbooks, a publication by the group formed for the purpose of developing a system of staging for cancer that is acceptable to the American medical profession and is compatible with other accepted classifications.",False,,"['6th', 'Not Reported', '5th', '7th', '1st', 'Unknown', '4th', '8th', '2nd', '3rd', '']",,Diagnosis +Primary Diagnosis,Primary Diagnosis,PrimaryDiagnosis,"Text term used to describe the patient's histologic diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",True,,"['Adenocarcinoma in tubular adenoma', 'Tumor cells NOS', 'Malignant lymphoma mixed cell type follicular', 'T-cell large granular lymphocytic leukemia', 'Kaposi sarcoma', 'Carcinoma in adenomatous polyp', 'Adenocarcinoma in situ in tubular adenoma', 'Mixed medullary-papillary carcinoma', 'Liposarcoma NOS', 'Carcinoma intestinal type', 'Classical Hodgkin lymphoma nodular sclerosis grade 1', 'Bile duct adenoma', 'Inflammatory carcinoma', 'Carcinoma in situ in a polyp NOS', 'Intravascular B-cell lymphoma', 'Melanotic psammomatous MPNST', 'Acinar cell carcinoma', 'Papillary renal cell carcinoma', 'Papillary serous cystadenoma NOS', 'Papillary adenoma NOS', 'Interstitial cell tumor benign', 'Mixed small cell carcinoma', 'Rhabdoid sarcoma', 'Malignant lymphoma mixed cell type diffuse', 'Chronic leukemia NOS', 'Intraductal papillary carcinoma', 'Intraductal tubular-papillary neoplasm high grade', 'Central neurocytoma', 'Undifferentiated spindle cell sarcoma', 'Bronchiolo-alveolar carcinoma indeterminate type', 'Pancreatic endocrine tumor NOS', 'Tubulocystic renal cell carcinoma', 'Basophil adenocarcinoma', 'Intraductal carcinoma solid type', 'Papillotubular adenoma', 'Undifferentiated epithelioid sarcoma', 'Renal medullary carcinoma', 'Chronic granulocytic leukemia Philadelphia chromosome (Ph1) positive', 'Unclassified tumor benign', 'Bronchial adenoma cylindroid', 'Classical Hodgkin lymphoma mixed cellularity NOS', 'Pigmented adenoma', 'Infiltrating duct and colloid carcinoma', 'Bronchial-associated lymphoid tissue lymphoma', 'Epidermoid carcinoma in situ NOS', 'Unknown', 'Carcinoma NOS', 'Malignancy', 'Undifferentiated leukaemia', 'Unclassified tumor borderline malignancy', 'Hodgkin lymphoma NOS', 'Papillary cystadenoma NOS', 'Medullary carcinoma NOS', 'Myeloma NOS', 'Acute basophilic leukaemia', 'Renal cell carcinoma NOS', 'Neoplasm secondary', 'Primary amyloidosis', 'Acute lymphoblastic leukemia NOS', 'Malignant melanoma in junctional nevus', 'Nevus NOS', 'Tumor malignant NOS', 'Basal cell adenoma', 'Bronchio-alveolar carcinoma mucinous', 'Mucosal-associated lymphoid tissue lymphoma', 'Pleomorphic lobular carcinoma in situ', 'Small cell carcinoma NOS', 'Dermal nevus', 'Liver cell adenoma', 'Malignant lymphoma lymphocytic diffuse NOS', 'Cerebellar liponeurocytoma', 'Acute lymphoblastic leukemia mature B-cell type', 'Adenocarcinoma combined with other types of carcinoma', 'Adenocarcinoma metastatic NOS', 'Carcinoma in a polyp NOS', 'Pleomorphic adenoma', 'Osteosarcoma NOS', 'Carcinosarcoma NOS', 'Lymphoblastic leukemia NOS', 'Unclassified tumor uncertain whether benign or malignant', 'Renal cell carcinoma unclassified', 'Neoplasm NOS', 'Acute lymphoblastic leukemia precursor cell type', 'Cerebellar sarcoma NOS', 'Renal cell carcinoma spindle cell', 'Small cell sarcoma', 'Bronchiolo-alveolar carcinoma goblet cell type', 'Combined small cell-adenocarcinoma', 'Precancerous melanosis NOS', 'Tumor NOS', 'Neoplasm malignant', 'Melanoma in situ', 'Melanotic neuroectodermal tumor', 'Intraductal carcinoma NOS', 'Lymphoma NOS', 'Tumor cells malignant', 'Hepatocholangiocarcinoma', 'Preleukemic syndrome', 'Papillomatosis glandular', 'Small congenital nevus', 'c-ALL', 'Hodgkin lymphoma nodular sclerosis NOS', 'Bronchiolo-alveolar adenocarcinoma NOS', 'Pancreatic microadenoma', 'Tubular carcinoid', 'Gastrinoma NOS', 'Papillary urothelial carcinoma', 'Carcinoma in situ in adenomatous polyp', 'Pancreatobiliary-type carcinoma', 'Small cell osteosarcoma', 'Adenocarcinoma of anal glands', 'Gastrointestinal stromal tumor malignant', 'Acute myeloid leukemia minimal differentiation', 'Ductal carcinoma NOS', 'Malignant melanoma in Hutchinson melanotic freckle', 'Malignant lymphoma nodular NOS', 'B-cell lymphocytic leukemia/small lymphocytic lymphoma', 'Malignant lymphoma NOS', 'Combined hepatocellular carcinoma and cholangiocarcinoma', 'Combined small cell-large carcinoma', 'Epithelial tumor malignant', 'Intraepidermal carcinoma NOS', 'Endometrioid carcinoma NOS', 'Acute leukemia Burkitt type', 'Pituitary adenoma NOS', 'Adenocarcinoma NOS', 'Papillary epidermoid carcinoma', 'Teratoma NOS', 'Combined small cell-squamous cell carcinoma', 'Lobular carcinoma NOS', 'Basophil carcinoma', 'Serous cystadenocarcinoma NOS', 'Glioma malignant', 'Diffuse astrocytoma IDH-wildtype', 'Renal cell carcinoma sarcomatoid', 'Hepatoid adenocarcinoma', 'Intraductal and lobular carcinoma', 'Malignant melanoma NOS', 'Peripheral T-cell lymphoma large cell', 'Chronic myelomonocytic leukemia Type 1', 'Combined/mixed carcinoid and adenocarcinoma', 'Intraductal carcinoma and lobular carcinoma in situ', 'Pancreatic endocrine tumor nonfunctioning', 'Tubulovillous adenoma NOS', 'Intraductal carcinoma noninfiltrating NOS', 'Tumorlet benign', 'Basal cell epithelioma', 'Endometrioid adenocarcinoma NOS', 'Large cell carcinoma NOS', 'Burkitt tumor', 'Papillary microcarcinoma', 'Melanotic neurofibroma', 'Paget disease and intraductal carcinoma of breast', 'Precursor B-cell lymphoblastic lymphoma', 'Pleomorphic carcinoma', 'Dysplastic nevus', 'Undifferentiated high-grade pleomorphic sarcoma', 'Acute myeloid leukemia NOS', 'Esophageal glandular dysplasia (intraepithelial neoplasia) low grade', 'Unclassified tumor malignant uncertain whether primary or metastatic', 'Mixed pineal tumor', 'Bile duct adenocarcinoma', 'Adenocarcinoma in adenomatous polyp', 'Lymphatic leukemic NOS', 'Papillotubular adenocarcinoma', 'Lobular adenocarcinoma', 'Melanocytoma eyeball', 'Melanoma malignant of soft parts', 'Therapy related myeloid neoplasm', 'Oat cell carcinoma', 'Duct carcinoma desmoplastic type', 'Melanotic MPNST', 'Neurofibromatosis NOS', 'Melanotic medulloblastoma', 'Skin appendage carcinoma', 'Hodgkin disease NOS', 'Diffuse melanocytosis', 'Preleukemia', 'Tumor cells benign', 'Chronic myelomonocytic leukemia Type II', 'Cervical intraepithelial neoplasia low grade', 'Tubulo-papillary adenoma', 'Adenocarcinoma of anal ducts', 'Papillary carcinoma in situ', 'Acute lymphocytic leukemia', 'Myeloid leukemia NOS', 'T-cell large granular lymphocytosis', 'Bronchial adenoma NOS', 'Pulmonary blastoma', 'Intraductal carcinoma clinging', 'Adult T-cell lymphoma/leukemia', 'Intraductal adenocarcinoma noninfiltrating NOS', 'Acute lymphatic leukemia', 'Infiltrating duct and cribriform carcinoma', 'Neoplasm metastatic', 'Basal cell tumor', 'Papilloma of bladder', 'Teratoma malignant NOS', 'Pancreatoblastoma', 'Infiltrating duct carcinoma NOS', 'Precursor T-cell lymphoblastic lymphoma', 'Basal cell carcinoma NOS', 'Malignant melanoma in precancerous melanosis', 'Inflammatory adenocarcinoma', 'Splenic B-cell lymphoma/leukemia unclassifiable', 'Squamous cell carcinoma adenoid', 'T-cell lymphoma NOS', 'Tubular adenoma NOS', 'Papillary adenocarcinoma NOS', 'Esophageal intraepithelial neoplasia high grade', 'Papillary squamous cell carcinoma', 'Pulmonary adenomatosis', 'Bile duct cystadenoma', 'Combined large cell neuroendocrine carcinoma', 'Neoplasm uncertain whether benign or malignant', 'Mammary carcinoma in situ', 'Melanoma NOS', 'Spindle cell melanoma NOS', 'Esophageal glandular dysplasia (intraepithelial neoplasia) high grade', 'Neuroendocrine carcinoma NOS', 'Meningeal melanoma', 'Burkitt-like lymphoma', 'Precursor cell lymphoblastic leukemia NOS', 'Acute lymphoid leukemia', 'Chondrosarcoma grade 2/3', 'Tubulopapillary adenocarcinoma', 'B lymphoblastic leukemia/lymphoma NOS', 'Non-lymphocytic leukemia NOS', 'Pleomorphic liposarcoma', 'Mixed medullary-follicular carcinoma', 'Bronchiolo-alveolar carcinoma NOS', 'Myelocytic leukemia NOS', 'Splenic lymphoma with villous lymphocytes', 'Transitional carcinoma', 'Melanocytic nevus', 'Liposarcoma well differentiated', 'Eosinophilic leukemia', 'Chronic myeloproliferative disease NOS', 'Adenocarcinoma in situ in a polyp NOS', 'Hodgkin lymphoma mixed cellularity NOS', 'Classical Hodgkin lymphoma nodular sclerosis grade 2', 'Eosinophilic granuloma', 'Tumor embolus', 'Mixed tumor NOS', 'Carcinoma diffuse type', 'Precursor T-cell lymphoblastic leukemia', 'Neurofibrosarcoma', 'Melanocytoma NOS', 'B-ALL', 'Bronchio-alveolar carcinoma mixed mucinous and non-mucinous', 'Acute myeloid leukemia MLL', 'Adenocarcinoma in situ non-mucinous', 'Malignant lymphoma lymphoblastic NOS', 'Papillary adenocarcinoma follicular variant', 'Tumor cells uncertain whether benign or malignant', 'Pleomorphic lipoma', 'Lymphocytic leukemia NOS', 'Astrocytoma anaplastic', 'Non-Hodgkin lymphoma NOS', 'Papillary serous adenocarcinoma', 'Meningioma malignant', 'Chronic lymphoid leukemia', 'Ductal carcinoma in situ NOS', 'Neuroepithelioma NOS', 'Melanotic progonoma', 'Melanotic schwannoma', 'Diffuse astrocytoma IDH-mutant', 'Small cell neuroendocrine carcinoma', 'Esophageal squamous intraepithelial neoplasia (dysplasia) high grade', 'Paget disease extramammary', 'Prostatic intraepithelial neoplasia grade III', 'Ewing sarcoma', 'Micropapillary carcinoma NOS', 'Epithelial tumor benign', 'Hepatocellular adenoma', 'Cementoma NOS', 'Malignant lymphoma mixed cell type nodular', 'Acute leukemia NOS', 'Bile duct carcinoma', 'Nephroblastoma NOS', 'Pagetoid reticulosis', 'Hepatocarcinoma', 'Not Reported', 'Neoplasm malignant uncertain whether primary or metastatic', 'Malignant melanoma regressing', 'Bronchiolo-alveolar carcinoma Clara cell and goblet cell type', 'Dermatofibroma NOS', 'Interstitial cell tumor malignant', 'Adenocarcinoma in situ NOS', 'Adenocarcinoma endocervical type', 'Meningioma anaplastic', 'B lymphoblastic leukemia/lymphoma with hypodiploidy (Hypodiploid ALL)', 'Intraductal tubulopapillary neoplasm', 'Tumor secondary', 'Chronic myelogenous leukemia Philadelphia chromosome (Ph 1) positive', 'Sclerosing hemangioma', 'Papillary transitional cell carcinoma', 'Tubular androblastoma NOS', 'Ependymoma NOS', 'Papillary tumor of the pineal region', 'Chronic myelocytic leukemia NOS', 'Papillary serous cystadenocarcinoma', 'Haemangiosarcoma', 'Papillary and follicular carcinoma', 'Chronic myelomonocytic leukemia in transformation', 'Carcinoma anaplastic NOS', 'Paget disease mammary', 'Liver cell carcinoma', 'Eosinophil adenocarcinoma', 'Sclerosing hepatic carcinoma', 'Tumor metastatic', 'Endometrial sarcoma NOS', 'Gastrin cell tumor', 'Chronic myeloproliferative disorder', 'Acute promyelocytic leukemia NOS', 'Malignant lymphoma Hodgkin', 'Classical Hodgkin lymphoma lymphocyte depletion NOS', 'Lobular carcinoma noninfiltrating', 'Mixed pancreatic endocrine and exocrine tumor malignant', 'Unclassified tumor malignant', 'Chondroma NOS', 'Basophil adenoma', 'Transitional cell carcinoma', 'Carcinoma metastatic NOS', 'Medullary adenocarcinoma', 'Adenocarcinoma in villous adenoma', 'Ganglioglioma NOS', 'Intradermal nevus', 'Osteoblastoma malignant', 'Papillary squamous cell carcinoma in situ', 'Undifferentiated pleomorphic sarcoma', 'Bronchiolar carcinoma', 'Pancreatic endocrine tumor benign', 'Malignant melanoma in congenital melanocytic nevus', 'Malignant lymphoma diffuse NOS', 'Composite Hodgkin and non-Hodgkin lymphoma', 'Monocytic leukemia NOS', 'Paraganglioma malignant', 'Splenic diffuse red pulp small B-cell lymphoma', 'B lymphoblastic leukemia/lymphoma with hyperdiploidy', 'Rodent ulcer', 'Hodgkin sarcoma', 'Familial adenomatous polyposis', 'Duct cell carcinoma', 'Rhabdomyosarcoma NOS', 'Eosinophil carcinoma', 'Pulmonary artery intimal sarcoma', 'Capillary hemangioma', 'Adult rhabdomyoma', 'Tubular carcinoma', 'Burkitt cell leukemia', 'Bronchiolo-alveolar carcinoma Clara cell', 'Papillary glioneuronal tumor', 'T lymphoblastic leukemia/lymphoma', 'Neuroblastoma NOS', 'Meningioma NOS', 'Adenocarcinoid tumor', 'Malignant lymphoma large cell NOS', 'Combined small cell carcinoma', 'Mucous adenocarcinoma', 'Peripheral T-cell lymphoma NOS', 'Renal carcinoma collecting duct type', 'Bile duct cystadenocarcinoma', 'Chronic myelogenous leukemia BCR-ABL positive', 'Intraductal tubular-papillary neoplasm low grade', 'Tumor benign', 'Adenocarcinoma intestinal type', 'Pro-B ALL', 'Malignant lymphoma large B-cell diffuse NOS', 'Secondary carcinoma', 'Gastrinoma malignant', 'Intracystic papilloma', 'Cancer', 'Intraductal papillary adenocarcinoma with invasion', 'Mixed squamous cell and glandular papilloma', 'Sarcoma NOS', 'Non-invasive low grade serous carcinoma', 'Serous surface papillary carcinoma', 'Pro-T ALL', 'Neurofibroma NOS', 'Pancreatobiliary neoplasm non-invasive', 'Bronchial adenoma carcinoid', 'Precursor B-cell lymphoblastic leukemia', 'Melanoameloblastoma', 'Mixed adenocarcinoma and epidermoid carcinoma', 'Splenic marginal zone lymphoma NOS', 'Intraepidermal squamous cell carcinoma Bowen type', 'Carcinoma undifferentiated NOS', 'Capillary lymphangioma', 'Chronic myelomonocytic leukemia NOS', 'Adenocarcinoma in a polyp NOS', 'Astrocytoma NOS', 'Glioblastoma', 'Adult T-cell lymphoma', 'Transitional cell carcinoma in situ', 'Carcinoma in pleomorphic adenoma', 'Renal cell adenocarcinoma', 'Medulloblastoma NOS', 'Papillomatosis NOS', 'Acute myelomonocytic leukemia', 'Malignant lymphoma immunoblastic NOS', 'Chronic lymphocytic leukemia B-cell type (includes all variants of BCLL)', 'Malignant lymphoma lymphocytic NOS', 'Nonpigmented nevus', 'Squamous cell carcinoma clear cell type', 'Mixed adenocarcinoma and squamous cell carcinoma', 'Diffuse large B-cell lymphoma NOS', 'Paraganglioma benign', 'Malignant lymphoma non-Hodgkin NOS', 'Classical Hodgkin lymphoma lymphocyte-rich', 'Intraductal micropapillary carcinoma', 'Secretory carcinoma of breast', 'Gastrin cell tumor malignant', 'Papilloma NOS', 'Infiltrating basal cell carcinoma NOS', 'Adenocarcinoma in polypoid adenoma', 'Chronic neutrophilic leukemia', 'Undifferentiated sarcoma', 'Neurosarcoma', 'Medullary osteosarcoma', 'Papillary carcinoma NOS', 'Chronic lymphocytic leukemia', 'Undifferentiated uterine sarcoma', 'Malignant lymphoma lymphocytic nodular NOS', 'Adenocarcinoma in situ mucinous', 'Multiple myeloma', 'Lobular and ductal carcinoma', 'Undifferentiated round cell sarcoma', 'Chronic lymphatic leukemia', 'Endometrioid adenofibroma NOS', 'Malignant lymphoma large B-cell NOS', 'Pancreatic endocrine tumor malignant', 'Cervical intraepithelial neoplasia grade III', 'Glioma NOS', 'Papillary adenofibroma', 'Classical Hodgkin lymphoma nodular sclerosis NOS', 'Non-small cell carcinoma', 'Squamous cell carcinoma NOS', 'Haemangioblastoma', 'Paraganglioma NOS', 'Bronchiolar adenocarcinoma', 'Liposarcoma differentiated', 'Mixed tumor malignant NOS', 'Burkitt lymphoma NOS (Includes all variants)', 'Renal cell carcinoma chromophobe type', 'Malignant melanoma in giant pigmented nevus', 'Chronic monocytic leukemia', 'Carcinoma in situ NOS', 'Lymphoblastoma', 'Tubulolobular carcinoma', 'Rhabdoid tumor NOS', 'Hepatocellular carcinoma NOS', 'Adenocarcinoma in situ in adenomatous polyp', 'Classical Hodgkin lymphoma nodular sclerosis cellular phase', 'Paget disease of breast', 'Squamous cell carcinoma in situ NOS', 'Classical Hodgkin lymphoma lymphocyte depletion diffuse fibrosis', 'Bronchiolo-alveolar carcinoma non-mucinous', 'Rhabdosarcoma', 'Astrocytoma low grade', 'Chronic myeloid leukemia NOS', 'Chronic granulocytic leukemia NOS', 'Endometrioid adenoma NOS', 'Typical carcinoid', 'Rhabdoid meningioma', 'Hodgkin paragranuloma NOS', 'Hodgkin granuloma', 'Duct adenocarcinoma NOS', 'Juvenile myelomonocytic leukemia', 'Adenocarcinoma diffuse type', 'Osteoblastoma NOS', 'Rhabdomyosarcoma with ganglionic differentiation', 'Eosinophil adenoma', 'Interstitial cell tumor NOS', 'Tubular adenocarcinoma', 'Myoepithelioma', 'Pigmented nevus NOS', 'Duct carcinoma NOS', 'Neoplasm benign', 'Rhabdomyoma NOS', 'Spindle cell carcinoma NOS', 'Pleomorphic lobular carcinoma', 'Lobular carcinoma in situ NOS', 'Central neuroblastoma', 'Adenocarcinoma pancreatobiliary type', 'Chronic granulocytic leukemia BCR/ABL', 'Pigmented basal cell carcinoma', 'Paget disease and infiltrating duct carcinoma of breast', 'Acute lymphoblastic leukemia-lymphoma NOS', 'Epidermoid carcinoma NOS', 'Hepatoid carcinoma', 'Papillary meningioma', 'High-grade serous carcinoma', 'Basal cell adenocarcinoma', 'Esophageal squamous intraepithelial neoplasia (dysplasia) low grade', 'Malignant lymphoma small B lymphocytic NOS', 'Pituitary carcinoma NOS', 'Tubular androblastoma with lipid storage', 'Meningeal melanocytoma', 'Duct adenoma NOS', 'Diffuse astrocytoma low grade', 'Intraductal papillary adenocarcinoma NOS', 'Splenic marginal zone B-cell lymphoma', 'Classical Hodgkin lymphoma lymphocyte depletion reticular', 'B cell lymphoma NOS']",,Diagnosis +Lymphatic Invasion Present,Lymphatic Invasion Present,LymphaticInvasionPresent,"A yes/no indicator to ask if small or thin-walled vessel invasion is present, indicating lymphatic involvement",False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,Diagnosis +Site of Resection or Biopsy,Site of Resection or Biopsy,SiteofResectionorBiopsy,"The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",True,,"['Paraurethral gland', 'Colon NOS', 'Frontal sinus', 'Overlapping lesion of tongue', 'Overlapping lesion of palate', 'Scrotum NOS', 'Bone marrow', 'Axillary tail of breast', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'unknown primary site', 'Broad ligament', 'Lateral floor of mouth', 'Overlapping lesion of vulva', 'Trigone of bladder', 'Lacrimal gland', 'Thorax NOS', 'Ampulla of Vater', 'Myometrium', 'Penis NOS', 'Female genital tract NOS', 'Submandibular gland', 'Anterior 2/3 of tongue NOS', 'Posterior wall of bladder', 'Thymus', 'Endocrine gland NOS', 'Stomach NOS', 'Unknown', 'Cerebrum', 'Splenic flexure of colon', 'Urachus', 'Skin of lip NOS', 'Mucosa of lip NOS', 'Accessory sinus NOS', 'Cortex of adrenal gland', 'Other ill-defined sites', 'Middle lobe lung', 'Pelvis NOS', 'Anus NOS', 'Upper-inner quadrant of breast', 'Posterior mediastinum', 'Esophagus NOS', 'Duodenum', 'Cervical esophagus', 'Optic nerve', 'Long bones of lower limb and associated joints', 'Middle ear', 'Breast NOS', 'Dorsal surface of tongue NOS', 'Lesser curvature of stomach NOS', 'Overlapping lesion of floor of mouth', 'Overlapping lesion of heart mediastinum and pleura', 'Eye NOS', 'Overlapping lesion of esophagus', 'Ciliary body', 'Ureteric orifice', 'Postcricoid region', 'External ear', 'Base of tongue NOS', 'Liver', 'Commissure of lip', 'Cloacogenic zone', 'Lower lobe lung', 'Transverse colon', 'Acoustic nerve', 'Supraglottis', 'Fallopian tube', 'Upper third of esophagus', 'Skin of scalp and neck', 'Choroid', 'Long bones of upper limb scapula and associated joints', 'Overlapping lesion of brain', 'Upper gum', 'Skin NOS', 'Hard palate', 'Ileum', 'Overlapping lesion of colon', 'Ascending colon', 'Lower gum', 'Pelvic bones sacrum coccyx and associated joints', 'Hepatic flexure of colon', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Vestibule of mouth', 'Cervix uteri', 'Bones of skull and face and associated joints', 'Overlapping lesion of lip oral cavity and pharynx', 'Endometrium', 'Sphenoid sinus', 'Overlapping lesion of ill-defined sites', 'Sigmoid colon', 'Peritoneum NOS', 'Specified parts of peritoneum', 'Meckel diverticulum', 'Rectosigmoid junction', 'Kidney NOS', 'Reticuloendothelial system NOS', 'Rectum NOS', 'Pylorus', 'Overlapping lesion of tonsil', 'Pleura NOS', 'Jejunum', 'Vallecula', 'Skin of lower limb and hip', 'Pelvic lymph nodes', 'External lower lip', 'Overlapping lesion of skin', 'Mucosa of upper lip', 'Ovary', 'Cauda equina', 'Lower limb NOS', 'Body of stomach', 'Overlapping lesion of larynx', 'Pancreas NOS', 'Overlapping lesion of lung', 'Overlapping lesion of major salivary glands', 'Uvula', 'Overlapping lesion of hypopharynx', 'Round ligament', 'Corpus uteri', 'Biliary tract NOS', 'Male genital organs NOS', 'Parametrium', 'External lip NOS', 'Overlapping lesion of accessory sinuses', 'Cardia NOS', 'Islets of Langerhans', 'Carotid body', 'Ventral surface of tongue NOS', 'Autonomic nervous system NOS', 'Overlapping lesion of corpus uteri', 'Spinal meninges', 'Posterior wall of nasopharynx', 'Placenta', 'Intrahepatic bile duct', 'Overlapping lesion of digestive system', 'Mediastinum NOS', 'Hematopoietic system NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Major salivary gland NOS', 'Cerebellum NOS', 'Overlapping lesion of stomach', 'Vulva NOS', 'Craniopharyngeal duct', 'Lung NOS', 'Greater curvature of stomach NOS', 'Upper-outer quadrant of breast', 'Gallbladder', 'Thoracic esophagus', 'Lymph nodes of axilla or arm', 'Ventricle NOS', 'Overlapping lesion of biliary tract', 'Hypopharynx NOS', 'Clitoris', 'Exocervix', 'Parietal lobe', 'Waldeyer ring', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Head face or neck NOS', 'Anterior wall of nasopharynx', 'Urethra', 'Overlapping lesion of nasopharynx', 'Maxillary sinus', 'Lymph nodes of inguinal region or leg', 'Ureter', 'Tonsillar pillar', 'Sublingual gland', 'Pituitary gland', 'Gastrointestinal tract NOS', 'Pineal gland', 'Meninges NOS', 'Lingual tonsil', 'Trachea', 'Pyriform sinus', 'Mucosa of lower lip', 'Not Reported', 'Posterior wall of hypopharynx', 'Urinary system NOS', 'Orbit NOS', 'Short bones of lower limb and associated joints', 'Connective subcutaneous and other soft tissues of thorax', 'Upper limb NOS', 'Gastric antrum', 'Lymph node NOS', 'Peripheral nerves and autonomic nervous system of thorax', 'Ill-defined sites within respiratory system', 'Other specified parts of male genital organs', 'Rib sternum clavicle and associated joints', 'Overlapping lesion of bladder', 'Appendix', 'Prostate gland', 'Lymph nodes of multiple regions', 'Lateral wall of nasopharynx', 'Branchial cleft', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Floor of mouth NOS', 'Connective subcutaneous and other soft tissues NOS', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Bladder neck', 'Border of tongue', 'Connective subcutaneous and other soft tissues of abdomen', 'Overlapping lesion of small intestine', 'Lateral wall of bladder', 'Soft palate NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Isthmus uteri', 'Nasal cavity', 'Endocervix', 'Tonsil NOS', 'Glottis', 'Retroperitoneum', 'Peripheral nerves and autonomic nervous system of pelvis', 'Frontal lobe', 'Vagina NOS', 'Undescended testis', 'Laryngeal cartilage', 'Eyelid', 'Hypopharyngeal aspect of aryepiglottic fold', 'Overlapping lesion of other and unspecified parts of mouth', 'Upper lobe lung', 'Lip NOS', 'Lymph nodes of head face and neck', 'Overlapping lesion of brain and central nervous system', 'Overlapping lesion of penis', 'Overlapping lesion of retroperitoneum and peritoneum', 'Parotid gland', 'Dome of bladder', 'Bone of limb NOS', 'Descended testis', 'Vertebral column', 'Fundus uteri', 'Connective subcutaneous and other soft tissues of pelvis', 'Epididymis', 'Intra-abdominal lymph nodes', 'Paraspinal', 'Prepuce', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Pharynx NOS', 'Overlapping lesion of endocrine glands and related structures', 'Gum NOS', 'Spinal cord', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Skin of upper limb and shoulder', 'Nasopharynx NOS', 'Parathyroid gland', 'Bone NOS', 'Mouth NOS', 'Abdomen NOS', 'Conjunctiva', 'Spermatic cord', 'External upper lip', 'Labium minus', 'Renal pelvis', 'Overlapping lesion of lip', 'Short bones of upper limb and associated joints', 'Main bronchus', 'Upper respiratory tract NOS', 'Body of penis', 'Small intestine NOS', 'Central portion of breast', 'Lower-inner quadrant of breast', 'Labium majus', 'Tonsillar fossa', 'Cecum', 'Glans penis', 'Tail of pancreas', 'Lower third of esophagus', 'Body of pancreas', 'Intestinal tract NOS', 'Brain stem', 'Overlapping lesion of rectum anus and anal canal', 'Posterior wall of oropharynx', 'Pancreatic duct', 'Blood', 'Temporal lobe', 'Anterior floor of mouth', 'Nervous system NOS', 'Cornea NOS', 'Palate NOS', 'Occipital lobe', 'Abdominal esophagus', 'Overlapping lesion of pancreas', 'Overlapping lesion of female genital organs', 'Cheek mucosa', 'Retina', 'Overlapping lesion of male genital organs', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Larynx NOS', 'Skin of other and unspecified parts of face', 'Spleen', 'Oropharynx NOS', 'Anal canal', 'Subglottis', 'Cerebral meninges', 'Lateral wall of oropharynx', 'Middle third of esophagus', 'Nipple', 'Medulla of adrenal gland', 'Overlapping lesion of eye and adnexa', 'Olfactory nerve', 'Ethmoid sinus', 'Overlapping lesion of cervix uteri', 'Descending colon', 'Brain NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Anterior wall of bladder', 'Mandible', 'Other specified parts of pancreas', 'Skin of trunk', 'Other specified parts of female genital organs', 'Uterus NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Intrathoracic lymph nodes', 'Heart', 'Adrenal gland NOS', 'Aortic body and other paraganglia', 'Extrahepatic bile duct', 'Overlapping lesion of breast', 'Superior wall of nasopharynx', 'Fundus of stomach', 'Anterior mediastinum', 'Tongue NOS', 'Cranial nerve NOS', 'Head of pancreas', 'Overlapping lesions of oropharynx', 'Overlapping lesion of bones joints and articular cartilage', 'Retromolar area', 'Testis NOS', 'Connective subcutaneous and other soft tissues of head face and neck', 'Bladder NOS', 'Overlapping lesion of urinary organs', 'Lower-outer quadrant of breast', 'Thyroid gland', 'Anterior surface of epiglottis', 'Uterine adnexa']",,Diagnosis +Tumor Depth,Tumor Depth,TumorDepth,"Numeric value that represents the depth of tumor invasion, measured in millimeters (mm).",False,,,,Diagnosis +Margin Distance,Margin Distance,MarginDistance,Numeric value (in centimeters) that represents the distance between the tumor and the surgical margin.,False,,,,Diagnosis +Vascular Invasion Type,Vascular Invasion Type,VascularInvasionType,Text term that represents the type of vascular tumor invasion.,False,,"['Not Reported', 'Intramural', 'Micro', 'Unknown', 'No Vascular Invasion', 'Macro', 'Extramural', '']",,Diagnosis +IRS Group,IRS Group,IRSGroup,"Text term used to describe the classification of rhabdomyosarcoma tumors, as defined by the Intergroup Rhabdomyosarcoma Study (IRS).",False,,"['Group Ia', 'Group II', 'Group IIc', 'Group IIIa', 'Not Reported', 'Group Ib', 'Group III', 'Unknown', 'Group I', 'Group IV', 'Group IIa', 'Group IIIb', '']",,Diagnosis +Non Nodal Tumor Deposits,Non Nodal Tumor Deposits,NonNodalTumorDeposits,The yes/no/unknown indicator used to describe the presence of tumor deposits in the pericolic or perirectal fat or in adjacent mesentery away from the leading edge of the tumor.,False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,Diagnosis +Days to Diagnosis,Days to Diagnosis,DaystoDiagnosis,Number of days between the date used for index and the date the patient was diagnosed with the malignant disease.,False,,,,Diagnosis +Prior Malignancy,Prior Malignancy,PriorMalignancy,The yes/no/unknown indicator used to describe the patient's history of prior cancer diagnosis.,False,,"['Not Reported', 'Yes', 'No', 'Unknown', 'Not Allowed To Collect', '']",,Diagnosis +Gleason Grade Group,Gleason Grade Group,GleasonGradeGroup,"The text term used to describe the overall grouping of grades defined by the Gleason grading classification, which is used to determine the aggressiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.",False,,"['Group 1', 'Group 4', 'Group 2', 'Group 3', 'Group 5', '']",,Diagnosis +Age at Diagnosis,Age at Diagnosis,AgeatDiagnosis,Age at the time of diagnosis expressed in number of days since birth.,True,,,,Diagnosis +INRG Stage,INRG Stage,INRGStage,"The text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Risk Group (INRG).",False,,"['Not Reported', 'L2', 'Ms', 'Unknown', 'm', 'L1', '']",,Diagnosis +AJCC Clinical T,AJCC Clinical T,AJCCClinicalT,Extent of the primary cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.,False,,"['T2', 'T4a', 'T3a', 'T2b', 'Tis (DCIS)', 'T3c', ""Tis (Paget's)"", 'T4', 'T1b2', 'T2a1', 'T1a2', 'T1b', 'T1b1', 'T1a1', 'Tis', 'TX', 'Unknown', 'T1mi', 'T4d', 'Tis (LCIS)', 'Not Reported', 'T3b', 'T2c', 'T1', 'T4b', 'T1a', 'T2a', 'T3d', 'T2a2', 'T2d', 'T4e', 'T0', 'T1c', 'Ta', 'T4c', 'T3', '']",,Diagnosis +Metastasis at Diagnosis Site,Metastasis at Diagnosis Site,MetastasisatDiagnosisSite,Text term to identify an anatomic site in which metastatic disease involvement is found.,False,,"['Adrenal Gland', 'Lung', 'Soft Tissue', 'Pleura', 'Scalp', 'Brain', 'Liver', 'Groin', 'Small Intestine', 'Axillary', 'Distant Organ', 'Bone', 'Peritoneal Cavity', 'Central Nervous System', 'Unknown', 'Abdomen', 'Ovary', 'Kidney', 'Not Reported', 'Colon', 'Mediastinum', 'Pelvis', 'Inguinal', 'Spinal Cord', 'Bone Marrow', 'Ascites', 'Peritoneum', 'Skin', 'Lymph Node NOS', 'Lymph Node', 'Cerebrospinal Fluid', 'Omentum', 'Distant Nodes', '']",,Diagnosis +Prior Treatment,Prior Treatment,PriorTreatment,A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received before the body specimen was collected.,False,,"['Not Reported', 'Yes', 'No', 'Unknown', 'Not Allowed To Collect', '']",,Diagnosis +Cog Rhabdomyosarcoma Risk Group,Cog Rhabdomyosarcoma Risk Group,CogRhabdomyosarcomaRiskGroup,"Text term used to describe the classification of rhabdomyosarcoma, as defined by the Children's Oncology Group (COG).",False,,"['Not Reported', 'High Risk', 'Intermediate Risk', 'Unknown', 'Low Risk', '']",,Diagnosis +Percent Tumor Invasion,Percent Tumor Invasion,PercentTumorInvasion,The percentage of tumor cells spread locally in a malignant neoplasm through infiltration or destruction of adjacent tissue.,False,,,,Diagnosis +INSS Stage,INSS Stage,INSSStage,"Text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Staging System (INSS).",False,,"['Stage 1', 'Not Reported', 'Stage 4', 'Stage 3', 'Unknown', 'Stage 2B', 'Stage 2A', 'Stage 4S', '']",,Diagnosis +Laterality,Laterality,Laterality,"For tumors in paired organs, designates the side on which the cancer originates.",False,,"['Not Reported', 'Bilateral', 'Midline', 'Unilateral', 'Unknown', 'Left', 'Right', '']",,Diagnosis +Pregnant at Diagnosis,Pregnant at Diagnosis,PregnantatDiagnosis,The text term used to indicate whether the patient was pregnant at the time they were diagnosed.,False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,Diagnosis +Tumor Confined to Organ of Origin,Tumor Confined to Organ of Origin,TumorConfinedtoOrganofOrigin,The yes/no/unknown indicator used to describe whether the tumor is confined to the organ where it originated and did not spread to a proximal or distant location within the body.,False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,Diagnosis +Lymph Nodes Tested,Lymph Nodes Tested,LymphNodesTested,The number of lymph nodes tested to determine whether lymph nodes were involved with disease as determined by a pathologic examination.,False,,,,Diagnosis +AJCC Pathologic T,AJCC Pathologic T,AJCCPathologicT,"Code of pathological T (primary tumor) to define the size or contiguous extension of the primary tumor (T), using staging criteria from the American Joint Committee on Cancer (AJCC).",False,,"['T2', 'T4a', 'T3a', 'T2b', 'Tis (DCIS)', 'T3c', ""Tis (Paget's)"", 'T4', 'T1b2', 'T2a1', 'T1a2', 'T1b', 'T1b1', 'T1a1', 'Tis', 'TX', 'Unknown', 'T1mi', 'T4d', 'Tis (LCIS)', 'Not Reported', 'T3b', 'T2c', 'T1', 'T4b', 'T1a', 'T2a', 'T3d', 'T2a2', 'T2d', 'T4e', 'T0', 'T1c', 'Ta', 'T4c', 'T3', '']",,Diagnosis +WHO CNS Grade,WHO CNS Grade,WHOCNSGrade,WHO CNS Grade,False,,"['Not Reported', 'Grade II', 'Grade IV', 'Grade Not Assigned', 'Unknown', 'Grade III', 'Grade I', '']",,Diagnosis +Method of Diagnosis,Method of Diagnosis,MethodofDiagnosis,Text term used to describe the method used to confirm the patients malignant diagnosis.,False,,"['Pap Smear', 'Bone Marrow Aspirate', 'Blood Draw', 'Enucleation', 'Incisional Biopsy', 'Cystoscopy', 'Biopsy', 'Fine Needle Aspiration', 'Ultrasound Guided Biopsy', 'Unknown', 'Cytology', 'Physical Exam', 'Debulking', 'Not Reported', 'Excisional Biopsy', 'Laparotomy', 'Pathologic Review', 'Surgical Resection', 'Core Biopsy', 'Diagnostic Imaging', 'Other', 'Dilation and Curettage Procedure', 'Laparoscopy', 'Autopsy', 'Thoracentesis', '']",,Diagnosis +INPC Histologic Group,INPC Histologic Group,INPCHistologicGroup,"The text term used to describe the classification of neuroblastomas distinguishing between favorable and unfavorable histologic groups. The histologic score, defined by the International Neuroblastoma Pathology Classification (INPC), is based on age, mitosis-karyorrhexis index (MKI), stromal content and degree of tumor cell differentiation.",False,,"['Unknown', 'Favorable', 'Not Reported', 'Unfavorable', '']",,Diagnosis +Peritoneal Fluid Cytological Status,Peritoneal Fluid Cytological Status,PeritonealFluidCytologicalStatus,The text term used to describe the malignant status of the peritoneal fluid determined by cytologic testing.,False,,"['Atypical', 'Not Reported', 'Unsatisfactory', 'Non-Malignant', 'Unknown', 'Malignant', '']",,Diagnosis +Days to Recurrence,Days to Recurrence,DaystoRecurrence,Number of days between the date used for index and the date the patient's disease recurred.,False,True,," If Progression or Recurrence is ""Yes - Progression or Recurrence"" then ""Days to Recurrence"" is required",Diagnosis +Days to Progression,Days to Progression,DaystoProgression,Number of days between the date used for index and the date the patient's disease progressed.,False,True,," If Progression or Recurrence is ""Yes - Progression or Recurrence"" then ""Days to Progression"" is required",Diagnosis +Progression or Recurrence Type,Progression or Recurrence Type,ProgressionorRecurrenceType,The text term used to describe the type of progressive or recurrent disease or relapsed disease.,False,True,"['Distant', 'Not Reported', 'Unknown', 'Biochemical', 'Regional', 'Local', '']"," If Progression or Recurrence is ""Yes - Progression or Recurrence"" then ""Progression or Recurrence Type"" is required",Diagnosis +Progression or Recurrence Anatomic Site,Progression or Recurrence Anatomic Site,ProgressionorRecurrenceAnatomicSite,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,False,True,"['Paraurethral gland', 'Colon NOS', 'Frontal sinus', 'Overlapping lesion of tongue', 'Overlapping lesion of palate', 'Scrotum NOS', 'Bone marrow', 'Axillary tail of breast', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'unknown primary site', 'Broad ligament', 'Lateral floor of mouth', 'Overlapping lesion of vulva', 'Trigone of bladder', 'Lacrimal gland', 'Thorax NOS', 'Ampulla of Vater', 'Myometrium', 'Penis NOS', 'Female genital tract NOS', 'Submandibular gland', 'Anterior 2/3 of tongue NOS', 'Posterior wall of bladder', 'Thymus', 'Endocrine gland NOS', 'Stomach NOS', 'Unknown', 'Cerebrum', 'Splenic flexure of colon', 'Urachus', 'Skin of lip NOS', 'Mucosa of lip NOS', 'Accessory sinus NOS', 'Cortex of adrenal gland', 'Other ill-defined sites', 'Middle lobe lung', 'Pelvis NOS', 'Anus NOS', 'Upper-inner quadrant of breast', 'Posterior mediastinum', 'Esophagus NOS', 'Duodenum', 'Cervical esophagus', 'Optic nerve', 'Long bones of lower limb and associated joints', 'Middle ear', 'Breast NOS', 'Dorsal surface of tongue NOS', 'Lesser curvature of stomach NOS', 'Overlapping lesion of floor of mouth', 'Overlapping lesion of heart mediastinum and pleura', 'Eye NOS', 'Overlapping lesion of esophagus', 'Ciliary body', 'Ureteric orifice', 'Postcricoid region', 'External ear', 'Base of tongue NOS', 'Liver', 'Commissure of lip', 'Cloacogenic zone', 'Lower lobe lung', 'Transverse colon', 'Acoustic nerve', 'Supraglottis', 'Fallopian tube', 'Upper third of esophagus', 'Skin of scalp and neck', 'Choroid', 'Long bones of upper limb scapula and associated joints', 'Overlapping lesion of brain', 'Upper gum', 'Skin NOS', 'Hard palate', 'Ileum', 'Overlapping lesion of colon', 'Ascending colon', 'Lower gum', 'Pelvic bones sacrum coccyx and associated joints', 'Hepatic flexure of colon', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Vestibule of mouth', 'Cervix uteri', 'Bones of skull and face and associated joints', 'Overlapping lesion of lip oral cavity and pharynx', 'Endometrium', 'Sphenoid sinus', 'Overlapping lesion of ill-defined sites', 'Sigmoid colon', 'Peritoneum NOS', 'Specified parts of peritoneum', 'Meckel diverticulum', 'Rectosigmoid junction', 'Kidney NOS', 'Reticuloendothelial system NOS', 'Rectum NOS', 'Pylorus', 'Overlapping lesion of tonsil', 'Pleura NOS', 'Jejunum', 'Vallecula', 'Skin of lower limb and hip', 'Pelvic lymph nodes', 'External lower lip', 'Overlapping lesion of skin', 'Mucosa of upper lip', 'Ovary', 'Cauda equina', 'Lower limb NOS', 'Body of stomach', 'Overlapping lesion of larynx', 'Pancreas NOS', 'Overlapping lesion of lung', 'Overlapping lesion of major salivary glands', 'Uvula', 'Overlapping lesion of hypopharynx', 'Round ligament', 'Corpus uteri', 'Biliary tract NOS', 'Male genital organs NOS', 'Parametrium', 'External lip NOS', 'Overlapping lesion of accessory sinuses', 'Cardia NOS', 'Islets of Langerhans', 'Carotid body', 'Ventral surface of tongue NOS', 'Autonomic nervous system NOS', 'Overlapping lesion of corpus uteri', 'Spinal meninges', 'Posterior wall of nasopharynx', 'Placenta', 'Intrahepatic bile duct', 'Overlapping lesion of digestive system', 'Mediastinum NOS', 'Hematopoietic system NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Major salivary gland NOS', 'Cerebellum NOS', 'Overlapping lesion of stomach', 'Vulva NOS', 'Craniopharyngeal duct', 'Lung NOS', 'Greater curvature of stomach NOS', 'Upper-outer quadrant of breast', 'Gallbladder', 'Thoracic esophagus', 'Lymph nodes of axilla or arm', 'Ventricle NOS', 'Overlapping lesion of biliary tract', 'Hypopharynx NOS', 'Clitoris', 'Exocervix', 'Parietal lobe', 'Waldeyer ring', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Head face or neck NOS', 'Anterior wall of nasopharynx', 'Urethra', 'Overlapping lesion of nasopharynx', 'Maxillary sinus', 'Lymph nodes of inguinal region or leg', 'Ureter', 'Tonsillar pillar', 'Sublingual gland', 'Pituitary gland', 'Gastrointestinal tract NOS', 'Pineal gland', 'Meninges NOS', 'Lingual tonsil', 'Trachea', 'Pyriform sinus', 'Mucosa of lower lip', 'Not Reported', 'Posterior wall of hypopharynx', 'Urinary system NOS', 'Orbit NOS', 'Short bones of lower limb and associated joints', 'Connective subcutaneous and other soft tissues of thorax', 'Upper limb NOS', 'Gastric antrum', 'Lymph node NOS', 'Peripheral nerves and autonomic nervous system of thorax', 'Ill-defined sites within respiratory system', 'Other specified parts of male genital organs', 'Rib sternum clavicle and associated joints', 'Overlapping lesion of bladder', 'Appendix', 'Prostate gland', 'Lymph nodes of multiple regions', 'Lateral wall of nasopharynx', 'Branchial cleft', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Floor of mouth NOS', 'Connective subcutaneous and other soft tissues NOS', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Bladder neck', 'Border of tongue', 'Connective subcutaneous and other soft tissues of abdomen', 'Overlapping lesion of small intestine', 'Lateral wall of bladder', 'Soft palate NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Isthmus uteri', 'Nasal cavity', 'Endocervix', 'Tonsil NOS', 'Glottis', 'Retroperitoneum', 'Peripheral nerves and autonomic nervous system of pelvis', 'Frontal lobe', 'Vagina NOS', 'Undescended testis', 'Laryngeal cartilage', 'Eyelid', 'Hypopharyngeal aspect of aryepiglottic fold', 'Overlapping lesion of other and unspecified parts of mouth', 'Upper lobe lung', 'Lip NOS', 'Lymph nodes of head face and neck', 'Overlapping lesion of brain and central nervous system', 'Overlapping lesion of penis', 'Overlapping lesion of retroperitoneum and peritoneum', 'Parotid gland', 'Dome of bladder', 'Bone of limb NOS', 'Descended testis', 'Vertebral column', 'Fundus uteri', 'Connective subcutaneous and other soft tissues of pelvis', 'Epididymis', 'Intra-abdominal lymph nodes', 'Prepuce', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Pharynx NOS', 'Overlapping lesion of endocrine glands and related structures', 'Gum NOS', 'Spinal cord', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Skin of upper limb and shoulder', 'Nasopharynx NOS', 'Parathyroid gland', 'Bone NOS', 'Mouth NOS', 'Abdomen NOS', 'Conjunctiva', 'Spermatic cord', 'External upper lip', 'Labium minus', 'Renal pelvis', 'Overlapping lesion of lip', 'Short bones of upper limb and associated joints', 'Main bronchus', 'Upper respiratory tract NOS', 'Body of penis', 'Small intestine NOS', 'Central portion of breast', 'Lower-inner quadrant of breast', 'Labium majus', 'Tonsillar fossa', 'Cecum', 'Glans penis', 'Tail of pancreas', 'Lower third of esophagus', 'Body of pancreas', 'Intestinal tract NOS', 'Brain stem', 'Overlapping lesion of rectum anus and anal canal', 'Posterior wall of oropharynx', 'Pancreatic duct', 'Blood', 'Temporal lobe', 'Anterior floor of mouth', 'Nervous system NOS', 'Cornea NOS', 'Palate NOS', 'Occipital lobe', 'Abdominal esophagus', 'Overlapping lesion of pancreas', 'Overlapping lesion of female genital organs', 'Cheek mucosa', 'Retina', 'Overlapping lesion of male genital organs', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Larynx NOS', 'Skin of other and unspecified parts of face', 'Spleen', 'Oropharynx NOS', 'Anal canal', 'Subglottis', 'Cerebral meninges', 'Lateral wall of oropharynx', 'Middle third of esophagus', 'Nipple', 'Medulla of adrenal gland', 'Overlapping lesion of eye and adnexa', 'Olfactory nerve', 'Ethmoid sinus', 'Overlapping lesion of cervix uteri', 'Descending colon', 'Brain NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Anterior wall of bladder', 'Mandible', 'Other specified parts of pancreas', 'Skin of trunk', 'Other specified parts of female genital organs', 'Uterus NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Intrathoracic lymph nodes', 'Heart', 'Adrenal gland NOS', 'Aortic body and other paraganglia', 'Extrahepatic bile duct', 'Overlapping lesion of breast', 'Superior wall of nasopharynx', 'Fundus of stomach', 'Anterior mediastinum', 'Tongue NOS', 'Cranial nerve NOS', 'Head of pancreas', 'Overlapping lesions of oropharynx', 'Overlapping lesion of bones joints and articular cartilage', 'Retromolar area', 'Testis NOS', 'Connective subcutaneous and other soft tissues of head face and neck', 'Bladder NOS', 'Overlapping lesion of urinary organs', 'Lower-outer quadrant of breast', 'Thyroid gland', 'Anterior surface of epiglottis', 'Uterine adnexa', '']"," If Progression or Recurrence is ""Yes - Progression or Recurrence"" then ""Progression or Recurrence Anatomic Site"" is required",Diagnosis +Days to Progression Free,Days to Progression Free,DaystoProgressionFree,Number of days between the date used for index and the date the patient's disease was formally confirmed as progression-free.,False,True,," If Progression or Recurrence is ""Yes - Progression or Recurrence"" then ""Days to Progression Free"" is required",Diagnosis +Treatment Outcome,Treatment Outcome,TreatmentOutcome,Text term that describes the patient's final outcome after the treatment was administered.,False,,"['Progressive Disease', 'Stable Disease', 'Very Good Partial Response', 'Not Reported', 'Treatment Ongoing', 'Complete Response', 'No Response', 'Persistent Disease', 'Partial Response', 'Mixed Response', 'Treatment Stopped Due to Toxicity', 'Unknown', 'No Measurable Disease', '']",,Therapy +Chemo Concurrent to Radiation,Chemo Concurrent to Radiation,ChemoConcurrenttoRadiation,The text term used to describe whether the patient was receiving chemotherapy concurrent to radiation.,False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,Therapy +Treatment Arm,Treatment Arm,TreatmentArm,Text term used to describe the treatment arm assigned to a patient at the time eligibility is determined.,False,,"['E4512', 'EA5142', 'A081105', '']",,Therapy +Treatment Effect Indicator,Treatment Effect Indicator,TreatmentEffectIndicator,The text term used to indicate whether the treatment had an effect on the patient.,False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,Therapy +Treatment Dose,Treatment Dose,TreatmentDose,The numeric value used to describe the dose of an agent the patient received.,False,,,,Therapy +Initial Disease Status,Initial Disease Status,InitialDiseaseStatus,The text term used to describe the status of the patient's malignancy when the treatment began.,False,,"['Progressive Disease', 'Initial Diagnosis', 'Not Reported', 'Recurrent Disease', 'Residual Disease', 'Unknown', '']",,Therapy +Days to Treatment End,Days to Treatment End,DaystoTreatmentEnd,Number of days between the date used for index and the date the treatment ended.,False,,,,Therapy +Regimen or Line of Therapy,Regimen or Line of Therapy,RegimenorLineofTherapy,The text term used to describe the regimen or line of therapy.,False,,,,Therapy +Treatment Frequency,Treatment Frequency,TreatmentFrequency,The text term used to describe the frequency the patient received an agent or regimen.,False,,"['Once Weekly', 'Not Reported', 'Every Hour', 'Three Times Daily', 'Five Times Daily', 'Twice Weekly', 'Four Times Daily', 'Unknown', 'Every Other Day', 'Every 24 Hours', 'Twice Daily', '']",,Therapy +Treatment Dose Units,Treatment Dose Units,TreatmentDoseUnits,The text term used to describe the dose units of an agent the patient received.,False,,"['cGy', 'Gy', '']",,Therapy +Therapeutic Agents,Therapeutic Agents,TherapeuticAgents,Text identification of the individual agent(s) used as part of a treatment regimen.,False,,,,Therapy +Treatment Type,Treatment Type,TreatmentType,Text term that describes the kind of treatment administered.,False,,,,Therapy +Reason Treatment Ended,Reason Treatment Ended,ReasonTreatmentEnded,The text term used to describe the reason a specific treatment or regimen ended.,False,,"['Adverse Therapy Event', 'Disease Progression', 'Other', 'Death', 'Withdrawal by Subject', 'Course of Therapy Completed', '']",,Therapy +Treatment Effect,Treatment Effect,TreatmentEffect,The text term used to describe the pathologic effect a treatment(s) had on the tumor.,False,,"['Not Reported', 'Unknown', 'Complete Necrosis (No Viable Tumor)', 'Incomplete Necrosis (Viable Tumor Present)', 'No Necrosis', '']",,Therapy +Treatment or Therapy,Treatment or Therapy,TreatmentorTherapy,A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received.,False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,Therapy +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,Therapy +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Therapy +Treatment Anatomic Site,Treatment Anatomic Site,TreatmentAnatomicSite,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,False,,"['Paraurethral gland', 'Colon NOS', 'Frontal sinus', 'Overlapping lesion of tongue', 'Overlapping lesion of palate', 'Scrotum NOS', 'Bone marrow', 'Axillary tail of breast', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'unknown primary site', 'Broad ligament', 'Lateral floor of mouth', 'Overlapping lesion of vulva', 'Trigone of bladder', 'Lacrimal gland', 'Thorax NOS', 'Ampulla of Vater', 'Myometrium', 'Penis NOS', 'Female genital tract NOS', 'Submandibular gland', 'Anterior 2/3 of tongue NOS', 'Posterior wall of bladder', 'Thymus', 'Endocrine gland NOS', 'Stomach NOS', 'Unknown', 'Cerebrum', 'Splenic flexure of colon', 'Urachus', 'Skin of lip NOS', 'Mucosa of lip NOS', 'Accessory sinus NOS', 'Cortex of adrenal gland', 'Other ill-defined sites', 'Middle lobe lung', 'Pelvis NOS', 'Anus NOS', 'Upper-inner quadrant of breast', 'Posterior mediastinum', 'Esophagus NOS', 'Duodenum', 'Cervical esophagus', 'Optic nerve', 'Long bones of lower limb and associated joints', 'Middle ear', 'Breast NOS', 'Dorsal surface of tongue NOS', 'Lesser curvature of stomach NOS', 'Overlapping lesion of floor of mouth', 'Overlapping lesion of heart mediastinum and pleura', 'Eye NOS', 'Overlapping lesion of esophagus', 'Ciliary body', 'Ureteric orifice', 'Postcricoid region', 'External ear', 'Base of tongue NOS', 'Liver', 'Commissure of lip', 'Cloacogenic zone', 'Lower lobe lung', 'Transverse colon', 'Acoustic nerve', 'Supraglottis', 'Fallopian tube', 'Upper third of esophagus', 'Skin of scalp and neck', 'Choroid', 'Long bones of upper limb scapula and associated joints', 'Overlapping lesion of brain', 'Upper gum', 'Skin NOS', 'Hard palate', 'Ileum', 'Overlapping lesion of colon', 'Ascending colon', 'Lower gum', 'Pelvic bones sacrum coccyx and associated joints', 'Hepatic flexure of colon', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Vestibule of mouth', 'Cervix uteri', 'Bones of skull and face and associated joints', 'Overlapping lesion of lip oral cavity and pharynx', 'Endometrium', 'Sphenoid sinus', 'Overlapping lesion of ill-defined sites', 'Sigmoid colon', 'Peritoneum NOS', 'Specified parts of peritoneum', 'Meckel diverticulum', 'Rectosigmoid junction', 'Kidney NOS', 'Reticuloendothelial system NOS', 'Rectum NOS', 'Pylorus', 'Overlapping lesion of tonsil', 'Pleura NOS', 'Jejunum', 'Vallecula', 'Skin of lower limb and hip', 'Pelvic lymph nodes', 'External lower lip', 'Overlapping lesion of skin', 'Mucosa of upper lip', 'Ovary', 'Cauda equina', 'Lower limb NOS', 'Body of stomach', 'Overlapping lesion of larynx', 'Pancreas NOS', 'Overlapping lesion of lung', 'Overlapping lesion of major salivary glands', 'Uvula', 'Overlapping lesion of hypopharynx', 'Round ligament', 'Corpus uteri', 'Biliary tract NOS', 'Male genital organs NOS', 'Parametrium', 'External lip NOS', 'Overlapping lesion of accessory sinuses', 'Cardia NOS', 'Islets of Langerhans', 'Carotid body', 'Ventral surface of tongue NOS', 'Autonomic nervous system NOS', 'Overlapping lesion of corpus uteri', 'Spinal meninges', 'Posterior wall of nasopharynx', 'Placenta', 'Intrahepatic bile duct', 'Overlapping lesion of digestive system', 'Mediastinum NOS', 'Hematopoietic system NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Major salivary gland NOS', 'Cerebellum NOS', 'Overlapping lesion of stomach', 'Vulva NOS', 'Craniopharyngeal duct', 'Lung NOS', 'Greater curvature of stomach NOS', 'Upper-outer quadrant of breast', 'Gallbladder', 'Thoracic esophagus', 'Lymph nodes of axilla or arm', 'Ventricle NOS', 'Overlapping lesion of biliary tract', 'Hypopharynx NOS', 'Clitoris', 'Exocervix', 'Parietal lobe', 'Waldeyer ring', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Head face or neck NOS', 'Anterior wall of nasopharynx', 'Urethra', 'Overlapping lesion of nasopharynx', 'Maxillary sinus', 'Lymph nodes of inguinal region or leg', 'Ureter', 'Tonsillar pillar', 'Sublingual gland', 'Pituitary gland', 'Gastrointestinal tract NOS', 'Pineal gland', 'Meninges NOS', 'Lingual tonsil', 'Trachea', 'Pyriform sinus', 'Mucosa of lower lip', 'Not Reported', 'Posterior wall of hypopharynx', 'Urinary system NOS', 'Orbit NOS', 'Short bones of lower limb and associated joints', 'Connective subcutaneous and other soft tissues of thorax', 'Upper limb NOS', 'Gastric antrum', 'Lymph node NOS', 'Peripheral nerves and autonomic nervous system of thorax', 'Ill-defined sites within respiratory system', 'Other specified parts of male genital organs', 'Rib sternum clavicle and associated joints', 'Overlapping lesion of bladder', 'Appendix', 'Prostate gland', 'Lymph nodes of multiple regions', 'Lateral wall of nasopharynx', 'Branchial cleft', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Floor of mouth NOS', 'Connective subcutaneous and other soft tissues NOS', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Bladder neck', 'Border of tongue', 'Connective subcutaneous and other soft tissues of abdomen', 'Overlapping lesion of small intestine', 'Lateral wall of bladder', 'Soft palate NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Isthmus uteri', 'Nasal cavity', 'Endocervix', 'Tonsil NOS', 'Glottis', 'Retroperitoneum', 'Peripheral nerves and autonomic nervous system of pelvis', 'Frontal lobe', 'Vagina NOS', 'Undescended testis', 'Laryngeal cartilage', 'Eyelid', 'Hypopharyngeal aspect of aryepiglottic fold', 'Overlapping lesion of other and unspecified parts of mouth', 'Upper lobe lung', 'Lip NOS', 'Lymph nodes of head face and neck', 'Overlapping lesion of brain and central nervous system', 'Overlapping lesion of penis', 'Overlapping lesion of retroperitoneum and peritoneum', 'Parotid gland', 'Dome of bladder', 'Bone of limb NOS', 'Descended testis', 'Vertebral column', 'Fundus uteri', 'Connective subcutaneous and other soft tissues of pelvis', 'Epididymis', 'Intra-abdominal lymph nodes', 'Prepuce', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Pharynx NOS', 'Overlapping lesion of endocrine glands and related structures', 'Gum NOS', 'Spinal cord', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Skin of upper limb and shoulder', 'Nasopharynx NOS', 'Parathyroid gland', 'Bone NOS', 'Mouth NOS', 'Abdomen NOS', 'Conjunctiva', 'Spermatic cord', 'External upper lip', 'Labium minus', 'Renal pelvis', 'Overlapping lesion of lip', 'Short bones of upper limb and associated joints', 'Main bronchus', 'Upper respiratory tract NOS', 'Body of penis', 'Small intestine NOS', 'Central portion of breast', 'Lower-inner quadrant of breast', 'Labium majus', 'Tonsillar fossa', 'Cecum', 'Glans penis', 'Tail of pancreas', 'Lower third of esophagus', 'Body of pancreas', 'Intestinal tract NOS', 'Brain stem', 'Overlapping lesion of rectum anus and anal canal', 'Posterior wall of oropharynx', 'Pancreatic duct', 'Blood', 'Temporal lobe', 'Anterior floor of mouth', 'Nervous system NOS', 'Cornea NOS', 'Palate NOS', 'Occipital lobe', 'Abdominal esophagus', 'Overlapping lesion of pancreas', 'Overlapping lesion of female genital organs', 'Cheek mucosa', 'Retina', 'Overlapping lesion of male genital organs', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Larynx NOS', 'Skin of other and unspecified parts of face', 'Spleen', 'Oropharynx NOS', 'Anal canal', 'Subglottis', 'Cerebral meninges', 'Lateral wall of oropharynx', 'Middle third of esophagus', 'Nipple', 'Medulla of adrenal gland', 'Overlapping lesion of eye and adnexa', 'Olfactory nerve', 'Ethmoid sinus', 'Overlapping lesion of cervix uteri', 'Descending colon', 'Brain NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Anterior wall of bladder', 'Mandible', 'Other specified parts of pancreas', 'Skin of trunk', 'Other specified parts of female genital organs', 'Uterus NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Intrathoracic lymph nodes', 'Heart', 'Adrenal gland NOS', 'Aortic body and other paraganglia', 'Extrahepatic bile duct', 'Overlapping lesion of breast', 'Superior wall of nasopharynx', 'Fundus of stomach', 'Anterior mediastinum', 'Tongue NOS', 'Cranial nerve NOS', 'Head of pancreas', 'Overlapping lesions of oropharynx', 'Overlapping lesion of bones joints and articular cartilage', 'Retromolar area', 'Testis NOS', 'Connective subcutaneous and other soft tissues of head face and neck', 'Bladder NOS', 'Overlapping lesion of urinary organs', 'Lower-outer quadrant of breast', 'Thyroid gland', 'Anterior surface of epiglottis', 'Uterine adnexa', '']",,Therapy +Number of Cycles,Number of Cycles,NumberofCycles,The numeric value used to describe the number of cycles of a specific treatment or regimen the patient received.,False,,,,Therapy +Treatment Intent Type,Treatment Intent Type,TreatmentIntentType,Text term to identify the reason for the administration of a treatment regimen. [Manually-curated],False,,"['Palliative', 'Cure', 'Not Reported', 'Cancer Control', 'Unknown', 'Prevention', 'Neoadjuvant', 'Adjuvant', '']",,Therapy +Days to Treatment Start,Days to Treatment Start,DaystoTreatmentStart,Number of days between the date used for index and the date the treatment started.,False,,,,Therapy +Loci Count,Loci Count,LociCount,Numeric value used to describe the number of loci tested.,False,,,,MolecularTest +Loci Abnormal Count,Loci Abnormal Count,LociAbnormalCount,Numeric value used to describe the number of loci determined to be abnormal.,False,,,,MolecularTest +Mismatch Repair Mutation,Mismatch Repair Mutation,MismatchRepairMutation,The yes/no/unknown indicator used to describe whether the mutation included in molecular testing was known to have an affect on the mismatch repair process. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,MolecularTest +Locus,Locus,Locus,Alphanumeric value used to describe the locus of a specific genetic variant. Example: NM_001126114.,False,,,,MolecularTest +Second Exon,Second Exon,SecondExon,"The second exon number involved in molecular variation. If a specific genetic variant is being reported, this property can be used to capture the second exon where that variant is located. This property is typically used for a translocation where two different locations are involved in the variation.",False,,,,MolecularTest +Second Gene Symbol,Second Gene Symbol,SecondGeneSymbol,"The text term used to describe a secondary gene targeted or included in molecular analysis. For rearrangements, this is should represent the location of the variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,,,MolecularTest +Specialized Molecular Test,Specialized Molecular Test,SpecializedMolecularTest,Text term used to describe a specific test that is not covered in the list of molecular analysis methods. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,,,MolecularTest +Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,MolecularTest +Gene Symbol,Gene Symbol,GeneSymbol,"The text term used to describe a gene targeted or included in molecular analysis. For rearrangements, this is should be used to represent the reference gene. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",True,,,,MolecularTest +Antigen,Antigen,Antigen,The text term used to describe an antigen included in molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['CD33', 'CD138', 'CD15', 'CD25', 'Mesothelin', 'CD14', 'CD20', 'CD79A', 'CD3', 'CCND1', 'NSE', 'CD23', 'CD34', 'CD22', 'Unknown', 'CD56', 'CD45', 'CA19-9', 'CD117', 'HLA-DR', 'CD30', 'Not Reported', 'CD5', 'CD7', 'Squamous Cell Carcinoma Antigen', 'CD10', 'BCL6', 'CD19', 'CA-125', 'CEA', '']",,MolecularTest +Histone Family,Histone Family,HistoneFamily,"The text term used to describe the family, or classification of a group of basic proteins found in chromatin, called histones.",False,,"['Not Reported', 'H3', 'H2A', 'H4', 'H1', 'Unknown', 'H2B', '']",,MolecularTest +Test Value,Test Value,TestValue,The text term or numeric value used to describe a specific result of a molecular test. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here,False,,,,MolecularTest +Exon,Exon,Exon,"Exon number targeted or included in a molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the exon where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,,,MolecularTest +Molecular Analysis Method,Molecular Analysis Method,MolecularAnalysisMethod,The text term used to describe the method used for molecular analysis. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,True,,"['Not Applicable', 'WGS', 'Targeted Sequencing', 'FISH', 'IHC', 'Unknown', 'Microarray', 'Cytogenetics NOS', 'Nuclear Staining', 'Microsatellite Analysis', 'Sequencing NOS', 'Comparative Genomic Hybridization', 'Not Reported', 'Flow Cytometry', 'Southern Blotting', 'ISH', 'RNA Sequencing', 'Other', 'RT-PCR', 'WXS', 'Karyotype']",,MolecularTest +Variant Origin,Variant Origin,VariantOrigin,The text term used to describe the biological origin of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Unknown', 'Germline', 'Somatic', '']",,MolecularTest +Test Result,Test Result,TestResult,The text term used to describe the result of the molecular test. If the test result was a numeric value see test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,True,,"['Equivocal', 'Copy Number Reported', 'Abnormal NOS', 'Not Reported', 'Low', 'Overexpressed', 'Test Value Reported', 'Intermediate', 'Not Applicable', 'Positive', 'Unknown', 'High', 'Normal', 'Negative', 'Loss of Expression']",,MolecularTest +Histone Variant,Histone Variant,HistoneVariant,"The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.",False,,"['H2A.Z', 'H2A.Z.1', 'H3t (H3.4)', 'mH2A.2', 'H2A-Bbd', 'Unknown', 'H3.5', 'H3.2', 'mH2A.1', 'Not Reported', 'H2A.Z.2.2', 'mH2A', 'H2A.Z.2', 'H3.Y', 'H3.X', 'H3.1', 'H3.3', 'CENP-A', 'H2A.X', '']",,MolecularTest +Molecular Consequence,Molecular Consequence,MolecularConsequence,The text term used to describe the molecular consequence of genetic variation. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Start Lost', 'Stop Lost', 'Splice Region Variant', 'Mature miRNA Variant', 'Intron Variant', 'Missense Variant', 'TFBS Amplification', 'Feature Elongation', 'Non-coding Transcript Variant', '3 Prime UTR Variant', 'Regulatory Region Ablation', 'Splice Acceptor Variant', 'Frameshift Variant', 'Inframe Insertion', 'Intergenic Variant', 'Regulatory Region Variant', 'Feature Truncation', 'Protein Altering Variant', 'Upstream Gene Variant', 'Transcript Amplification', 'Stop Retained Variant', 'NMD Transcript Variant', 'Regulatory Region Amplification', 'Splice Donor Variant', 'Inframe Deletion', 'Non-coding Transcript Exon Variant', 'Coding Sequence Variant', 'TF Binding Site Variant', 'TFBS Ablation', 'Stop Gain', 'Downstream Gene Variant', 'Transcript Ablation', '5 Prime UTR Variant', 'Synonymous Variant', 'Incomplete Terminal Codon Variant', '']",,MolecularTest +Blood Test Normal Range Upper,Blood Test Normal Range Upper,BloodTestNormalRangeUpper,Numeric value used to describe the upper limit of the normal range used to describe a healthy individual at the institution where the test was completed.,False,,,,MolecularTest +Stop Days from Index,Stop Days from Index,StopDaysfromIndex,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'",False,,,,MolecularTest +Test Units,Test Units,TestUnits,The text term used to describe the units of the test value for a molecular test. This property is used in conjunction with test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,,,MolecularTest +Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,MolecularTest +Copy Number,Copy Number,CopyNumber,"Numeric value used to describe the number of times a section of the genome is repeated or copied within an insertion, duplication or deletion variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,,,MolecularTest +Variant Type,Variant Type,VariantType,The text term used to describe the type of genetic variation.,False,,"['Chrimerism', 'Inversion', 'Extension', 'Loss', 'Splice', 'Unknown', 'Substitution', 'Insertion', 'Partial Methylation', 'Translocation', 'Amplification', 'Duplication', 'Not Reported', 'Mosaicism', 'Conversion', 'Hypermethylation', 'Methylation', 'Repeated Sequences', 'Alleles', 'Deletion-Insertion', 'Gain', 'Other', 'Rearrangement', 'Deletion', '']",,MolecularTest +Ploidy,Ploidy,Ploidy,Text term used to describe the number of sets of homologous chromosomes.,False,,"['Not Reported', 'Diploid', 'Hypodiploid', 'Unknown', 'Near Diploid', 'Hyperdiploid', 'Aneuploid', 'Tetraploid', '']",,MolecularTest +Pathogenicity,Pathogenicity,Pathogenicity,The text used to describe a variant's level of involvement in the cause of the patient's disease according to the standards outlined by the American College of Medical Genetics and Genomics (ACMG).,False,,"['Benign', 'Uncertain Significance', 'Likely Pathogenic', 'Pathogenic', 'Likely Benign', '']",,MolecularTest +Transcript,Transcript,Transcript,Alphanumeric value used to describe the transcript of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,,,MolecularTest +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,MolecularTest +Zygosity,Zygosity,Zygosity,The text term used to describe the zygosity of a specific genetic variant.,False,,"['Hemizygous', 'Homozygous', 'Not Reported', 'Heterozygous', 'Nullizygous', 'Unknown', '']",,MolecularTest +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MolecularTest +Cell Count,Cell Count,CellCount,Numeric value used to describe the number of cells used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,,,MolecularTest +Cytoband,Cytoband,Cytoband,"Alphanumeric value used to describe the cytoband or chromosomal location targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the cytoband where the variant is located. Format: [chromosome][chromosome arm].[band+sub-bands]. Example: 17p13.1. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,,,MolecularTest +AA Change,AA Change,AAChange,Alphanumeric value used to describe the amino acid change for a specific genetic variant. Example: R116Q. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,,,MolecularTest +Intron,Intron,Intron,"Intron number targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the intron where that variant is located.",False,,,,MolecularTest +Blood Test Normal Range Lower,Blood Test Normal Range Lower,BloodTestNormalRangeLower,Numeric value used to describe the lower limit of the normal range used to describe a healthy individual at the institution where the test was completed.,False,,,,MolecularTest +Test Analyte Type,Test Analyte Type,TestAnalyteType,The text term used to describe the type of analyte used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Protein Analyte', 'Not Reported', 'Total RNA', 'Unknown', 'miRNA', 'mRNA', 'DNA', '']",,MolecularTest +Clonality,Clonality,Clonality,The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Clonal', 'Non-clonal', '']",,MolecularTest +Clinical Biospecimen Type,Clinical Biospecimen Type,ClinicalBiospecimenType,"The text term used to describe the biological material used for testing, diagnostic, treatment or research purposes. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,"['Serum', 'Granulocyte', 'Pleural Fluid', 'Soft Tissue', 'Connective Tissue', 'Muscle Tissue', 'Blood', 'Feces', 'Buccal Mucosa', 'Embryonic Fluid', 'Nerve Tissue', 'Unknown', 'Not Reported', 'Embryonic Tissue', 'Urine', 'Bone Marrow', 'Peritoneal Fluid', 'Buffy Coat', 'Skin', 'Plasma', 'Saliva', 'Tissue NOS', 'Cerebrospinal Fluid', 'Uninvolved Tissue NOS', '']",,MolecularTest +Chromosome,Chromosome,Chromosome,"The text term used to describe a chromosome targeted or included in molecular testing. If a specific genetic variant is being reported, this property can be used to capture the chromosome where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,"['chr4', 'chrX', 'chr3', 'chr13', 'chr1', 'chr19', 'chr5', 'Unknown', 'chr16', 'chr7', 'chr10', 'chr12', 'Not Reported', 'chrM', 'chrY', 'chr2', 'chr21', 'chr23', 'chr17', 'chr11', 'chr15', 'chr9', 'chr22', 'chr6', 'chr14', 'chr8', 'chr20', 'chr18', '']",,MolecularTest +Laboratory Test,Laboratory Test,LaboratoryTest,"The text term used to describe the medical testing used to diagnose, treat or further understand a patient's disease.",False,,"['Blood Urea Nitrogen', 'Hemoglobin', 'Lymphocytes', 'Calcium', 'C-Reactive Protein', 'Human Papillomavirus', 'Kappa', 'Lambda', 'Total Bilirubin', 'Beta 2 Microglobulin', 'Cellularity', 'Eosinophil', 'M Protein', 'Immunoglobulin M', 'Epstein-Barr Virus', 'Leukocytes', 'Unknown', 'Metamyelocytes', 'Myeloblasts', 'Circulating Tumor Cells', 'Prolymphocytes', 'Alpha Fetoprotein', 'Basophil', 'Not Reported', 'Segmented Neutrophil', 'Testosterone', 'Immunoglobulin G', 'Total Protein', 'Creatinine', 'Glucose', 'Serum Free Immunoglobulin Light Chain', 'HPV-E6/E7', 'Hematocrit', 'Lymphoblasts', 'Promonocytes', 'B-cell genotyping', 'Myelocytes', 'Neutrophil Bands', 'NOS', 'Luteinizing Hormone', 'Immunoglobulin A', 'Absolute Neutrophil', 'Albumin', 'Promyelocytes', 'Lactate Dehydrogenase', 'Human Chorionic Gonadotropin', 'Platelets', '']",,MolecularTest +Lysis Buffer,Lysis Buffer,LysisBuffer,scRNA-seq specific: Type of lysis buffer used,False,,,,Biospecimen +Dysplasia Fraction,Dysplasia Fraction,DysplasiaFraction,Resulting value to represent the number of pieces of dysplasia divided by the total number of pieces. [Text: max length 5],False,,,,Biospecimen +Method of Nucleic Acid Isolation,Method of Nucleic Acid Isolation,MethodofNucleicAcidIsolation,"Bulk RNA & DNA-seq specific: method used for nucleic acid isolation. E.g. Qiagen Allprep, Qiagen miRNAeasy. [Text - max length 100]",False,,,,Biospecimen +Fixative Type,Fixative Type,FixativeType,Text term to identify the type of fixative used to preserve a tissue specimen,True,,"['95% Ethanol', 'Dimidoester', 'Acetone', 'RNAlater', 'Polaxamer', 'Glutaraldehyde', 'Cryo-store', 'Carbodiimide', 'OCT media', 'None', 'Formalin', 'Methacarn', 'Unknown', 'NP40 lysis buffer', 'PAXgene tissue', 'Para-benzoquinone', 'Alcohol', 'TCL lysis buffer', 'Dimethylacetamide', 'Saline', 'Other', ""Carnoy's Fixative""]",,Biospecimen +Histology Assessment By,Histology Assessment By,HistologyAssessmentBy,Text term describing who (in what role) made the histological assessments of the sample,False,,"['Unknown', 'Research Scientist', 'Pathologist', 'Other', '']",,Biospecimen +Biospecimen Type,Biospecimen Type,BiospecimenType,Biospecimen Type,True,,"['Bone Marrow Biospecimen Type', 'Tissue Biospecimen Type', 'Stool Biospecimen Type', 'Fluids Biospecimen Type', 'Cells Biospecimen Type', 'Urine Biospecimen Type', 'Blood Biospecimen Type', 'Ascites Biospecimen Type', 'Analyte Biospecimen Type', 'Mouth Rinse Biospecimen Type', 'Sputum Biospecimen Type']",,Biospecimen +Degree of Dysplasia,Degree of Dysplasia,DegreeofDysplasia,Information related to the presence of cells that look abnormal under a microscope but are not cancer. Records the degree of dysplasia for the cyst or lesion under consideration.,False,,"['Normal or basal cell hyperplasia or metaplasia', 'Carcinoma in Situ', 'Unknown', 'Severe dysplasia', 'Mild dysplasia', 'Moderate dysplasia', '']",,Biospecimen +Slicing Method,Slicing Method,SlicingMethod,Imaging specific: the method by which the tissue was sliced.,False,,"['Tissue molds', 'Not Reported', 'Vibratome', 'Sectioning', 'Other', 'Unknown', 'Sliding microtome', 'Cryosectioning', '']",,Biospecimen +Percent Monocyte Infiltration,Percent Monocyte Infiltration,PercentMonocyteInfiltration,Numeric value to represent the percentage of monocyte infiltration in a sample or specimen.,False,,,,Biospecimen +HTAN Parent ID,HTAN Parent ID,HTANParentID,HTAN ID of parent from which the biospecimen was obtained. Parent could be another biospecimen or a research participant.,True,,,,Biospecimen +Percent Eosinophil Infiltration,Percent Eosinophil Infiltration,PercentEosinophilInfiltration,Numeric value to represent the percentage of infiltration by eosinophils in a tumor sample or specimen.,False,,,,Biospecimen +Percent Tumor Nuclei,Percent Tumor Nuclei,PercentTumorNuclei,Numeric value to represent the percentage of tumor nuclei in a malignant neoplasm sample or specimen.,False,,,,Biospecimen +Percent Necrosis,Percent Necrosis,PercentNecrosis,Numeric value to represent the percentage of cell death in a malignant tumor sample or specimen.,False,,,,Biospecimen +Percent Granulocyte Infiltration,Percent Granulocyte Infiltration,PercentGranulocyteInfiltration,Numeric value to represent the percentage of infiltration by granulocytes in a tumor sample or specimen.,False,,,,Biospecimen +Percent Stromal Cells,Percent Stromal Cells,PercentStromalCells,"Numeric value to represent the percentage of reactive cells that are present in a malignant tumor sample or specimen but are not malignant such as fibroblasts, vascular structures, etc.",False,,,,Biospecimen +Source HTAN Biospecimen ID,Source HTAN Biospecimen ID,SourceHTANBiospecimenID,This is the HTAN ID that may have been assigned to the biospecimen at the site of biospecimen origin (e.g. BU).,False,,,,Biospecimen +HTAN Biospecimen ID,HTAN Biospecimen ID,HTANBiospecimenID,HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,Biospecimen +Collection Days from Index,Collection Days from Index,CollectionDaysfromIndex,Number of days from the research participant's index date that the biospecimen was obtained.,True,,,,Biospecimen +Site Data Source,Site Data Source,SiteDataSource,"Text to identify the data source for the specimen/sample from within the HTAN center, if applicable. Any identifier used within the center to identify data sources. No PHI/PII is allowed.",False,,,,Biospecimen +Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,Biospecimen +Number Proliferating Cells,Number Proliferating Cells,NumberProliferatingCells,Numeric value that represents the count of proliferating cells determined during pathologic review of the sample slide(s).,False,,,,Biospecimen +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,Biospecimen +Preinvasive Morphology,Preinvasive Morphology,PreinvasiveMorphology,"Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the HTAN",False,,"['Melanoma in situ - superficial spreading', 'Invasive melanoma - other', 'Benign tumor NOS', 'No diagnosis possible', 'Melanoma in situ - lentigo maligna type', 'Normal WDA', 'Persistent melanoma in situ', 'Atypical adenomatous hyperplasia', 'Squamous Carcinoma in situ', 'Invasive melanoma - nevoid', 'Invasive melanoma - nodular type', 'Severe dysplasia', 'Reserve cell hyperplasia', 'Melanocytic hyperplasia', 'Squamous metaplasia - immature', 'Melanoma in situ - acral-lentiginous', 'Melanoma in situ - arising in a giant congenital nevus', 'Atypical melanocytic proliferation', 'Carcinoma NOS', 'Mild dysplasia', 'Squamous metaplasia - mature', 'Moderate dysplasia', 'Invasive melanoma - acral lentiginous', 'Melanoma in situ - not otherwise classified', 'Adenocarcinoma in situ - mucinous', 'Invasive melanoma - desmoplastic', 'Hamartoma', 'Scar - no residual melanoma', 'Invasive melanoma - superficial spreading', 'Adenocarcinoma in situ - non mucinous', 'Invasive melanoma - lentigo maligna', '']",,Biospecimen +Storage Method,Storage Method,StorageMethod,The method by which a biomaterial was stored after preservation or before another protocol was used.,True,,"['RNAlater at 25C', '4C in vacuum chamber', 'RNAlater at 4C', 'Frozen at -80C', 'Cut slide', 'Frozen at -70C', 'Fresh', 'Frozen in vapor phase', 'Not Applicable', 'Ambient temperature', 'Refrigerated at 4 degrees', 'Unknown', 'Paraffin block', 'Refrigerated vacuum chamber', 'Frozen in liquid nitrogen', 'Desiccant at 4C', 'RNAlater at -20C', 'Frozen at -150C']",,Biospecimen +Processing Days from Index,Processing Days from Index,ProcessingDaysfromIndex,Number of days from the research participant's index date that the biospecimen was processed,True,,,,Biospecimen +Percent Inflam Infiltration,Percent Inflam Infiltration,PercentInflamInfiltration,"Numeric value to represent local response to cellular injury, marked by capillary dilatation, edema and leukocyte infiltration; clinically, inflammation is manifest by redness, heat, pain, swelling and loss of function, with the need to heal damaged tissue.",False,,,,Biospecimen +Fiducial Marker,Fiducial Marker,FiducialMarker,Imaging specific: fiducial markers for the alignment of images taken across multiple rounds of imaging.,False,,"['Grid Slides - Hemocytometer', 'Not Reported', 'Nuclear Stain - DAPI', 'Other', 'Unknown', 'Fluorescent Beads', 'Adhesive Markers', '']",,Biospecimen +Acquisition Method Type,Acquisition Method Type,AcquisitionMethodType,Records the method of acquisition or source for the specimen under consideration.,True,,"['Blood draw', 'Core needle biopsy', 'Lymphadenectomy - Regional Nodes', 'Biopsy', 'Endoscopic biopsy', 'Shave Biopsy', 'Other Acquisition Method', 'Re-excision', 'BAL (bronchial alveolar lavage)', 'Not specified', 'Induced sputum', 'Cytobrush', 'Sentinel Node Biopsy', 'Surgical Resection', 'Excision', 'Fine Needle Aspirate', 'Punch Biopsy', 'Non induced sputum', 'Fluid collection', 'Forceps biopsy', 'Autopsy']",,Biospecimen +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Biospecimen +Adjacent Biospecimen IDs,Adjacent Biospecimen IDs,AdjacentBiospecimenIDs,"List of HTAN Identifiers (separated by commas) of adjacent biospecimens cut from the same sample; for example HTA3_3000_3, HTA3_3000_4, ...",False,,,,Biospecimen +Tumor Infiltrating Lymphocytes,Tumor Infiltrating Lymphocytes,TumorInfiltratingLymphocytes,Measure of Tumor-Infiltrating Lymphocytes [Number],False,,,,Biospecimen +Percent Normal Cells,Percent Normal Cells,PercentNormalCells,Numeric value to represent the percentage of normal cell content in a malignant tumor sample or specimen.,False,,,,Biospecimen +Percent Tumor Cells,Percent Tumor Cells,PercentTumorCells,Numeric value that represents the percentage of infiltration by tumor cells in a sample.,False,,,,Biospecimen +Mounting Medium,Mounting Medium,MountingMedium,"The solution in which the specimen is embedded, generally under a cover glass. It may be liquid, gum or resinous, soluble in water, alcohol or other solvents and be sealed from the external atmosphere by non-soluble ringing media",False,,"['Antifade with DAPI', 'Not Reported', 'Non-Aqueous Solvent based', 'Antifade without DAPI', 'PBS', 'Xylene', 'Unknown', 'Aqueous water based', 'Toluene', '']",,Biospecimen +Collection Media,Collection Media,CollectionMedia,Material Specimen is collected into post procedure,False,,"['None', 'PBS', 'PBS+Serum', 'RPMI', 'DMEM+Serum', 'RPMI+Serum', 'DMEM', '']",,Biospecimen +Processing Location,Processing Location,ProcessingLocation,"Site with an HTAN center where specimen processing occurs, if applicable. Any identifier used within the center to identify processing location. No PHI/PII is allowed.",False,,,,Biospecimen +Percent Lymphocyte Infiltration,Percent Lymphocyte Infiltration,PercentLymphocyteInfiltration,Numeric value to represent the percentage of infiltration by lymphocytes in a solid tissue normal sample or specimen.,False,,,,Biospecimen +Percent Neutrophil Infiltration,Percent Neutrophil Infiltration,PercentNeutrophilInfiltration,Numeric value to represent the percentage of infiltration by neutrophils in a tumor sample or specimen.,False,,,,Biospecimen +Histology Assessment Medium,Histology Assessment Medium,HistologyAssessmentMedium,The method of assessment used to characterize histology,False,,"['Unknown', 'Microscopy', 'Digital', 'Other', '']",,Biospecimen +Biospecimen Dimension 3,Biospecimen Dimension 3,BiospecimenDimension3,"Third dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,," If Biospecimen is ""Bone"" OR ""Tissue"" then ""Biospecimen Dimension 3"" is required",Biospecimen +Preservation Method,Preservation Method,PreservationMethod,Text term that represents the method used to preserve the sample.,False,True,"['Negative 80 Deg C', 'Formalin fixed-unbuffered', 'Formalin fixed-buffered', 'Formalin fixed paraffin embedded - FFPE', 'Fresh dissociated and single cell sorted', 'Fresh', 'Frozen', 'Cryopreservation in liquid nitrogen - dead tissue', 'Unknown', 'Liquid Nitrogen', 'OCT', 'Cryopreserved', 'Methacarn fixed paraffin embedded - MFPE', 'Not Reported', 'Cryopreservation in dry ice - dead tissue', 'Snap Frozen', 'Fresh dissociated and single cell sorted into plates', 'Fresh dissociated and single cell sorted into plates in NP40 buffer', 'Fresh dissociated', 'Cryopreservation in liquid nitrogen - live cells', '']"," If Biospecimen is ""Bone"" OR ""Tissue"" OR ""Urine"" then ""Preservation Method"" is required",Biospecimen +Portion Weight,Portion Weight,PortionWeight,"Numeric value that represents the sample portion weight, measured in milligrams.",False,True,," If Biospecimen is ""Bone"" OR ""Tissue"" OR ""Urine"" then ""Portion Weight"" is required",Biospecimen +Site of Resection or Biopsy,Site of Resection or Biopsy,SiteofResectionorBiopsy,"The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",False,True,"['Paraurethral gland', 'Colon NOS', 'Frontal sinus', 'Overlapping lesion of tongue', 'Overlapping lesion of palate', 'Scrotum NOS', 'Bone marrow', 'Axillary tail of breast', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'unknown primary site', 'Broad ligament', 'Lateral floor of mouth', 'Overlapping lesion of vulva', 'Trigone of bladder', 'Lacrimal gland', 'Thorax NOS', 'Ampulla of Vater', 'Myometrium', 'Penis NOS', 'Female genital tract NOS', 'Submandibular gland', 'Anterior 2/3 of tongue NOS', 'Posterior wall of bladder', 'Thymus', 'Endocrine gland NOS', 'Stomach NOS', 'Unknown', 'Cerebrum', 'Splenic flexure of colon', 'Urachus', 'Skin of lip NOS', 'Mucosa of lip NOS', 'Accessory sinus NOS', 'Cortex of adrenal gland', 'Other ill-defined sites', 'Middle lobe lung', 'Pelvis NOS', 'Anus NOS', 'Upper-inner quadrant of breast', 'Posterior mediastinum', 'Esophagus NOS', 'Duodenum', 'Cervical esophagus', 'Optic nerve', 'Long bones of lower limb and associated joints', 'Middle ear', 'Breast NOS', 'Dorsal surface of tongue NOS', 'Lesser curvature of stomach NOS', 'Overlapping lesion of floor of mouth', 'Overlapping lesion of heart mediastinum and pleura', 'Eye NOS', 'Overlapping lesion of esophagus', 'Ciliary body', 'Ureteric orifice', 'Postcricoid region', 'External ear', 'Base of tongue NOS', 'Liver', 'Commissure of lip', 'Cloacogenic zone', 'Lower lobe lung', 'Transverse colon', 'Acoustic nerve', 'Supraglottis', 'Fallopian tube', 'Upper third of esophagus', 'Skin of scalp and neck', 'Choroid', 'Long bones of upper limb scapula and associated joints', 'Overlapping lesion of brain', 'Upper gum', 'Skin NOS', 'Hard palate', 'Ileum', 'Overlapping lesion of colon', 'Ascending colon', 'Lower gum', 'Pelvic bones sacrum coccyx and associated joints', 'Hepatic flexure of colon', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Vestibule of mouth', 'Cervix uteri', 'Bones of skull and face and associated joints', 'Overlapping lesion of lip oral cavity and pharynx', 'Endometrium', 'Sphenoid sinus', 'Overlapping lesion of ill-defined sites', 'Sigmoid colon', 'Peritoneum NOS', 'Specified parts of peritoneum', 'Meckel diverticulum', 'Rectosigmoid junction', 'Kidney NOS', 'Reticuloendothelial system NOS', 'Rectum NOS', 'Pylorus', 'Overlapping lesion of tonsil', 'Pleura NOS', 'Jejunum', 'Vallecula', 'Skin of lower limb and hip', 'Pelvic lymph nodes', 'External lower lip', 'Overlapping lesion of skin', 'Mucosa of upper lip', 'Ovary', 'Cauda equina', 'Lower limb NOS', 'Body of stomach', 'Overlapping lesion of larynx', 'Pancreas NOS', 'Overlapping lesion of lung', 'Overlapping lesion of major salivary glands', 'Uvula', 'Overlapping lesion of hypopharynx', 'Round ligament', 'Corpus uteri', 'Biliary tract NOS', 'Male genital organs NOS', 'Parametrium', 'External lip NOS', 'Overlapping lesion of accessory sinuses', 'Cardia NOS', 'Islets of Langerhans', 'Carotid body', 'Ventral surface of tongue NOS', 'Autonomic nervous system NOS', 'Overlapping lesion of corpus uteri', 'Spinal meninges', 'Posterior wall of nasopharynx', 'Placenta', 'Intrahepatic bile duct', 'Overlapping lesion of digestive system', 'Mediastinum NOS', 'Hematopoietic system NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Major salivary gland NOS', 'Cerebellum NOS', 'Overlapping lesion of stomach', 'Vulva NOS', 'Craniopharyngeal duct', 'Lung NOS', 'Greater curvature of stomach NOS', 'Upper-outer quadrant of breast', 'Gallbladder', 'Thoracic esophagus', 'Lymph nodes of axilla or arm', 'Ventricle NOS', 'Overlapping lesion of biliary tract', 'Hypopharynx NOS', 'Clitoris', 'Exocervix', 'Parietal lobe', 'Waldeyer ring', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Head face or neck NOS', 'Anterior wall of nasopharynx', 'Urethra', 'Overlapping lesion of nasopharynx', 'Maxillary sinus', 'Lymph nodes of inguinal region or leg', 'Ureter', 'Tonsillar pillar', 'Sublingual gland', 'Pituitary gland', 'Gastrointestinal tract NOS', 'Pineal gland', 'Meninges NOS', 'Lingual tonsil', 'Trachea', 'Pyriform sinus', 'Mucosa of lower lip', 'Not Reported', 'Posterior wall of hypopharynx', 'Urinary system NOS', 'Orbit NOS', 'Short bones of lower limb and associated joints', 'Connective subcutaneous and other soft tissues of thorax', 'Upper limb NOS', 'Gastric antrum', 'Lymph node NOS', 'Peripheral nerves and autonomic nervous system of thorax', 'Ill-defined sites within respiratory system', 'Other specified parts of male genital organs', 'Rib sternum clavicle and associated joints', 'Overlapping lesion of bladder', 'Appendix', 'Prostate gland', 'Lymph nodes of multiple regions', 'Lateral wall of nasopharynx', 'Branchial cleft', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Floor of mouth NOS', 'Connective subcutaneous and other soft tissues NOS', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Bladder neck', 'Border of tongue', 'Connective subcutaneous and other soft tissues of abdomen', 'Overlapping lesion of small intestine', 'Lateral wall of bladder', 'Soft palate NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Isthmus uteri', 'Nasal cavity', 'Endocervix', 'Tonsil NOS', 'Glottis', 'Retroperitoneum', 'Peripheral nerves and autonomic nervous system of pelvis', 'Frontal lobe', 'Vagina NOS', 'Undescended testis', 'Laryngeal cartilage', 'Eyelid', 'Hypopharyngeal aspect of aryepiglottic fold', 'Overlapping lesion of other and unspecified parts of mouth', 'Upper lobe lung', 'Lip NOS', 'Lymph nodes of head face and neck', 'Overlapping lesion of brain and central nervous system', 'Overlapping lesion of penis', 'Overlapping lesion of retroperitoneum and peritoneum', 'Parotid gland', 'Dome of bladder', 'Bone of limb NOS', 'Descended testis', 'Vertebral column', 'Fundus uteri', 'Connective subcutaneous and other soft tissues of pelvis', 'Epididymis', 'Intra-abdominal lymph nodes', 'Paraspinal', 'Prepuce', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Pharynx NOS', 'Overlapping lesion of endocrine glands and related structures', 'Gum NOS', 'Spinal cord', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Skin of upper limb and shoulder', 'Nasopharynx NOS', 'Parathyroid gland', 'Bone NOS', 'Mouth NOS', 'Abdomen NOS', 'Conjunctiva', 'Spermatic cord', 'External upper lip', 'Labium minus', 'Renal pelvis', 'Overlapping lesion of lip', 'Short bones of upper limb and associated joints', 'Main bronchus', 'Upper respiratory tract NOS', 'Body of penis', 'Small intestine NOS', 'Central portion of breast', 'Lower-inner quadrant of breast', 'Labium majus', 'Tonsillar fossa', 'Cecum', 'Glans penis', 'Tail of pancreas', 'Lower third of esophagus', 'Body of pancreas', 'Intestinal tract NOS', 'Brain stem', 'Overlapping lesion of rectum anus and anal canal', 'Posterior wall of oropharynx', 'Pancreatic duct', 'Blood', 'Temporal lobe', 'Anterior floor of mouth', 'Nervous system NOS', 'Cornea NOS', 'Palate NOS', 'Occipital lobe', 'Abdominal esophagus', 'Overlapping lesion of pancreas', 'Overlapping lesion of female genital organs', 'Cheek mucosa', 'Retina', 'Overlapping lesion of male genital organs', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Larynx NOS', 'Skin of other and unspecified parts of face', 'Spleen', 'Oropharynx NOS', 'Anal canal', 'Subglottis', 'Cerebral meninges', 'Lateral wall of oropharynx', 'Middle third of esophagus', 'Nipple', 'Medulla of adrenal gland', 'Overlapping lesion of eye and adnexa', 'Olfactory nerve', 'Ethmoid sinus', 'Overlapping lesion of cervix uteri', 'Descending colon', 'Brain NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Anterior wall of bladder', 'Mandible', 'Other specified parts of pancreas', 'Skin of trunk', 'Other specified parts of female genital organs', 'Uterus NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Intrathoracic lymph nodes', 'Heart', 'Adrenal gland NOS', 'Aortic body and other paraganglia', 'Extrahepatic bile duct', 'Overlapping lesion of breast', 'Superior wall of nasopharynx', 'Fundus of stomach', 'Anterior mediastinum', 'Tongue NOS', 'Cranial nerve NOS', 'Head of pancreas', 'Overlapping lesions of oropharynx', 'Overlapping lesion of bones joints and articular cartilage', 'Retromolar area', 'Testis NOS', 'Connective subcutaneous and other soft tissues of head face and neck', 'Bladder NOS', 'Overlapping lesion of urinary organs', 'Lower-outer quadrant of breast', 'Thyroid gland', 'Anterior surface of epiglottis', 'Uterine adnexa', '']"," If Biospecimen is ""Bone"" OR ""Tissue"" OR ""Urine"" then ""Site of Resection or Biopsy"" is required",Biospecimen +Specimen Laterality,Specimen Laterality,SpecimenLaterality,"For tumors in paired organs, designates the side on which the specimen was obtained.",False,True,"['Not Reported', 'Bilateral', 'Not Applicable', 'Unknown', 'Left', 'Right', '']"," If Biospecimen is ""Bone"" OR ""Tissue"" OR ""Urine"" then ""Specimen Laterality"" is required",Biospecimen +Ischemic Temperature,Ischemic Temperature,IschemicTemperature,Specify whether specimen experienced warm or cold ischemia.,False,True,"['4C wet ice', 'Ambient air', 'Cold Ischemia', 'Warm Ischemia', 'Unknown', 'Liquid Nitrogen', 'Negative -20C', 'Dry Ice', '']"," If Biospecimen is ""Bone"" OR ""Tissue"" OR ""Urine"" OR ""Analyte"" then ""Ischemic Temperature"" is required",Biospecimen +Tumor Tissue Type,Tumor Tissue Type,TumorTissueType,Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint (add rows to select multiple values along with timepoints),False,True,"['Not analyzed', 'Local recurrence', 'Metastatic', 'Premalignant - in situ', 'primary', 'Post therapy neoadjuvant', 'Normal adjacent', 'Post therapy', 'Normal', 'Recurrent', 'Not Otherwise Specified', 'Premalignant', 'Normal distant', 'Additional Primary', 'Post therapy adjuvant', 'Atypia - hyperplasia', '']"," If Biospecimen is ""Bone"" OR ""Tissue"" OR ""Urine"" then ""Tumor Tissue Type"" is required",Biospecimen +Histologic Morphology Code,Histologic Morphology Code,HistologicMorphologyCode,"Histologic Morphology Code, based on ICD-O-3. Any valid ICD-O-3 morphology code. See https://seer.cancer.gov/icd-o-3/ and https://seer.cancer.gov/icd-o-3/sitetype.icdo3.20200629.xlsx. Examples: 80510",False,True,," If Biospecimen is ""Bone"" OR ""Tissue"" OR ""Urine"" then ""Histologic Morphology Code"" is required",Biospecimen +Biospecimen Dimension 1,Biospecimen Dimension 1,BiospecimenDimension1,"First dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,," If Biospecimen is ""Bone"" OR ""Tissue"" then ""Biospecimen Dimension 1"" is required",Biospecimen +Total Volume,Total Volume,TotalVolume,Numeric value for the total amount of sample or specimen,False,True,," If Biospecimen is ""Bone"" OR ""Tissue"" OR ""Urine"" then ""Total Volume"" is required",Biospecimen +Section Number in Sequence,Section Number in Sequence,SectionNumberinSequence,"Numeric value (integer, including ranges) provided to a sample in a series of sections (list all adjacent sections in the Adjacent Biospecimen IDs field)",False,True,," If Biospecimen is ""Bone"" OR ""Tissue"" then ""Section Number in Sequence"" is required",Biospecimen +Ischemic Time,Ischemic Time,IschemicTime,"Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value.",False,True,," If Biospecimen is ""Bone"" OR ""Tissue"" OR ""Urine"" OR ""Analyte"" then ""Ischemic Time"" is required",Biospecimen +Biospecimen Dimension 2,Biospecimen Dimension 2,BiospecimenDimension2,"Second dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,," If Biospecimen is ""Bone"" OR ""Tissue"" then ""Biospecimen Dimension 2"" is required",Biospecimen +Shipping Condition Type,Shipping Condition Type,ShippingConditionType,Text descriptor of the shipping environment of a biospecimen.,False,True,"['Ambient Pack', 'Other Shipping Environment', 'Ice Pack', 'Cold Pack', 'Liquid Nitrogen', 'Not Shipped', 'Dry Ice', 'Specimen at Room Temperature', '']"," If Biospecimen is ""Blood"" OR ""Analyte"" then ""Shipping Condition Type"" is required",Biospecimen +Slide Charge Type,Slide Charge Type,SlideChargeType,A description of the charge on the glass slide.,False,True,"['Not applicable', 'Uncharged', 'Charged', 'Other', 'Coverslip', '']"," If Biospecimen is ""Analyte"" then ""Slide Charge Type"" is required",Biospecimen +Fixation Duration,Fixation Duration,FixationDuration,"The length of time, from beginning to end, required to process or preserve biospecimens in fixative (measured in minutes)",False,True,," If Biospecimen is ""Analyte"" then ""Fixation Duration"" is required",Biospecimen +Section Thickness Value,Section Thickness Value,SectionThicknessValue,"Numeric value to describe the thickness of a slice to tissue taken from a biospecimen, measured in microns (um).",False,True,," If Biospecimen is ""Analyte"" then ""Section Thickness Value"" is required",Biospecimen +Sectioning Days from Index,Sectioning Days from Index,SectioningDaysfromIndex,Number of days from the research participant's index date that the biospecimen was sectioned after collection,False,True,," If Biospecimen is ""Analyte"" then ""Sectioning Days from Index"" is required",Biospecimen +Analyte Type,Analyte Type,AnalyteType,The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen,False,True,"['cfDNA Analyte', 'RNA Analyte', 'PBMCs or Plasma or Serum Analyte', 'PBMCs', 'Plasma', 'DNA Analyte', 'cDNA Libraries Analyte', 'Total RNA Analyte', 'Serum Analyte', 'Tissue Section Analyte', 'Tissue Block Analyte', '']"," If Biospecimen is ""Analyte"" then ""Analyte Type"" is required",Biospecimen +Acquisition Method Other Specify,Acquisition Method Other Specify,AcquisitionMethodOtherSpecify,A custom acquisition method [Text - max length 100 characters],False,True,," If Acquisition is ""Other Acquisition Method"" then ""Acquisition Method Other Specify"" is required",Biospecimen +Dimensions Unit,Dimensions Unit,DimensionsUnit,"Unit of measurement used for dimension CDEs in metric system (i.e. cm, mm, etc)",False,,"['cm', 'mm', '']",,Biospecimen +Total Volume Unit,Total Volume Unit,TotalVolumeUnit,Unit of measurement used for the total amount of sample or specimen,False,,"['mL', 'cubic millimeter', 'square centimeter', '']",,Biospecimen +Precancerous Condition Type,Precancerous Condition Type,PrecancerousConditionType,The classification of pre-cancerous cells found in a specific collection of data being studied by the Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions (MCL).,False,,"['Benign tumor NOS', 'No diagnosis possible', 'Pancreatic Intraductal Papillary-Mucinous Neoplasm', 'Normal WDA', 'Persistent melanoma in situ', 'Atypical adenomatous hyperplasia', 'Invasive melanoma - nevoid', 'Invasive melanoma - nodular type', 'Severe dysplasia', 'Reserve cell hyperplasia', 'Melanocytic hyperplasia', 'Squamous metaplasia - immature', 'Atypical melanocytic proliferation', 'Carcinoma NOS', 'Mild dysplasia', 'Superficial spreading', 'Ductal Carcinoma In Situ', 'Squamous metaplasia - mature', 'Moderate dysplasia', 'Invasive melanoma - acral lentiginous', 'Adenocarcinoma in situ - mucinous', 'Pancreatic Intraepithelial Neoplasia', 'Acral-lentiginous', 'Invasive melanoma - desmoplastic', 'Hamartoma', 'Atypical Adenomatous Lung Hyperplasia', 'Scar - no residual melanoma', 'Invasive melanoma - superficial spreading', 'Melanoma in situ not otherwise classified', 'Lentigo maligna type', 'Invasive melanoma', 'Melanoma in situ arising in a giant congenital nevus', 'Other', 'Adenocarcinoma in situ - non mucinous', 'Invasive melanoma - lentigo maligna', 'Melanoma in situ', 'Prostatic Intraepithelial Neoplasia', '']",,ClinicalDataTier2 +Mutational Signatures,Mutational Signatures,MutationalSignatures,"Mutational signatures identified in the patient, includes signatures linked to selected exogenous carcinogens, endogenous and enzymatic modification of DNA or defective DNA repair. Note: Include only outputs of tests that were completed clinically for the participant and only include data from a diagnostic array that was completed prior to research sequencing was done. ",False,,"['transcriptional strand bias', 'Signature 2', 'Not Applicable', 'methylated CpG sequences mutagenesis(deamination of 5-methyl-cytosine)', 'Signature 1A', 'Alkylating Agents (Temozolomide) induced mutations', 'Signature 15', 'Signature 11', 'Data not available', 'Signature 17', 'Signature 10', 'Signature 16', 'Signature 21', 'microsatellite instability (additions and deletions)', 'Signature 3', 'Signature 18', 'Signature 19', 'Unknown', 'Activation Induced Deaminases (AID) associated mutations', 'Signature 4', 'localized substitution hypermutation (kataegis)', 'Ig gene hypermutation', 'altered activity of the error-prone polymerase POLε (POLE)', 'Signature 1B', 'Signature 5', 'Signature 20', 'UV light induced mutations', 'Not Reported', 'Signature 12', 'APOBEC enzymes associated mutations', 'Signature 6', 'Signature 9', 'Signature 14', 'Signature 13', 'Other', 'Signature 7', 'Tobacco use associated mutations', 'age of cancer diagnosis', 'DNA MMR Deficiency', 'Signature 8', '']",,ClinicalDataTier2 +COVID19 Occurrence Indicator,COVID19 Occurrence Indicator,COVID19OccurrenceIndicator,The indicator that describes whether or not a COVID-19 infectious disorder occurred.,False,,"['Yes', 'No', 'Not Applicable', 'Unknown', 'Not Done', '']",,ClinicalDataTier2 +Ecig vape use,Ecig vape use,Ecigvapeuse,"Use of non-traditional cigarette nicotine delivery device (electronic cigarette, ENDS - electronic nicotine delivery system)",False,,"['Unknown', 'Current', 'Former', 'Never', '']",,ClinicalDataTier2 +Extent of Tumor Resection,Extent of Tumor Resection,ExtentofTumorResection,"The degree to which the lesion has been cut out, or resected.",False,,"['Partial debulking', 'Not Reported', 'Not Applicable', 'Open Biopsy', 'Other', 'Optimal debulking', 'Subtotal Resection', 'Segmental', 'Suboptimal', 'Unknown', 'Minor', 'Extensive Subtotal', 'Gross Total Resection', 'NTR', 'Suboptimal debulking', '']",,ClinicalDataTier2 +Chewing tobacco daily use count,Chewing tobacco daily use count,Chewingtobaccodailyusecount,"The quantity of daily use of tobacco, in the form of a plug, usually flavored, for chewing rather than smoking.",False,,,,ClinicalDataTier2 +Education Level,Education Level,EducationLevel,Highest level of education that the patient completed (direct patient-derived information),False,,"['Data not available', 'Grade school', ""Bachelor's degree"", 'High school graduate (including equivalency)', ""Master's degree"", 'Doctoral degree or professional degree', 'Graduate or professional degree', 'Some college or associate degree', 'No formal education', 'Not high school graduate', '']",,ClinicalDataTier2 +Hereditary Cancer Predisposition Syndrome,Hereditary Cancer Predisposition Syndrome,HereditaryCancerPredispositionSyndrome,History of presence of inherited genetic predisposition syndrome that confers heightened susceptibility to cancer in the patient.,False,,"['Tyrosinemia', 'von Hippel-Lindau Syndrome', 'Carney complex', 'Not Applicable', 'Gorlin syndrome', 'Familial adenomatous polyposis', 'Familial prostate cancer', 'Hereditary paraganglioma–pheochromocytoma syndrome', 'Rhabdoid tumor predisposition syndrome type II', 'Familial gastrointestinal stromal tumor', 'Multiple endocrine neoplasia type I', 'Glycogen Storage Disease', 'Tuberous sclerosis complex', 'Li-Fraumeni syndrome', 'Hereditary diffuse gastric cancer', 'Multiple endocrine neoplasia type II', 'Rhabdoid tumor predisposition syndrome type I', 'Beckwith-Wiedemann', 'Hereditary breast–ovarian cancer syndrome', 'Hereditary renal oncocytoma', 'Rubinstein-Taybi syndrome', 'Unknown', 'Hereditary mixed polyposis syndrome', 'Hereditary retinoblastoma', 'Peutz–Jeghers syndrome', 'Melanoma–astrocytoma syndrome', 'Cirrhosis unknown etiology', 'Alpha-1 antitrypsin', 'Familial pancreatic cancer', 'Lynch syndrome', 'Turcot syndrome', 'Serrated polyposis syndrome', 'Not Reported', 'Birt-Hogg-Dube syndrome', 'Biliary disorder', 'Hereditary papillary renal cell carcinoma', 'Juvenile polyposis syndrome', 'SDH associated renal cancer', 'Hereditary papillary RCC', 'Cowden syndrome', 'Constitutional mismatch repair deficiency', 'BAP1 mutant disease', 'Attenuated familial adenomatous polyposis', 'MUTYH-associated polyposis', 'Hereditary melanoma', 'Hereditary leiomyoma-renal cell carcinoma', 'Fanconi anemia', 'Familial renal cancer', 'Nevoid basal cell carcinoma syndrome', '']",,ClinicalDataTier2 +Cancer Incidence,Cancer Incidence,CancerIncidence,"Incidence of specific cancer type in a defined area (a number between 0 and 100). The rate of incident cases per population of 100,000 persons of a specific type of cancer as designated in the ""primary_diagnosis"" data element in the county where the patient resides, using the most recent 2013-2017 NCI Cancer Atlas derived data. Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the asociated county on the right side of the result field. On the https://gis.cancer.gov/canceratlas/tableview/ website, choose ""Incidence"" from the Topic dropdown menu, state of interest from the Area menu, ""All Races"" from the Race menu, and the cancer type (""Both Sexes"" when possible) from the Statistic menu. Find the county of interest and enter the numeric Age-Adjusted Rate per 100,000 as the value.",False,,,,ClinicalDataTier2 +Sentinel Node Positive Assessment Count,Sentinel Node Positive Assessment Count,SentinelNodePositiveAssessmentCount,The number or amount of metastatic neoplasms related to the confirmed presence of disease or specific microorganisms during examination of the first rounded mass of lymphatic tissue to which cancer is likely to spread from the primary tumor.,False,,,,ClinicalDataTier2 +Rural vs Urban,Rural vs Urban,RuralvsUrban,"Density of population in the county of residence, based on census data (updated last on 4/28/20). Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the associated county on the right side of the result field. Go to https://www2.census.gov/programs-surveys/acs/data/covid_19/Data_Profiles_for_HHS/050-County_By_State/. Select the dp02_XX.csv file where XX = the two letter abbreviation for the appropriate state. On row 166 find the total population for the appropriate county. If the total population is <2,500 enter a value of ""Rural Population""; if 2,500 - 50,000 enter a value of ""Urban Cluster""; or if >50,000 enter ""Urban Population""",False,,"['Rural Population (population <2500)', 'Urban Cluster (population 2500 - 50000)', 'Urban Population (population >50000)', '']",,ClinicalDataTier2 +Type of smoke exposure cumulative years,Type of smoke exposure cumulative years,Typeofsmokeexposurecumulativeyears,The number of cumulative years of the patient's specific type of smoke exposure,False,,,,ClinicalDataTier2 +Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,ClinicalDataTier2 +COVID19 Current Status,COVID19 Current Status,COVID19CurrentStatus,The patient's current COVID-19 status of sign or symptom events or interventions,False,,"['Patient currently has symptoms', 'Status unknown due to other reasons', 'Patient never had any symptoms of COVID-19', 'Patient had symptoms but now is fully recovered', 'Status unknown due to lack of disease/tumor assessment due to COVID-19 diagnosis', 'Status unknown due to general COVID-19 related travel restrictions', '']",,ClinicalDataTier2 +Cancer Incidence Location,Cancer Incidence Location,CancerIncidenceLocation,"The county and state in which the patient lives and to which the cancer_incidence data correlates. Record as ""County, State"" as they appear in the incidence box from which the cancer_incidence data is obtained in the https://gis.cancer.gov/canceratlas/tableview/ website",False,,,,ClinicalDataTier2 +Satellite Metastasis Present Indicator,Satellite Metastasis Present Indicator,SatelliteMetastasisPresentIndicator,A yes/no indicator to ask if intransit metastases or satellite lesions are present.,False,,"['No', 'Unknown', 'Yes', '']",,ClinicalDataTier2 +COVID19 Cancer Treatment Followup,COVID19 Cancer Treatment Followup,COVID19CancerTreatmentFollowup,Indicator that describes if cancer treatment was modified for the patient due to COVID-19 infectious disorder,False,,"['Not Applicable', 'No', 'Unknown', 'Yes', '']",,ClinicalDataTier2 +Second hand smoke exposure years,Second hand smoke exposure years,Secondhandsmokeexposureyears,The number of cumulative years of the patient's exposure to second-hand cigarette smoke,False,,,,ClinicalDataTier2 +Concomitant Medication Received Type,Concomitant Medication Received Type,ConcomitantMedicationReceivedType,An enumerated list of the type of concomitant medication received by the patient.,False,,"['Intravaginal estrogen preparations', 'Prophylactic antiplatelet therapy', 'Not Applicable', 'Antifungal', 'Antidepressants-weak CYP2D2 inhibitors or non-inhibitors', 'Non-steroidal anti-inflammatory agents', 'Diabetes-Insulin', 'Anticonvulsant', 'Diabetes-Metformin containing agents', 'Growth factor', 'Unknown', 'Anticoagulant agents', 'Antidepressants-Strong CYP2D6 inhibitors', 'COX-2 inhibitor', 'Opioids', 'Prescription medications for relief of hot flashes', 'Prescription medications for memory', 'Not Reported', 'Antidepressants-Moderate CYP2D6 inhibitors', 'Anxiolytics or sedatives', 'Tricyclic antidepressants', 'Decadron', 'Aspirin', 'Lipid-lowering drugs', 'Corticosteroid', 'Non-prescription supplements for relief of hot flashes', 'Antiplatelet agents', 'Other', 'Non-prescription supplements for memory', 'Bisphosphonates for treatment/prevention of bone loss', '']",,ClinicalDataTier2 +Ecig vape 30 day use num,Ecig vape 30 day use num,Ecigvape30dayusenum,Number of days e-cigarettes or vaping device was used in the last 30 days,False,,,,ClinicalDataTier2 +Other Biopsy Resection Site,Other Biopsy Resection Site,OtherBiopsyResectionSite,A description of the location on or within the human body where the surgical biopsy/resection procedure was performed (Not covered under HTAN Clinical Data Tier 1),False,,,,ClinicalDataTier2 +COVID19 Antibody Testing,COVID19 Antibody Testing,COVID19AntibodyTesting,Text term that demonstrates the test results of immunoglobulin M (IgM) and immunoglobulin G (IgG) antibodies to the SARS-CoV-2 virus in subject serum samples.,False,,"['SARS-CoV-2 IgG antibody positive', 'SARS-CoV-2 IgM antibody negative', 'SARS-CoV-2 IgG antibody negative', 'Not Applicable', 'SARS-CoV-2 IgM antibody positive', 'Unknown', 'SARS-CoV-2 IgG/IgM antibody positive', 'SARS-CoV-2 IgG/IgM antibody negative', 'Not Done', '']",,ClinicalDataTier2 +Immunosuppression,Immunosuppression,Immunosuppression,The indicator that describes whether or not immunosuppressive therapy was administered.,False,,"['Yes', 'No', 'Not Applicable', 'Unknown', 'Not Done', '']",,ClinicalDataTier2 +Ecig vape times per day,Ecig vape times per day,Ecigvapetimesperday,e-cig frequency of use (times per day—one “time” consists of around 15 puffs or lasts around 10 minutes),False,,,,ClinicalDataTier2 +Stop Days from Index,Stop Days from Index,StopDaysfromIndex,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'",False,,,,ClinicalDataTier2 +Lab Tests for MMR Status,Lab Tests for MMR Status,LabTestsforMMRStatus,Laboratory tests used to evaluate the status of mismatch repair pathways,False,,"['PCR to evaluate microsatellite instability', 'Not Applicable', 'Other', 'Unknown', 'BRAF\xa0sequencing', 'IHC staining for mismatch repair proteins', 'MLH1\xa0promoter methylation analysis', '']",,ClinicalDataTier2 +Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,ClinicalDataTier2 +Cancer Associated Gene Mutations,Cancer Associated Gene Mutations,CancerAssociatedGeneMutations,Type of inherited germline or other gene mutations that confers heightened susceptibility to cancer identified in patient history,False,,"['Not Applicable', 'GREM1 mutation', 'MSH6 mutation', 'NF2 mutation', 'CHK mutation', 'SMARCB1 mutation', 'PolD mutation', 'PRKAR1A mutation', 'HOXB13 mutation', 'NF1 mutation', 'PolE mutation', 'RB1 mutation', 'KIT mutation', 'PAX5 mutation', 'STK11 mutation', 'MLH1 mutation', 'p14ARF mutation', 'EGFR mutation', 'MEN1 mutation', 'SMARCA4 mutation', 'BRCA2 mutation', 'MAX mutation', 'ALK mutation', 'BRAF mutation', 'Unknown', 'ATRX mutation', 'MUTYH mutation', 'VHL mutation', 'H3K27M mutation', 'BMPR1A mutation', 'FLCN mutation', 'ETV6 mutation', 'PHOX2B mutation', 'BRCA1 mutation', 'IKZF1 mutation', 'CDKN2A mutation', 'Not Reported', 'SETD2 mutation', 'PALB2 mutation', 'POT1 mutation', 'KRAS mutation', 'APC mutation', 'SDHB mutation', 'TMEM127 mutation', 'PDGFRA mutation', 'RET mutation', 'ROS1 mutation', 'ACVR1 mutation', 'PMS2 mutation', 'SDHAF2 mutation', 'SMAD4 mutation', 'BAP1 mutation', 'PTEN mutation', 'FH mutation', 'BLM mutation', 'TSC1 mutation', 'BRCA1 and 2 mutation', 'MET mutation', 'CDKN2A and p14ARF mutation', 'TSC2 mutation', 'SDHC mutation', 'TP53 mutation', 'H3G34R/V mutation', 'CDH1 mutation', 'SDHD mutation', 'MSH2 mutation', 'PTCH mutation', 'ARF mutation', 'ATM mutation', '']",,ClinicalDataTier2 +Country of Birth,Country of Birth,CountryofBirth,Country where the patient was born.,False,,"['Belize', 'Monaco', 'Bahrain', 'Iraq', 'South Africa', 'Vietnam', 'Niue', 'Poland', 'Albania', 'Burundi', 'Spain', 'Bhutan', 'Saudi Arabia', 'Madagascar', 'Gambia', 'Switzerland', 'Laos', 'Saint Lucia', 'Myanmar', 'Mayotte', 'Guadeloupe', 'South Korea', 'Tokelau', 'Syria', 'Pakistan', 'Isle of Man', 'Yemen', 'Svalbard & Jan Mayen Islands', 'Jersey', 'Bosnia and Herzegovina', 'Eritrea', 'Guinea', 'Philippines', 'Guinea-Bissau', 'Azerbaijan', 'Somalia', 'Sudan', 'Cambodia', 'Cuba', 'Rwanda', 'Tonga', 'Saint Kitts and Nevis', 'Finland', 'Paraguay', 'Malawi', 'Falkland Islands (Malvinas)', 'Federated States of Micronesia', 'Niger', 'Colombia', 'Democratic Republic of the Congo', 'North Macedonia', 'Haiti', 'Timor-Leste', 'Austria', 'Chad', 'Iceland', 'Dominica', 'Malta', 'Denmark', 'Kosovo', 'Martinique', 'Bangladesh', 'San Marino', 'South Sudan', 'Georgia', 'Nigeria', 'Gibraltar', 'Nauru', 'Tajikistan', 'Montserrat', 'Sweden', 'Antigua and Barbuda', 'Indonesia', 'Sri Lanka', 'Greece', 'Gabon', 'Japan', 'Mauritania', 'Nicaragua', 'China', 'Cape Verde', 'Unknown', 'Grenada', 'French Polynesia', 'Moldova', 'Cayman Islands', 'Dominican Republic', 'Liechtenstein', 'Senegal', 'Holy See', 'Mali', 'Vanuatu', 'India', 'Bermuda', 'Netherlands', 'Ireland', 'Zambia', 'North Korea', 'Macau', 'Romania', 'Solomon Islands', 'Suriname', 'Nepal', 'Croatia', 'Reunion', 'Ghana', 'Saint Helena Ascension and Tristan da Cunha', 'Israel', 'Faroe Islands', 'Greenland', 'State of Palestine', 'Wallis and Futuna', 'Ecuador', 'French Guiana', 'Angola', 'Aruba', 'Guyana', 'Kuwait', 'Taiwan', 'Singapore', 'Togo', 'Andorra', 'Lebanon', 'Northern Mariana Islands', 'Armenia', 'Iran', 'New Zealand', 'Bolivia', 'Cameroon', 'Norway', 'Panama', 'Papua New Guinea', 'Qatar', 'Tanzania', 'Portugal', 'Slovakia', 'Equatorial Guinea', 'Estonia', 'Mongolia', 'Chile', 'Burkina Faso', 'Ethiopia', 'Hungary', 'Djibouti', 'Kenya', 'Kiribati', 'Botswana', 'Australia', 'Guam', 'Congo', 'Belarus', 'Uruguay', 'Czech Republic (Czechia)', 'Lesotho', 'United Kingdom', 'Lithuania', 'Russia', 'Thailand', 'Oman', 'Benin', 'Tunisia', 'Uganda', 'Namibia', 'Honduras', 'Algeria', 'Turkey', 'Morocco', 'Barbados', 'Sierra Leone', 'Venezuela', 'Saint Pierre and Miquelon', 'Kyrgyzstan', 'Trinidad and Tobago', 'Serbia', 'Peru', 'Comoros', 'Canada', 'Hong Kong', 'Liberia', 'Malaysia', 'Puerto Rico', 'Brazil', 'Virgin Islands British', 'Zimbabwe', 'Latvia', 'Eswatini', ""Cote d'Ivoire"", 'United Arab Emirates', 'Bahamas', 'Curacao', 'Slovenia', 'Central African Republic', 'Guatemala', 'Jordan', 'Egypt', 'Germany', 'Mozambique', 'Fiji', 'Turkmenistan', 'Mexico', 'Brunei', 'France', 'Kazakhstan', 'Argentina', 'Uzbekistan', 'Samoa', 'Bulgaria', 'Virgin Islands U.S.', 'Maldives', 'Cyprus', 'Costa Rica', 'Italy', 'Libya', 'Jamaica', 'Tuvalu', 'United States', 'Saint Vincent and the Grenadines', 'Palau', 'Western Sahara', 'Guernsey', 'Mauritius', 'El Salvador', 'Afghanistan', 'Belgium', 'Luxembourg', 'Ukraine', 'Marshall Islands', 'Montenegro', 'Cook Islands', 'Seychelles', 'Sao Tome and Principe', 'New Caledonia', 'Anguilla', '']",,ClinicalDataTier2 +Family Member Vital Status Indicator,Family Member Vital Status Indicator,FamilyMemberVitalStatusIndicator,The response indicates whether the family member of the patient with a history of cancer is alive. (Extension to GDC attributes in Family History Tier 1),False,,"['Unknown', 'Not Reported', 'Vital Status Dead', 'Vital Status Alive', '']",,ClinicalDataTier2 +Known Genetic Predisposition Mutation,Known Genetic Predisposition Mutation,KnownGeneticPredispositionMutation,A yes/no/unknown indicator to identify whether there is a known genetic predisposition mutation present in the patient.,False,,"['No', 'Unknown', 'Yes', '']",,ClinicalDataTier2 +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,ClinicalDataTier2 +COVID19 Complications Severity,COVID19 Complications Severity,COVID19ComplicationsSeverity,Text term that retrospectively indicates the worst complications during COVID-19 infectious disorder in the patient.,False,,"['Pulmonary complications', 'Not Applicable', 'Other', 'Unknown', 'Systemic complications', 'Cardiac complications', '']",,ClinicalDataTier2 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ClinicalDataTier2 +Tumor Extranodal Extension Indicator,Tumor Extranodal Extension Indicator,TumorExtranodalExtensionIndicator,The indicator to determine extranodal involvement or extent of the disease.,False,,"['Not applicable', 'Present - minimal', 'Absent', 'No source documentation', 'NO', 'YES', 'unspecified', 'UNKNOWN', 'Indeterminate', 'Present - extensive', 'Not sampled or dissected', 'Present', '']",,ClinicalDataTier2 +COVID19 Positive Lab Test Indicator,COVID19 Positive Lab Test Indicator,COVID19PositiveLabTestIndicator,The indicator that describes whether or not there was a COVID-19 positive test result.,False,,"['Yes', 'No', 'Not Applicable', 'Unknown', 'Not Done', '']",,ClinicalDataTier2 +Mode of Cancer Detection,Mode of Cancer Detection,ModeofCancerDetection,"Text term used to describe the mode of cancer detection, like standard of care screening or random detection",False,,"['Incidentaloma', 'Interval Cancer', 'Data not available', 'Clinical Examination of unrelated cancer symptoms', 'Standard of Care Screening', '']",,ClinicalDataTier2 +Prior Sites of Radiation,Prior Sites of Radiation,PriorSitesofRadiation,The anatomic location to which radiation treatment was administered to a patient prior to enrollment on a protocol.,False,,"['Conjunctiva', 'Lymph Node(s) Parotid', 'Lung', 'Patella', 'Nasopharynx', 'Descending Colon', 'Lymph Node(s) Axilla', 'Dermal', 'Lymph Node(s) Subclavicular', 'Ureter', 'Chest Wall', 'Pericardium', 'Esophagus Mucosa Only', 'Frontal Cortex', 'Epidural Space', 'Lymph Node(s) Inguinal', 'Periorbital Soft Tissue', 'Skin upper extremity local', 'Arm', 'Joint', 'Genitourinary NOS', 'Ligament', 'Foreskin', 'Bone', 'Lymph Node(s) Iliac-Common', 'Central Nervous System', 'Lymph Node(s) Occipital', 'Retro-Orbital Region', 'Pancreas', 'Buttock', 'Ankle', 'Esophagogastric Junction', 'Cecum', 'Distant Site', 'Not Reported', 'Ileocecal Valve', 'Venous', 'Alveolar Ridge', 'Bile Duct', 'Colon Mucosa Only', 'Hilar', 'Lymph Node(s) Paraaortic', 'Prostate', 'Axilla', 'Frontal Lobe', 'Large Bowel', 'Carina', 'Chin', 'Pylorus', 'Sigmoid Colon', 'Elbow', 'Ischium', 'Nasal Cavity', 'Anorectum', 'Gastrointestinal Tract', 'Spinal Column', 'Adipose', 'Head and Neck', 'Scapula', 'Acetabulum', 'Mediastinal Soft Tissue', 'Other', 'Ganglia', 'Lymph Node(s) Hilar', 'Testis', 'Lymph Node(s) Submandibular', 'Leg', 'Jejunum', 'Ampulla of Vater', 'Small Bowel Mucosa Only', 'Appendix', 'Abdominal Wall', 'Primary tumor site', 'Soft Tissue', 'Lymph Node(s) Scalene', 'Pleura', 'Aortic Body', 'Blood', 'Hepatic Vein', 'Sinus', 'Mesentery', 'Brain', 'Fallopian Tube', 'Hippocampus', 'Bladder', 'Ascending Colon Hepatic Flexure', 'Brow', 'Transverse Colon', 'Adrenal', 'Laryngopharynx', 'Thymus', 'Artery', 'Skin total', 'Antrum', 'Pharynx', 'Islet Cells', 'Unknown', 'Urinary Tract', 'Autonomic Nervous System', 'Clavicle', 'Cerebrum', 'Abdomen total', 'Uterus', 'Vein', 'Ovary', 'Cell-Line', 'Small Finger', 'Thorax', 'Eye', 'Bowel', 'Lymph Node(s) Epitrochlear', 'Kidney', 'Fibula', 'Retina', 'Back', 'Lymph Node(s) Internal Mammary', 'Finger', 'Rectosigmoid Junction', 'Tibia', 'Ilium', 'Lumbar Spine', 'Spinal Cord', 'Thumb', 'Bone Marrow', 'Leptomeninges', 'Peritoneum', 'Vertebra', 'Bone non-spine', 'Lymph Node(s) Splenic', 'Ring Finger', 'Round Ligament', 'Spleen', 'Paraspinal Ganglion', 'Uvula', 'Lymph Node(s) Femoral', 'Lymph Node(s) Pelvic', 'Gastroesophageal Junction', 'Skull', 'Rib', 'Pituitary Gland', 'Anus', 'Anal Sphincter', 'Shoulder', 'Retroperitoneum', 'Parametrium', 'Hypopharynx', 'Cerebral Cortex', 'Ocular Orbits', 'Omentum', 'Hepatic Duct', 'Parathyroid', 'Aqueous Fluid', 'Endocrine Gland', 'Wrist', 'Carotid Artery', 'Mantle', 'Cervical Spine', 'Occipital Cortex', 'Ear Pinna (External)', 'Duodenum', 'Ascending Colon', 'Tonsil', 'Prostate Seminal Vesicles and Lymph Nodes', 'Throat', 'Epitrochlear', 'Buccal Mucosa', 'Lymph Node(s) Retroperitoneal', 'Placenta', 'Groin', 'Penis', 'Subcutaneous Tissue', 'Cardia', 'Peritoneal Cavity', 'Bronchiole', 'Small Bowel', 'Lymph Node(s) Distant', 'Spine', 'Hand', 'Vagina', 'Lymph Node(s) Regional', 'Umbilical Cord', 'Blood Vessel', 'Lymph Node(s) Cervical', 'Popliteal Fossa', 'Rectum', 'Index Finger', 'Regional Site', 'Oropharynx', 'Synovium', 'Mandible', 'Cerebellum', 'Nerve(s) Cranial', 'Breast', 'Colon', 'Mediastinum', 'Nails', 'Pelvis', 'Salivary Gland', 'Ascites', 'Skin', 'Palate', 'Neck', 'Lymph Node', 'Tonsil (Pharyngeal)', 'Head Face Or Neck Nos', 'Chest', 'Hepatic', 'Lacrimal Gland', 'Capillary', 'Forearm', 'Muscle', 'Fibroblasts', 'Fluid', 'Skin lower extremity local', 'Gallbladder', 'Body total', 'Lymph Node(s) Mediastinal', 'Lymph Node(s) Supraclavicular', 'Scrotum', 'Gastrointestinal Intestine', 'Sternum', 'Cervix', 'Oral Cavity Mucosa Only', 'Humerus', 'Adenoid', 'Carotid Body', 'Calf', 'Esophagus', 'Femoral Vein', 'Aorta', 'Femur', 'Foot', 'Primary Tumor Field', 'Heart', 'Antecubital Fossa', 'Connective Tissue', 'Hip', 'Sacrum', 'Trachea / Major Bronchi', 'Cartilage', 'Larynx', 'Scalp', 'Sciatic Nerve', 'Vulva', 'White Blood Cells', 'Epididymis', 'Liver', 'Nerve', 'Skin trunk local', 'Lymph Node(s) Iliac-External', 'Stomach', 'Clitoris', 'Hard Palate', 'Stomach Mucosa Only', 'Femoral Artery', 'Nasal Soft Tissue', 'Broad Ligament', 'Ear', 'Vas Deferens', 'Auditory Canal', 'Bronchus', 'Tendon', 'Lymph Node(s) Popliteal', 'Mesothelium', 'Oral Cavity', 'Ear Canal', 'Middle Finger', 'Common Duct', 'Thyroid', 'Fundus of Stomach', 'Tongue', 'Amniotic Fluid', 'Ileum', 'Pouch', 'Splenic Flexure', 'Pineal', 'Sinus(es) Maxillary', 'Thoracic Spine', 'Knee', 'Parotid Gland', 'Gum', 'Thigh', 'Urethra', 'Forehead', 'Jaw', 'Buccal Cavity', 'Floor of Mouth', 'Skeletal Muscle', 'Seminal Vesicle', 'Temporal Cortex', 'Diaphragm', 'Lymph Node(s) Mesenteric', 'Lymph Node(s) Mammary', 'Maxilla', 'Pineal Gland', 'Mitochondria', 'Lip', 'Cerebrospinal Fluid', 'Trunk', 'Brain Stem', 'Prostate Bed', '']",,ClinicalDataTier2 +Mismatch Repair System Status,Mismatch Repair System Status,MismatchRepairSystemStatus,The text that best describes the condition or state of MMR (mismatch repair system) in the patient,False,,"['unknown or other', 'Mismatch repair deficiency MMRD', 'Microsatellite stable MSS', 'Microsatellite instability high MSIH', 'Mismatch repair proficiency MMPP', '']",,ClinicalDataTier2 +Sentinel Lymph Node Count,Sentinel Lymph Node Count,SentinelLymphNodeCount,Numeric count of sentinel lymph nodes.,False,,,,ClinicalDataTier2 +Medically Underserved Area,Medically Underserved Area,MedicallyUnderservedArea,"Areas or populations designated by HRSA as having too few primary care providers, high infant mortality, high poverty or a high elderly population: Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/ - enter the zip code in the main text field and use the associated county on the right side of the result field. Go to data.hrsa.gov website and select ""Query Data"". Pick the Medically Underserved Areas/Populations (MUA/P) data source in the step 1 menu and select ""View Data"". Enter the name of the county (_______ county) in the first ""Service Area"" column, adding the state in the 5th column may help direct you to the data. If the designation type in the third column is ""medically underserved area"" enter ""Yes"" as the value. If the county generates a ""No data available in table"" enter ""No"" as the value. A value of ""Unknown"" indicates that sufficient data was not available to look up the value. If value is yes, complete the Medically_underserved_score data element.",False,,"['Medically Underserved Area - Yes', 'Medically Underserved Area - Unknown', 'Medically Underserved Area - No', '']",,ClinicalDataTier2 +Medically Underserved Score,Medically Underserved Score,MedicallyUnderservedScore,"Index of Medical Underservice (IMU) score, a number between 0 and 100, where 0 represents completely underserved and 100 represents best served or least underserved. Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the asociated county on the right side of the result field. Go to data.hrsa.gov website and select Query Data. Pick the Medically Underserved Areas/Populations (MUA/P) data source in the step 1 menu and select View Data. Enter the name of the county (______ county) in the first ""Service Area"" column, adding the state in the 5th column may help direct you to the data. Enter the Index of Medical Underservice Score in the fourth column to one decimal place as the value.",False,True,," If Medically Underserved Area is ""Medically Underserved Area - Yes"" then ""Medically Underserved Score"" is required",ClinicalDataTier2 +Days to Recurrence,Days to Recurrence,DaystoRecurrence,Number of days between the date used for index and the date the patient's disease recurred.,True,,,,SRRSClinicalDataTier2 +Days to Last Known Disease Status,Days to Last Known Disease Status,DaystoLastKnownDiseaseStatus,"Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days.",True,,,,SRRSClinicalDataTier2 +Vital Status,Vital Status,VitalStatus,The survival state of the person registered on the protocol.,True,,"['Alive', 'Unknown', 'Dead', 'Not Reported']",,SRRSClinicalDataTier2 +NCI Atlas Cancer Site,NCI Atlas Cancer Site,NCIAtlasCancerSite,"The primary tumor site used to calculate the incidence rate using the NCI Cancer Atlas, a digital atlas which provides geographical data related to cancer utilizing the Surveillance, Epidemiology, and End Results (SEER) Program cancer incidence rates for 2013 to 2017",False,,"['Colon And Rectum', 'Bladder', 'Leukemia', 'Thyroid Gland', 'Prostate Gland', 'Stomach', 'Cervix Uteri', 'Lung And Bronchus', 'Uterus', 'Pancreas', 'Ovary', 'In situ Female Breast', 'Oral Cavity And Pharynx', ""Non-Hodgkin's Lymphoma"", 'Malignant Childhood Neoplasm', 'Liver And Bile Duct', 'Cutaneous Melanoma', 'Female Breast', 'Brain And Other Nervous System', 'Less Than Age', 'Kidney And Renal Pelvis', 'Esophagus', '']",,SRRSClinicalDataTier2 +Tissue or Organ of Origin,Tissue or Organ of Origin,TissueorOrganofOrigin,"The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",True,,"['Paraurethral gland', 'Colon NOS', 'Frontal sinus', 'Overlapping lesion of tongue', 'Overlapping lesion of palate', 'Scrotum NOS', 'Bone marrow', 'Axillary tail of breast', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'unknown primary site', 'Broad ligament', 'Lateral floor of mouth', 'Overlapping lesion of vulva', 'Trigone of bladder', 'Lacrimal gland', 'Thorax NOS', 'Ampulla of Vater', 'Myometrium', 'Penis NOS', 'Female genital tract NOS', 'Submandibular gland', 'Anterior 2/3 of tongue NOS', 'Posterior wall of bladder', 'Thymus', 'Endocrine gland NOS', 'Stomach NOS', 'Unknown', 'Cerebrum', 'Splenic flexure of colon', 'Urachus', 'Skin of lip NOS', 'Mucosa of lip NOS', 'Accessory sinus NOS', 'Cortex of adrenal gland', 'Other ill-defined sites', 'Middle lobe lung', 'Pelvis NOS', 'Anus NOS', 'Upper-inner quadrant of breast', 'Posterior mediastinum', 'Esophagus NOS', 'Duodenum', 'Cervical esophagus', 'Optic nerve', 'Long bones of lower limb and associated joints', 'Middle ear', 'Breast NOS', 'Dorsal surface of tongue NOS', 'Lesser curvature of stomach NOS', 'Overlapping lesion of floor of mouth', 'Overlapping lesion of heart mediastinum and pleura', 'Eye NOS', 'Overlapping lesion of esophagus', 'Ciliary body', 'Ureteric orifice', 'Postcricoid region', 'External ear', 'Base of tongue NOS', 'Liver', 'Commissure of lip', 'Cloacogenic zone', 'Lower lobe lung', 'Transverse colon', 'Acoustic nerve', 'Supraglottis', 'Fallopian tube', 'Upper third of esophagus', 'Skin of scalp and neck', 'Choroid', 'Long bones of upper limb scapula and associated joints', 'Overlapping lesion of brain', 'Upper gum', 'Skin NOS', 'Hard palate', 'Ileum', 'Overlapping lesion of colon', 'Ascending colon', 'Lower gum', 'Pelvic bones sacrum coccyx and associated joints', 'Hepatic flexure of colon', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Vestibule of mouth', 'Cervix uteri', 'Bones of skull and face and associated joints', 'Overlapping lesion of lip oral cavity and pharynx', 'Endometrium', 'Sphenoid sinus', 'Overlapping lesion of ill-defined sites', 'Sigmoid colon', 'Peritoneum NOS', 'Specified parts of peritoneum', 'Meckel diverticulum', 'Rectosigmoid junction', 'Kidney NOS', 'Reticuloendothelial system NOS', 'Rectum NOS', 'Pylorus', 'Overlapping lesion of tonsil', 'Pleura NOS', 'Jejunum', 'Vallecula', 'Skin of lower limb and hip', 'Pelvic lymph nodes', 'External lower lip', 'Overlapping lesion of skin', 'Mucosa of upper lip', 'Ovary', 'Cauda equina', 'Lower limb NOS', 'Body of stomach', 'Overlapping lesion of larynx', 'Pancreas NOS', 'Overlapping lesion of lung', 'Overlapping lesion of major salivary glands', 'Uvula', 'Overlapping lesion of hypopharynx', 'Round ligament', 'Corpus uteri', 'Biliary tract NOS', 'Male genital organs NOS', 'Parametrium', 'External lip NOS', 'Overlapping lesion of accessory sinuses', 'Cardia NOS', 'Islets of Langerhans', 'Carotid body', 'Ventral surface of tongue NOS', 'Autonomic nervous system NOS', 'Overlapping lesion of corpus uteri', 'Spinal meninges', 'Posterior wall of nasopharynx', 'Placenta', 'Intrahepatic bile duct', 'Overlapping lesion of digestive system', 'Mediastinum NOS', 'Hematopoietic system NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Major salivary gland NOS', 'Cerebellum NOS', 'Overlapping lesion of stomach', 'Vulva NOS', 'Craniopharyngeal duct', 'Lung NOS', 'Greater curvature of stomach NOS', 'Upper-outer quadrant of breast', 'Gallbladder', 'Thoracic esophagus', 'Lymph nodes of axilla or arm', 'Ventricle NOS', 'Overlapping lesion of biliary tract', 'Hypopharynx NOS', 'Clitoris', 'Exocervix', 'Parietal lobe', 'Waldeyer ring', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Head face or neck NOS', 'Anterior wall of nasopharynx', 'Urethra', 'Overlapping lesion of nasopharynx', 'Maxillary sinus', 'Lymph nodes of inguinal region or leg', 'Ureter', 'Tonsillar pillar', 'Sublingual gland', 'Pituitary gland', 'Gastrointestinal tract NOS', 'Pineal gland', 'Meninges NOS', 'Lingual tonsil', 'Trachea', 'Pyriform sinus', 'Mucosa of lower lip', 'Not Reported', 'Posterior wall of hypopharynx', 'Urinary system NOS', 'Orbit NOS', 'Short bones of lower limb and associated joints', 'Connective subcutaneous and other soft tissues of thorax', 'Upper limb NOS', 'Gastric antrum', 'Lymph node NOS', 'Peripheral nerves and autonomic nervous system of thorax', 'Ill-defined sites within respiratory system', 'Other specified parts of male genital organs', 'Rib sternum clavicle and associated joints', 'Overlapping lesion of bladder', 'Appendix', 'Prostate gland', 'Lymph nodes of multiple regions', 'Lateral wall of nasopharynx', 'Branchial cleft', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Floor of mouth NOS', 'Connective subcutaneous and other soft tissues NOS', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Bladder neck', 'Border of tongue', 'Connective subcutaneous and other soft tissues of abdomen', 'Overlapping lesion of small intestine', 'Lateral wall of bladder', 'Soft palate NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Isthmus uteri', 'Nasal cavity', 'Endocervix', 'Tonsil NOS', 'Glottis', 'Retroperitoneum', 'Peripheral nerves and autonomic nervous system of pelvis', 'Frontal lobe', 'Vagina NOS', 'Undescended testis', 'Laryngeal cartilage', 'Eyelid', 'Hypopharyngeal aspect of aryepiglottic fold', 'Overlapping lesion of other and unspecified parts of mouth', 'Upper lobe lung', 'Lip NOS', 'Lymph nodes of head face and neck', 'Overlapping lesion of brain and central nervous system', 'Overlapping lesion of penis', 'Overlapping lesion of retroperitoneum and peritoneum', 'Parotid gland', 'Dome of bladder', 'Bone of limb NOS', 'Descended testis', 'Vertebral column', 'Fundus uteri', 'Connective subcutaneous and other soft tissues of pelvis', 'Epididymis', 'Intra-abdominal lymph nodes', 'Paraspinal', 'Prepuce', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Pharynx NOS', 'Overlapping lesion of endocrine glands and related structures', 'Gum NOS', 'Spinal cord', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Skin of upper limb and shoulder', 'Nasopharynx NOS', 'Parathyroid gland', 'Bone NOS', 'Mouth NOS', 'Abdomen NOS', 'Conjunctiva', 'Spermatic cord', 'External upper lip', 'Labium minus', 'Renal pelvis', 'Overlapping lesion of lip', 'Short bones of upper limb and associated joints', 'Main bronchus', 'Upper respiratory tract NOS', 'Body of penis', 'Small intestine NOS', 'Central portion of breast', 'Lower-inner quadrant of breast', 'Labium majus', 'Tonsillar fossa', 'Cecum', 'Glans penis', 'Tail of pancreas', 'Lower third of esophagus', 'Body of pancreas', 'Intestinal tract NOS', 'Brain stem', 'Overlapping lesion of rectum anus and anal canal', 'Posterior wall of oropharynx', 'Pancreatic duct', 'Blood', 'Temporal lobe', 'Anterior floor of mouth', 'Nervous system NOS', 'Cornea NOS', 'Palate NOS', 'Occipital lobe', 'Abdominal esophagus', 'Overlapping lesion of pancreas', 'Overlapping lesion of female genital organs', 'Cheek mucosa', 'Retina', 'Overlapping lesion of male genital organs', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Larynx NOS', 'Skin of other and unspecified parts of face', 'Spleen', 'Oropharynx NOS', 'Anal canal', 'Subglottis', 'Cerebral meninges', 'Lateral wall of oropharynx', 'Middle third of esophagus', 'Nipple', 'Medulla of adrenal gland', 'Overlapping lesion of eye and adnexa', 'Olfactory nerve', 'Ethmoid sinus', 'Overlapping lesion of cervix uteri', 'Descending colon', 'Brain NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Anterior wall of bladder', 'Mandible', 'Other specified parts of pancreas', 'Skin of trunk', 'Other specified parts of female genital organs', 'Uterus NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Intrathoracic lymph nodes', 'Heart', 'Adrenal gland NOS', 'Aortic body and other paraganglia', 'Extrahepatic bile duct', 'Overlapping lesion of breast', 'Superior wall of nasopharynx', 'Fundus of stomach', 'Anterior mediastinum', 'Tongue NOS', 'Cranial nerve NOS', 'Head of pancreas', 'Overlapping lesions of oropharynx', 'Overlapping lesion of bones joints and articular cartilage', 'Retromolar area', 'Testis NOS', 'Connective subcutaneous and other soft tissues of head face and neck', 'Bladder NOS', 'Overlapping lesion of urinary organs', 'Lower-outer quadrant of breast', 'Thyroid gland', 'Anterior surface of epiglottis', 'Uterine adnexa']",,SRRSClinicalDataTier2 +Age at Diagnosis,Age at Diagnosis,AgeatDiagnosis,Age at the time of diagnosis expressed in number of days since birth.,True,,,,SRRSClinicalDataTier2 +Education Level,Education Level,EducationLevel,Highest level of education that the patient completed (direct patient-derived information),False,,"['Data not available', 'Grade school', ""Bachelor's degree"", 'High school graduate (including equivalency)', ""Master's degree"", 'Doctoral degree or professional degree', 'Graduate or professional degree', 'Some college or associate degree', 'No formal education', 'Not high school graduate', '']",,SRRSClinicalDataTier2 +Days to Follow Up,Days to Follow Up,DaystoFollowUp,Number of days between the date used for index and the date of the patient's last follow-up appointment or contact.,True,,,,SRRSClinicalDataTier2 +Years Smoked,Years Smoked,YearsSmoked,Numeric value (or unknown) to represent the number of years a person has been smoking.,True,,,,SRRSClinicalDataTier2 +Rural vs Urban,Rural vs Urban,RuralvsUrban,"Density of population in the county of residence, based on census data (updated last on 4/28/20). Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the associated county on the right side of the result field. Go to https://www2.census.gov/programs-surveys/acs/data/covid_19/Data_Profiles_for_HHS/050-County_By_State/. Select the dp02_XX.csv file where XX = the two letter abbreviation for the appropriate state. On row 166 find the total population for the appropriate county. If the total population is <2,500 enter a value of ""Rural Population""; if 2,500 - 50,000 enter a value of ""Urban Cluster""; or if >50,000 enter ""Urban Population""",False,,"['Rural Population (population <2500)', 'Urban Cluster (population 2500 - 50000)', 'Urban Population (population >50000)', '']",,SRRSClinicalDataTier2 +Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,SRRSClinicalDataTier2 +Cancer Incidence Location,Cancer Incidence Location,CancerIncidenceLocation,"The county and state in which the patient lives and to which the cancer_incidence data correlates. Record as ""County, State"" as they appear in the incidence box from which the cancer_incidence data is obtained in the https://gis.cancer.gov/canceratlas/tableview/ website",False,,,,SRRSClinicalDataTier2 +Morphology,Morphology,Morphology,"The third edition of the International Classification of Diseases for Oncology, published in 2000 used principally in tumor and cancer registries for coding the site (topography) and the histology (morphology) of neoplasms. The study of the structure of the cells and their arrangement to constitute tissues and, finally, the association among these to form organs. In pathology, the microscopic process of identifying normal and abnormal morphologic characteristics in tissues, by employing various cytochemical and immunocytochemical stains. A system of numbered categories for representation of data.",True,,,,SRRSClinicalDataTier2 +Race,Race,Race,"An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation withina a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution.",True,,"['white', 'Not Reported', 'american indian or alaska native', 'asian', 'Other', 'Unknown', 'native hawaiian or other pacific islander', 'not allowed to collect', 'black or african american']",,SRRSClinicalDataTier2 +Days to Last Follow up,Days to Last Follow up,DaystoLastFollowup,"Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days.",True,,,,SRRSClinicalDataTier2 +Tumor Grade,Tumor Grade,TumorGrade,"Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.",True,,"['Low Grade', 'Not Reported', 'High Grade', 'Intermediate Grade', 'Not Applicable', 'GX', 'G2', 'Unknown', 'GB', 'G3', 'G4', 'G1']",,SRRSClinicalDataTier2 +Gene Symbol,Gene Symbol,GeneSymbol,"The text term used to describe a gene targeted or included in molecular analysis. For rearrangements, this is should be used to represent the reference gene. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",True,,,,SRRSClinicalDataTier2 +Primary Diagnosis,Primary Diagnosis,PrimaryDiagnosis,"Text term used to describe the patient's histologic diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",True,,"['Adenocarcinoma in tubular adenoma', 'Tumor cells NOS', 'Malignant lymphoma mixed cell type follicular', 'T-cell large granular lymphocytic leukemia', 'Kaposi sarcoma', 'Carcinoma in adenomatous polyp', 'Adenocarcinoma in situ in tubular adenoma', 'Mixed medullary-papillary carcinoma', 'Liposarcoma NOS', 'Carcinoma intestinal type', 'Classical Hodgkin lymphoma nodular sclerosis grade 1', 'Bile duct adenoma', 'Inflammatory carcinoma', 'Carcinoma in situ in a polyp NOS', 'Intravascular B-cell lymphoma', 'Melanotic psammomatous MPNST', 'Acinar cell carcinoma', 'Papillary renal cell carcinoma', 'Papillary serous cystadenoma NOS', 'Papillary adenoma NOS', 'Interstitial cell tumor benign', 'Mixed small cell carcinoma', 'Rhabdoid sarcoma', 'Malignant lymphoma mixed cell type diffuse', 'Chronic leukemia NOS', 'Intraductal papillary carcinoma', 'Intraductal tubular-papillary neoplasm high grade', 'Central neurocytoma', 'Undifferentiated spindle cell sarcoma', 'Bronchiolo-alveolar carcinoma indeterminate type', 'Pancreatic endocrine tumor NOS', 'Tubulocystic renal cell carcinoma', 'Basophil adenocarcinoma', 'Intraductal carcinoma solid type', 'Papillotubular adenoma', 'Undifferentiated epithelioid sarcoma', 'Renal medullary carcinoma', 'Chronic granulocytic leukemia Philadelphia chromosome (Ph1) positive', 'Unclassified tumor benign', 'Bronchial adenoma cylindroid', 'Classical Hodgkin lymphoma mixed cellularity NOS', 'Pigmented adenoma', 'Infiltrating duct and colloid carcinoma', 'Bronchial-associated lymphoid tissue lymphoma', 'Epidermoid carcinoma in situ NOS', 'Unknown', 'Carcinoma NOS', 'Malignancy', 'Undifferentiated leukaemia', 'Unclassified tumor borderline malignancy', 'Hodgkin lymphoma NOS', 'Papillary cystadenoma NOS', 'Medullary carcinoma NOS', 'Myeloma NOS', 'Acute basophilic leukaemia', 'Renal cell carcinoma NOS', 'Neoplasm secondary', 'Primary amyloidosis', 'Acute lymphoblastic leukemia NOS', 'Malignant melanoma in junctional nevus', 'Nevus NOS', 'Tumor malignant NOS', 'Basal cell adenoma', 'Bronchio-alveolar carcinoma mucinous', 'Mucosal-associated lymphoid tissue lymphoma', 'Pleomorphic lobular carcinoma in situ', 'Small cell carcinoma NOS', 'Dermal nevus', 'Liver cell adenoma', 'Malignant lymphoma lymphocytic diffuse NOS', 'Cerebellar liponeurocytoma', 'Acute lymphoblastic leukemia mature B-cell type', 'Adenocarcinoma combined with other types of carcinoma', 'Adenocarcinoma metastatic NOS', 'Carcinoma in a polyp NOS', 'Pleomorphic adenoma', 'Osteosarcoma NOS', 'Carcinosarcoma NOS', 'Lymphoblastic leukemia NOS', 'Unclassified tumor uncertain whether benign or malignant', 'Renal cell carcinoma unclassified', 'Neoplasm NOS', 'Acute lymphoblastic leukemia precursor cell type', 'Cerebellar sarcoma NOS', 'Renal cell carcinoma spindle cell', 'Small cell sarcoma', 'Bronchiolo-alveolar carcinoma goblet cell type', 'Combined small cell-adenocarcinoma', 'Precancerous melanosis NOS', 'Tumor NOS', 'Neoplasm malignant', 'Melanoma in situ', 'Melanotic neuroectodermal tumor', 'Intraductal carcinoma NOS', 'Lymphoma NOS', 'Tumor cells malignant', 'Hepatocholangiocarcinoma', 'Preleukemic syndrome', 'Papillomatosis glandular', 'Small congenital nevus', 'c-ALL', 'Hodgkin lymphoma nodular sclerosis NOS', 'Bronchiolo-alveolar adenocarcinoma NOS', 'Pancreatic microadenoma', 'Tubular carcinoid', 'Gastrinoma NOS', 'Papillary urothelial carcinoma', 'Carcinoma in situ in adenomatous polyp', 'Pancreatobiliary-type carcinoma', 'Small cell osteosarcoma', 'Adenocarcinoma of anal glands', 'Gastrointestinal stromal tumor malignant', 'Acute myeloid leukemia minimal differentiation', 'Ductal carcinoma NOS', 'Malignant melanoma in Hutchinson melanotic freckle', 'Malignant lymphoma nodular NOS', 'B-cell lymphocytic leukemia/small lymphocytic lymphoma', 'Malignant lymphoma NOS', 'Combined hepatocellular carcinoma and cholangiocarcinoma', 'Combined small cell-large carcinoma', 'Epithelial tumor malignant', 'Intraepidermal carcinoma NOS', 'Endometrioid carcinoma NOS', 'Acute leukemia Burkitt type', 'Pituitary adenoma NOS', 'Adenocarcinoma NOS', 'Papillary epidermoid carcinoma', 'Teratoma NOS', 'Combined small cell-squamous cell carcinoma', 'Lobular carcinoma NOS', 'Basophil carcinoma', 'Serous cystadenocarcinoma NOS', 'Glioma malignant', 'Diffuse astrocytoma IDH-wildtype', 'Renal cell carcinoma sarcomatoid', 'Hepatoid adenocarcinoma', 'Intraductal and lobular carcinoma', 'Malignant melanoma NOS', 'Peripheral T-cell lymphoma large cell', 'Chronic myelomonocytic leukemia Type 1', 'Combined/mixed carcinoid and adenocarcinoma', 'Intraductal carcinoma and lobular carcinoma in situ', 'Pancreatic endocrine tumor nonfunctioning', 'Tubulovillous adenoma NOS', 'Intraductal carcinoma noninfiltrating NOS', 'Tumorlet benign', 'Basal cell epithelioma', 'Endometrioid adenocarcinoma NOS', 'Large cell carcinoma NOS', 'Burkitt tumor', 'Papillary microcarcinoma', 'Melanotic neurofibroma', 'Paget disease and intraductal carcinoma of breast', 'Precursor B-cell lymphoblastic lymphoma', 'Pleomorphic carcinoma', 'Dysplastic nevus', 'Undifferentiated high-grade pleomorphic sarcoma', 'Acute myeloid leukemia NOS', 'Esophageal glandular dysplasia (intraepithelial neoplasia) low grade', 'Unclassified tumor malignant uncertain whether primary or metastatic', 'Mixed pineal tumor', 'Bile duct adenocarcinoma', 'Adenocarcinoma in adenomatous polyp', 'Lymphatic leukemic NOS', 'Papillotubular adenocarcinoma', 'Lobular adenocarcinoma', 'Melanocytoma eyeball', 'Melanoma malignant of soft parts', 'Therapy related myeloid neoplasm', 'Oat cell carcinoma', 'Duct carcinoma desmoplastic type', 'Melanotic MPNST', 'Neurofibromatosis NOS', 'Melanotic medulloblastoma', 'Skin appendage carcinoma', 'Hodgkin disease NOS', 'Diffuse melanocytosis', 'Preleukemia', 'Tumor cells benign', 'Chronic myelomonocytic leukemia Type II', 'Cervical intraepithelial neoplasia low grade', 'Tubulo-papillary adenoma', 'Adenocarcinoma of anal ducts', 'Papillary carcinoma in situ', 'Acute lymphocytic leukemia', 'Myeloid leukemia NOS', 'T-cell large granular lymphocytosis', 'Bronchial adenoma NOS', 'Pulmonary blastoma', 'Intraductal carcinoma clinging', 'Adult T-cell lymphoma/leukemia', 'Intraductal adenocarcinoma noninfiltrating NOS', 'Acute lymphatic leukemia', 'Infiltrating duct and cribriform carcinoma', 'Neoplasm metastatic', 'Basal cell tumor', 'Papilloma of bladder', 'Teratoma malignant NOS', 'Pancreatoblastoma', 'Infiltrating duct carcinoma NOS', 'Precursor T-cell lymphoblastic lymphoma', 'Basal cell carcinoma NOS', 'Malignant melanoma in precancerous melanosis', 'Inflammatory adenocarcinoma', 'Splenic B-cell lymphoma/leukemia unclassifiable', 'Squamous cell carcinoma adenoid', 'T-cell lymphoma NOS', 'Tubular adenoma NOS', 'Papillary adenocarcinoma NOS', 'Esophageal intraepithelial neoplasia high grade', 'Papillary squamous cell carcinoma', 'Pulmonary adenomatosis', 'Bile duct cystadenoma', 'Combined large cell neuroendocrine carcinoma', 'Neoplasm uncertain whether benign or malignant', 'Mammary carcinoma in situ', 'Melanoma NOS', 'Spindle cell melanoma NOS', 'Esophageal glandular dysplasia (intraepithelial neoplasia) high grade', 'Neuroendocrine carcinoma NOS', 'Meningeal melanoma', 'Burkitt-like lymphoma', 'Precursor cell lymphoblastic leukemia NOS', 'Acute lymphoid leukemia', 'Chondrosarcoma grade 2/3', 'Tubulopapillary adenocarcinoma', 'B lymphoblastic leukemia/lymphoma NOS', 'Non-lymphocytic leukemia NOS', 'Pleomorphic liposarcoma', 'Mixed medullary-follicular carcinoma', 'Bronchiolo-alveolar carcinoma NOS', 'Myelocytic leukemia NOS', 'Splenic lymphoma with villous lymphocytes', 'Transitional carcinoma', 'Melanocytic nevus', 'Liposarcoma well differentiated', 'Eosinophilic leukemia', 'Chronic myeloproliferative disease NOS', 'Adenocarcinoma in situ in a polyp NOS', 'Hodgkin lymphoma mixed cellularity NOS', 'Classical Hodgkin lymphoma nodular sclerosis grade 2', 'Eosinophilic granuloma', 'Tumor embolus', 'Mixed tumor NOS', 'Carcinoma diffuse type', 'Precursor T-cell lymphoblastic leukemia', 'Neurofibrosarcoma', 'Melanocytoma NOS', 'B-ALL', 'Bronchio-alveolar carcinoma mixed mucinous and non-mucinous', 'Acute myeloid leukemia MLL', 'Adenocarcinoma in situ non-mucinous', 'Malignant lymphoma lymphoblastic NOS', 'Papillary adenocarcinoma follicular variant', 'Tumor cells uncertain whether benign or malignant', 'Pleomorphic lipoma', 'Lymphocytic leukemia NOS', 'Astrocytoma anaplastic', 'Non-Hodgkin lymphoma NOS', 'Papillary serous adenocarcinoma', 'Meningioma malignant', 'Chronic lymphoid leukemia', 'Ductal carcinoma in situ NOS', 'Neuroepithelioma NOS', 'Melanotic progonoma', 'Melanotic schwannoma', 'Diffuse astrocytoma IDH-mutant', 'Small cell neuroendocrine carcinoma', 'Esophageal squamous intraepithelial neoplasia (dysplasia) high grade', 'Paget disease extramammary', 'Prostatic intraepithelial neoplasia grade III', 'Ewing sarcoma', 'Micropapillary carcinoma NOS', 'Epithelial tumor benign', 'Hepatocellular adenoma', 'Cementoma NOS', 'Malignant lymphoma mixed cell type nodular', 'Acute leukemia NOS', 'Bile duct carcinoma', 'Nephroblastoma NOS', 'Pagetoid reticulosis', 'Hepatocarcinoma', 'Not Reported', 'Neoplasm malignant uncertain whether primary or metastatic', 'Malignant melanoma regressing', 'Bronchiolo-alveolar carcinoma Clara cell and goblet cell type', 'Dermatofibroma NOS', 'Interstitial cell tumor malignant', 'Adenocarcinoma in situ NOS', 'Adenocarcinoma endocervical type', 'Meningioma anaplastic', 'B lymphoblastic leukemia/lymphoma with hypodiploidy (Hypodiploid ALL)', 'Intraductal tubulopapillary neoplasm', 'Tumor secondary', 'Chronic myelogenous leukemia Philadelphia chromosome (Ph 1) positive', 'Sclerosing hemangioma', 'Papillary transitional cell carcinoma', 'Tubular androblastoma NOS', 'Ependymoma NOS', 'Papillary tumor of the pineal region', 'Chronic myelocytic leukemia NOS', 'Papillary serous cystadenocarcinoma', 'Haemangiosarcoma', 'Papillary and follicular carcinoma', 'Chronic myelomonocytic leukemia in transformation', 'Carcinoma anaplastic NOS', 'Paget disease mammary', 'Liver cell carcinoma', 'Eosinophil adenocarcinoma', 'Sclerosing hepatic carcinoma', 'Tumor metastatic', 'Endometrial sarcoma NOS', 'Gastrin cell tumor', 'Chronic myeloproliferative disorder', 'Acute promyelocytic leukemia NOS', 'Malignant lymphoma Hodgkin', 'Classical Hodgkin lymphoma lymphocyte depletion NOS', 'Lobular carcinoma noninfiltrating', 'Mixed pancreatic endocrine and exocrine tumor malignant', 'Unclassified tumor malignant', 'Chondroma NOS', 'Basophil adenoma', 'Transitional cell carcinoma', 'Carcinoma metastatic NOS', 'Medullary adenocarcinoma', 'Adenocarcinoma in villous adenoma', 'Ganglioglioma NOS', 'Intradermal nevus', 'Osteoblastoma malignant', 'Papillary squamous cell carcinoma in situ', 'Undifferentiated pleomorphic sarcoma', 'Bronchiolar carcinoma', 'Pancreatic endocrine tumor benign', 'Malignant melanoma in congenital melanocytic nevus', 'Malignant lymphoma diffuse NOS', 'Composite Hodgkin and non-Hodgkin lymphoma', 'Monocytic leukemia NOS', 'Paraganglioma malignant', 'Splenic diffuse red pulp small B-cell lymphoma', 'B lymphoblastic leukemia/lymphoma with hyperdiploidy', 'Rodent ulcer', 'Hodgkin sarcoma', 'Familial adenomatous polyposis', 'Duct cell carcinoma', 'Rhabdomyosarcoma NOS', 'Eosinophil carcinoma', 'Pulmonary artery intimal sarcoma', 'Capillary hemangioma', 'Adult rhabdomyoma', 'Tubular carcinoma', 'Burkitt cell leukemia', 'Bronchiolo-alveolar carcinoma Clara cell', 'Papillary glioneuronal tumor', 'T lymphoblastic leukemia/lymphoma', 'Neuroblastoma NOS', 'Meningioma NOS', 'Adenocarcinoid tumor', 'Malignant lymphoma large cell NOS', 'Combined small cell carcinoma', 'Mucous adenocarcinoma', 'Peripheral T-cell lymphoma NOS', 'Renal carcinoma collecting duct type', 'Bile duct cystadenocarcinoma', 'Chronic myelogenous leukemia BCR-ABL positive', 'Intraductal tubular-papillary neoplasm low grade', 'Tumor benign', 'Adenocarcinoma intestinal type', 'Pro-B ALL', 'Malignant lymphoma large B-cell diffuse NOS', 'Secondary carcinoma', 'Gastrinoma malignant', 'Intracystic papilloma', 'Cancer', 'Intraductal papillary adenocarcinoma with invasion', 'Mixed squamous cell and glandular papilloma', 'Sarcoma NOS', 'Non-invasive low grade serous carcinoma', 'Serous surface papillary carcinoma', 'Pro-T ALL', 'Neurofibroma NOS', 'Pancreatobiliary neoplasm non-invasive', 'Bronchial adenoma carcinoid', 'Precursor B-cell lymphoblastic leukemia', 'Melanoameloblastoma', 'Mixed adenocarcinoma and epidermoid carcinoma', 'Splenic marginal zone lymphoma NOS', 'Intraepidermal squamous cell carcinoma Bowen type', 'Carcinoma undifferentiated NOS', 'Capillary lymphangioma', 'Chronic myelomonocytic leukemia NOS', 'Adenocarcinoma in a polyp NOS', 'Astrocytoma NOS', 'Glioblastoma', 'Adult T-cell lymphoma', 'Transitional cell carcinoma in situ', 'Carcinoma in pleomorphic adenoma', 'Renal cell adenocarcinoma', 'Medulloblastoma NOS', 'Papillomatosis NOS', 'Acute myelomonocytic leukemia', 'Malignant lymphoma immunoblastic NOS', 'Chronic lymphocytic leukemia B-cell type (includes all variants of BCLL)', 'Malignant lymphoma lymphocytic NOS', 'Nonpigmented nevus', 'Squamous cell carcinoma clear cell type', 'Mixed adenocarcinoma and squamous cell carcinoma', 'Diffuse large B-cell lymphoma NOS', 'Paraganglioma benign', 'Malignant lymphoma non-Hodgkin NOS', 'Classical Hodgkin lymphoma lymphocyte-rich', 'Intraductal micropapillary carcinoma', 'Secretory carcinoma of breast', 'Gastrin cell tumor malignant', 'Papilloma NOS', 'Infiltrating basal cell carcinoma NOS', 'Adenocarcinoma in polypoid adenoma', 'Chronic neutrophilic leukemia', 'Undifferentiated sarcoma', 'Neurosarcoma', 'Medullary osteosarcoma', 'Papillary carcinoma NOS', 'Chronic lymphocytic leukemia', 'Undifferentiated uterine sarcoma', 'Malignant lymphoma lymphocytic nodular NOS', 'Adenocarcinoma in situ mucinous', 'Multiple myeloma', 'Lobular and ductal carcinoma', 'Undifferentiated round cell sarcoma', 'Chronic lymphatic leukemia', 'Endometrioid adenofibroma NOS', 'Malignant lymphoma large B-cell NOS', 'Pancreatic endocrine tumor malignant', 'Cervical intraepithelial neoplasia grade III', 'Glioma NOS', 'Papillary adenofibroma', 'Classical Hodgkin lymphoma nodular sclerosis NOS', 'Non-small cell carcinoma', 'Squamous cell carcinoma NOS', 'Haemangioblastoma', 'Paraganglioma NOS', 'Bronchiolar adenocarcinoma', 'Liposarcoma differentiated', 'Mixed tumor malignant NOS', 'Burkitt lymphoma NOS (Includes all variants)', 'Renal cell carcinoma chromophobe type', 'Malignant melanoma in giant pigmented nevus', 'Chronic monocytic leukemia', 'Carcinoma in situ NOS', 'Lymphoblastoma', 'Tubulolobular carcinoma', 'Rhabdoid tumor NOS', 'Hepatocellular carcinoma NOS', 'Adenocarcinoma in situ in adenomatous polyp', 'Classical Hodgkin lymphoma nodular sclerosis cellular phase', 'Paget disease of breast', 'Squamous cell carcinoma in situ NOS', 'Classical Hodgkin lymphoma lymphocyte depletion diffuse fibrosis', 'Bronchiolo-alveolar carcinoma non-mucinous', 'Rhabdosarcoma', 'Astrocytoma low grade', 'Chronic myeloid leukemia NOS', 'Chronic granulocytic leukemia NOS', 'Endometrioid adenoma NOS', 'Typical carcinoid', 'Rhabdoid meningioma', 'Hodgkin paragranuloma NOS', 'Hodgkin granuloma', 'Duct adenocarcinoma NOS', 'Juvenile myelomonocytic leukemia', 'Adenocarcinoma diffuse type', 'Osteoblastoma NOS', 'Rhabdomyosarcoma with ganglionic differentiation', 'Eosinophil adenoma', 'Interstitial cell tumor NOS', 'Tubular adenocarcinoma', 'Myoepithelioma', 'Pigmented nevus NOS', 'Duct carcinoma NOS', 'Neoplasm benign', 'Rhabdomyoma NOS', 'Spindle cell carcinoma NOS', 'Pleomorphic lobular carcinoma', 'Lobular carcinoma in situ NOS', 'Central neuroblastoma', 'Adenocarcinoma pancreatobiliary type', 'Chronic granulocytic leukemia BCR/ABL', 'Pigmented basal cell carcinoma', 'Paget disease and infiltrating duct carcinoma of breast', 'Acute lymphoblastic leukemia-lymphoma NOS', 'Epidermoid carcinoma NOS', 'Hepatoid carcinoma', 'Papillary meningioma', 'High-grade serous carcinoma', 'Basal cell adenocarcinoma', 'Esophageal squamous intraepithelial neoplasia (dysplasia) low grade', 'Malignant lymphoma small B lymphocytic NOS', 'Pituitary carcinoma NOS', 'Tubular androblastoma with lipid storage', 'Meningeal melanocytoma', 'Duct adenoma NOS', 'Diffuse astrocytoma low grade', 'Intraductal papillary adenocarcinoma NOS', 'Splenic marginal zone B-cell lymphoma', 'Classical Hodgkin lymphoma lymphocyte depletion reticular', 'B cell lymphoma NOS']",,SRRSClinicalDataTier2 +Molecular Analysis Method,Molecular Analysis Method,MolecularAnalysisMethod,The text term used to describe the method used for molecular analysis. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,True,,"['Not Applicable', 'WGS', 'Targeted Sequencing', 'FISH', 'IHC', 'Unknown', 'Microarray', 'Cytogenetics NOS', 'Nuclear Staining', 'Microsatellite Analysis', 'Sequencing NOS', 'Comparative Genomic Hybridization', 'Not Reported', 'Flow Cytometry', 'Southern Blotting', 'ISH', 'RNA Sequencing', 'Other', 'RT-PCR', 'WXS', 'Karyotype']",,SRRSClinicalDataTier2 +Test Result,Test Result,TestResult,The text term used to describe the result of the molecular test. If the test result was a numeric value see test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,True,,"['Equivocal', 'Copy Number Reported', 'Abnormal NOS', 'Not Reported', 'Low', 'Overexpressed', 'Test Value Reported', 'Intermediate', 'Not Applicable', 'Positive', 'Unknown', 'High', 'Normal', 'Negative', 'Loss of Expression']",,SRRSClinicalDataTier2 +Pack Years Smoked,Pack Years Smoked,PackYearsSmoked,Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes smoked per day x number of years smoked divided by 20.,True,,,,SRRSClinicalDataTier2 +Site of Resection or Biopsy,Site of Resection or Biopsy,SiteofResectionorBiopsy,"The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",True,,"['Paraurethral gland', 'Colon NOS', 'Frontal sinus', 'Overlapping lesion of tongue', 'Overlapping lesion of palate', 'Scrotum NOS', 'Bone marrow', 'Axillary tail of breast', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'unknown primary site', 'Broad ligament', 'Lateral floor of mouth', 'Overlapping lesion of vulva', 'Trigone of bladder', 'Lacrimal gland', 'Thorax NOS', 'Ampulla of Vater', 'Myometrium', 'Penis NOS', 'Female genital tract NOS', 'Submandibular gland', 'Anterior 2/3 of tongue NOS', 'Posterior wall of bladder', 'Thymus', 'Endocrine gland NOS', 'Stomach NOS', 'Unknown', 'Cerebrum', 'Splenic flexure of colon', 'Urachus', 'Skin of lip NOS', 'Mucosa of lip NOS', 'Accessory sinus NOS', 'Cortex of adrenal gland', 'Other ill-defined sites', 'Middle lobe lung', 'Pelvis NOS', 'Anus NOS', 'Upper-inner quadrant of breast', 'Posterior mediastinum', 'Esophagus NOS', 'Duodenum', 'Cervical esophagus', 'Optic nerve', 'Long bones of lower limb and associated joints', 'Middle ear', 'Breast NOS', 'Dorsal surface of tongue NOS', 'Lesser curvature of stomach NOS', 'Overlapping lesion of floor of mouth', 'Overlapping lesion of heart mediastinum and pleura', 'Eye NOS', 'Overlapping lesion of esophagus', 'Ciliary body', 'Ureteric orifice', 'Postcricoid region', 'External ear', 'Base of tongue NOS', 'Liver', 'Commissure of lip', 'Cloacogenic zone', 'Lower lobe lung', 'Transverse colon', 'Acoustic nerve', 'Supraglottis', 'Fallopian tube', 'Upper third of esophagus', 'Skin of scalp and neck', 'Choroid', 'Long bones of upper limb scapula and associated joints', 'Overlapping lesion of brain', 'Upper gum', 'Skin NOS', 'Hard palate', 'Ileum', 'Overlapping lesion of colon', 'Ascending colon', 'Lower gum', 'Pelvic bones sacrum coccyx and associated joints', 'Hepatic flexure of colon', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Vestibule of mouth', 'Cervix uteri', 'Bones of skull and face and associated joints', 'Overlapping lesion of lip oral cavity and pharynx', 'Endometrium', 'Sphenoid sinus', 'Overlapping lesion of ill-defined sites', 'Sigmoid colon', 'Peritoneum NOS', 'Specified parts of peritoneum', 'Meckel diverticulum', 'Rectosigmoid junction', 'Kidney NOS', 'Reticuloendothelial system NOS', 'Rectum NOS', 'Pylorus', 'Overlapping lesion of tonsil', 'Pleura NOS', 'Jejunum', 'Vallecula', 'Skin of lower limb and hip', 'Pelvic lymph nodes', 'External lower lip', 'Overlapping lesion of skin', 'Mucosa of upper lip', 'Ovary', 'Cauda equina', 'Lower limb NOS', 'Body of stomach', 'Overlapping lesion of larynx', 'Pancreas NOS', 'Overlapping lesion of lung', 'Overlapping lesion of major salivary glands', 'Uvula', 'Overlapping lesion of hypopharynx', 'Round ligament', 'Corpus uteri', 'Biliary tract NOS', 'Male genital organs NOS', 'Parametrium', 'External lip NOS', 'Overlapping lesion of accessory sinuses', 'Cardia NOS', 'Islets of Langerhans', 'Carotid body', 'Ventral surface of tongue NOS', 'Autonomic nervous system NOS', 'Overlapping lesion of corpus uteri', 'Spinal meninges', 'Posterior wall of nasopharynx', 'Placenta', 'Intrahepatic bile duct', 'Overlapping lesion of digestive system', 'Mediastinum NOS', 'Hematopoietic system NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Major salivary gland NOS', 'Cerebellum NOS', 'Overlapping lesion of stomach', 'Vulva NOS', 'Craniopharyngeal duct', 'Lung NOS', 'Greater curvature of stomach NOS', 'Upper-outer quadrant of breast', 'Gallbladder', 'Thoracic esophagus', 'Lymph nodes of axilla or arm', 'Ventricle NOS', 'Overlapping lesion of biliary tract', 'Hypopharynx NOS', 'Clitoris', 'Exocervix', 'Parietal lobe', 'Waldeyer ring', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Head face or neck NOS', 'Anterior wall of nasopharynx', 'Urethra', 'Overlapping lesion of nasopharynx', 'Maxillary sinus', 'Lymph nodes of inguinal region or leg', 'Ureter', 'Tonsillar pillar', 'Sublingual gland', 'Pituitary gland', 'Gastrointestinal tract NOS', 'Pineal gland', 'Meninges NOS', 'Lingual tonsil', 'Trachea', 'Pyriform sinus', 'Mucosa of lower lip', 'Not Reported', 'Posterior wall of hypopharynx', 'Urinary system NOS', 'Orbit NOS', 'Short bones of lower limb and associated joints', 'Connective subcutaneous and other soft tissues of thorax', 'Upper limb NOS', 'Gastric antrum', 'Lymph node NOS', 'Peripheral nerves and autonomic nervous system of thorax', 'Ill-defined sites within respiratory system', 'Other specified parts of male genital organs', 'Rib sternum clavicle and associated joints', 'Overlapping lesion of bladder', 'Appendix', 'Prostate gland', 'Lymph nodes of multiple regions', 'Lateral wall of nasopharynx', 'Branchial cleft', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Floor of mouth NOS', 'Connective subcutaneous and other soft tissues NOS', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Bladder neck', 'Border of tongue', 'Connective subcutaneous and other soft tissues of abdomen', 'Overlapping lesion of small intestine', 'Lateral wall of bladder', 'Soft palate NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Isthmus uteri', 'Nasal cavity', 'Endocervix', 'Tonsil NOS', 'Glottis', 'Retroperitoneum', 'Peripheral nerves and autonomic nervous system of pelvis', 'Frontal lobe', 'Vagina NOS', 'Undescended testis', 'Laryngeal cartilage', 'Eyelid', 'Hypopharyngeal aspect of aryepiglottic fold', 'Overlapping lesion of other and unspecified parts of mouth', 'Upper lobe lung', 'Lip NOS', 'Lymph nodes of head face and neck', 'Overlapping lesion of brain and central nervous system', 'Overlapping lesion of penis', 'Overlapping lesion of retroperitoneum and peritoneum', 'Parotid gland', 'Dome of bladder', 'Bone of limb NOS', 'Descended testis', 'Vertebral column', 'Fundus uteri', 'Connective subcutaneous and other soft tissues of pelvis', 'Epididymis', 'Intra-abdominal lymph nodes', 'Paraspinal', 'Prepuce', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Pharynx NOS', 'Overlapping lesion of endocrine glands and related structures', 'Gum NOS', 'Spinal cord', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Skin of upper limb and shoulder', 'Nasopharynx NOS', 'Parathyroid gland', 'Bone NOS', 'Mouth NOS', 'Abdomen NOS', 'Conjunctiva', 'Spermatic cord', 'External upper lip', 'Labium minus', 'Renal pelvis', 'Overlapping lesion of lip', 'Short bones of upper limb and associated joints', 'Main bronchus', 'Upper respiratory tract NOS', 'Body of penis', 'Small intestine NOS', 'Central portion of breast', 'Lower-inner quadrant of breast', 'Labium majus', 'Tonsillar fossa', 'Cecum', 'Glans penis', 'Tail of pancreas', 'Lower third of esophagus', 'Body of pancreas', 'Intestinal tract NOS', 'Brain stem', 'Overlapping lesion of rectum anus and anal canal', 'Posterior wall of oropharynx', 'Pancreatic duct', 'Blood', 'Temporal lobe', 'Anterior floor of mouth', 'Nervous system NOS', 'Cornea NOS', 'Palate NOS', 'Occipital lobe', 'Abdominal esophagus', 'Overlapping lesion of pancreas', 'Overlapping lesion of female genital organs', 'Cheek mucosa', 'Retina', 'Overlapping lesion of male genital organs', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Larynx NOS', 'Skin of other and unspecified parts of face', 'Spleen', 'Oropharynx NOS', 'Anal canal', 'Subglottis', 'Cerebral meninges', 'Lateral wall of oropharynx', 'Middle third of esophagus', 'Nipple', 'Medulla of adrenal gland', 'Overlapping lesion of eye and adnexa', 'Olfactory nerve', 'Ethmoid sinus', 'Overlapping lesion of cervix uteri', 'Descending colon', 'Brain NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Anterior wall of bladder', 'Mandible', 'Other specified parts of pancreas', 'Skin of trunk', 'Other specified parts of female genital organs', 'Uterus NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Intrathoracic lymph nodes', 'Heart', 'Adrenal gland NOS', 'Aortic body and other paraganglia', 'Extrahepatic bile duct', 'Overlapping lesion of breast', 'Superior wall of nasopharynx', 'Fundus of stomach', 'Anterior mediastinum', 'Tongue NOS', 'Cranial nerve NOS', 'Head of pancreas', 'Overlapping lesions of oropharynx', 'Overlapping lesion of bones joints and articular cartilage', 'Retromolar area', 'Testis NOS', 'Connective subcutaneous and other soft tissues of head face and neck', 'Bladder NOS', 'Overlapping lesion of urinary organs', 'Lower-outer quadrant of breast', 'Thyroid gland', 'Anterior surface of epiglottis', 'Uterine adnexa']",,SRRSClinicalDataTier2 +Stop Days from Index,Stop Days from Index,StopDaysfromIndex,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'",False,,,,SRRSClinicalDataTier2 +Treatment Type,Treatment Type,TreatmentType,Text term that describes the kind of treatment administered.,False,,,,SRRSClinicalDataTier2 +Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,SRRSClinicalDataTier2 +Country of Birth,Country of Birth,CountryofBirth,Country where the patient was born.,False,,"['Belize', 'Monaco', 'Bahrain', 'Iraq', 'South Africa', 'Vietnam', 'Niue', 'Poland', 'Albania', 'Burundi', 'Spain', 'Bhutan', 'Saudi Arabia', 'Madagascar', 'Gambia', 'Switzerland', 'Laos', 'Saint Lucia', 'Myanmar', 'Mayotte', 'Guadeloupe', 'South Korea', 'Tokelau', 'Syria', 'Pakistan', 'Isle of Man', 'Yemen', 'Svalbard & Jan Mayen Islands', 'Jersey', 'Bosnia and Herzegovina', 'Eritrea', 'Guinea', 'Philippines', 'Guinea-Bissau', 'Azerbaijan', 'Somalia', 'Sudan', 'Cambodia', 'Cuba', 'Rwanda', 'Tonga', 'Saint Kitts and Nevis', 'Finland', 'Paraguay', 'Malawi', 'Falkland Islands (Malvinas)', 'Federated States of Micronesia', 'Niger', 'Colombia', 'Democratic Republic of the Congo', 'North Macedonia', 'Haiti', 'Timor-Leste', 'Austria', 'Chad', 'Iceland', 'Dominica', 'Malta', 'Denmark', 'Kosovo', 'Martinique', 'Bangladesh', 'San Marino', 'South Sudan', 'Georgia', 'Nigeria', 'Gibraltar', 'Nauru', 'Tajikistan', 'Montserrat', 'Sweden', 'Antigua and Barbuda', 'Indonesia', 'Sri Lanka', 'Greece', 'Gabon', 'Japan', 'Mauritania', 'Nicaragua', 'China', 'Cape Verde', 'Unknown', 'Grenada', 'French Polynesia', 'Moldova', 'Cayman Islands', 'Dominican Republic', 'Liechtenstein', 'Senegal', 'Holy See', 'Mali', 'Vanuatu', 'India', 'Bermuda', 'Netherlands', 'Ireland', 'Zambia', 'North Korea', 'Macau', 'Romania', 'Solomon Islands', 'Suriname', 'Nepal', 'Croatia', 'Reunion', 'Ghana', 'Saint Helena Ascension and Tristan da Cunha', 'Israel', 'Faroe Islands', 'Greenland', 'State of Palestine', 'Wallis and Futuna', 'Ecuador', 'French Guiana', 'Angola', 'Aruba', 'Guyana', 'Kuwait', 'Taiwan', 'Singapore', 'Togo', 'Andorra', 'Lebanon', 'Northern Mariana Islands', 'Armenia', 'Iran', 'New Zealand', 'Bolivia', 'Cameroon', 'Norway', 'Panama', 'Papua New Guinea', 'Qatar', 'Tanzania', 'Portugal', 'Slovakia', 'Equatorial Guinea', 'Estonia', 'Mongolia', 'Chile', 'Burkina Faso', 'Ethiopia', 'Hungary', 'Djibouti', 'Kenya', 'Kiribati', 'Botswana', 'Australia', 'Guam', 'Congo', 'Belarus', 'Uruguay', 'Czech Republic (Czechia)', 'Lesotho', 'United Kingdom', 'Lithuania', 'Russia', 'Thailand', 'Oman', 'Benin', 'Tunisia', 'Uganda', 'Namibia', 'Honduras', 'Algeria', 'Turkey', 'Morocco', 'Barbados', 'Sierra Leone', 'Venezuela', 'Saint Pierre and Miquelon', 'Kyrgyzstan', 'Trinidad and Tobago', 'Serbia', 'Peru', 'Comoros', 'Canada', 'Hong Kong', 'Liberia', 'Malaysia', 'Puerto Rico', 'Brazil', 'Virgin Islands British', 'Zimbabwe', 'Latvia', 'Eswatini', ""Cote d'Ivoire"", 'United Arab Emirates', 'Bahamas', 'Curacao', 'Slovenia', 'Central African Republic', 'Guatemala', 'Jordan', 'Egypt', 'Germany', 'Mozambique', 'Fiji', 'Turkmenistan', 'Mexico', 'Brunei', 'France', 'Kazakhstan', 'Argentina', 'Uzbekistan', 'Samoa', 'Bulgaria', 'Virgin Islands U.S.', 'Maldives', 'Cyprus', 'Costa Rica', 'Italy', 'Libya', 'Jamaica', 'Tuvalu', 'United States', 'Saint Vincent and the Grenadines', 'Palau', 'Western Sahara', 'Guernsey', 'Mauritius', 'El Salvador', 'Afghanistan', 'Belgium', 'Luxembourg', 'Ukraine', 'Marshall Islands', 'Montenegro', 'Cook Islands', 'Seychelles', 'Sao Tome and Principe', 'New Caledonia', 'Anguilla', '']",,SRRSClinicalDataTier2 +Gender,Gender,Gender,"Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.]",True,,"['Not Reported', 'unspecified', 'Unknown', 'female', 'male']",,SRRSClinicalDataTier2 +Progression or Recurrence,Progression or Recurrence,ProgressionorRecurrence,Yes/No/unknown indicator to identify whether a patient has had a new tumor event after initial treatment.,True,,"['No', 'Yes - Progression or Recurrence', 'Unknown', 'Not Reported']",,SRRSClinicalDataTier2 +Tumor Largest Dimension Diameter,Tumor Largest Dimension Diameter,TumorLargestDimensionDiameter,"Numeric value used to describe the maximum diameter or dimension of the primary tumor, measured in centimeters.",False,,,,SRRSClinicalDataTier2 +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,SRRSClinicalDataTier2 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,SRRSClinicalDataTier2 +Last Known Disease Status,Last Known Disease Status,LastKnownDiseaseStatus,Text term that describes the last known state or condition of an individual's neoplasm.,True,,"['With tumor', 'Not Reported', 'Not Applicable', 'unknown tumor status', 'Distant met recurrence/progression', 'Loco-regional recurrence/progression', 'Tumor free', 'Biochemical evidence of disease without structural correlate', 'Not Allowed To Collect']",,SRRSClinicalDataTier2 +Ethnicity,Ethnicity,Ethnicity,"An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.",True,,"['Not Reported', 'Unknown', 'hispanic or latino', 'not hispanic or latino', 'not allowed to collect']",,SRRSClinicalDataTier2 +Cancer Incidence,Cancer Incidence,CancerIncidence,"Incidence of specific cancer type in a defined area (a number between 0 and 100). The rate of incident cases per population of 100,000 persons of a specific type of cancer as designated in the ""primary_diagnosis"" data element in the county where the patient resides, using the most recent 2013-2017 NCI Cancer Atlas derived data. Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the asociated county on the right side of the result field. On the https://gis.cancer.gov/canceratlas/tableview/ website, choose ""Incidence"" from the Topic dropdown menu, state of interest from the Area menu, ""All Races"" from the Race menu, and the cancer type (""Both Sexes"" when possible) from the Statistic menu. Find the county of interest and enter the numeric Age-Adjusted Rate per 100,000 as the value.",False,,,,SRRSClinicalDataTier2 +Medically Underserved Area,Medically Underserved Area,MedicallyUnderservedArea,"Areas or populations designated by HRSA as having too few primary care providers, high infant mortality, high poverty or a high elderly population: Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/ - enter the zip code in the main text field and use the associated county on the right side of the result field. Go to data.hrsa.gov website and select ""Query Data"". Pick the Medically Underserved Areas/Populations (MUA/P) data source in the step 1 menu and select ""View Data"". Enter the name of the county (_______ county) in the first ""Service Area"" column, adding the state in the 5th column may help direct you to the data. If the designation type in the third column is ""medically underserved area"" enter ""Yes"" as the value. If the county generates a ""No data available in table"" enter ""No"" as the value. A value of ""Unknown"" indicates that sufficient data was not available to look up the value. If value is yes, complete the Medically_underserved_score data element.",False,,"['Medically Underserved Area - Yes', 'Medically Underserved Area - Unknown', 'Medically Underserved Area - No', '']",,SRRSClinicalDataTier2 +Year of Death,Year of Death,YearofDeath,Numeric value to represent the year of the death of an individual.,False,True,," If Vital Status is ""Dead"" then ""Year of Death"" is required",SRRSClinicalDataTier2 +Cause of Death Source,Cause of Death Source,CauseofDeathSource,The text term used to describe the source used to determine the patient's cause of death.,False,True,"['Medical Record', 'Not Reported', 'Unknown', 'Death Certificate', 'Autopsy', 'Social Security Death Index', '']"," If Vital Status is ""Dead"" then ""Cause of Death Source"" is required",SRRSClinicalDataTier2 +Cause of Death,Cause of Death,CauseofDeath,The cause of death,False,True,"['Cancer Related', 'Not Reported', 'Renal Disorder NOS', 'Not Applicable', 'Spinal Muscular Atrophy', 'End-stage Renal Disease', 'Not Cancer Related', 'Unknown', 'Infection', 'Surgical Complications', 'Cardiovascular Disorder NOS', 'Toxicity', '']"," If Vital Status is ""Dead"" then ""Cause of Death"" is required",SRRSClinicalDataTier2 +Days to Death,Days to Death,DaystoDeath,Number of days between the date used for index and the date from a person's date of death represented as a calculated number of days.,False,True,," If Vital Status is ""Dead"" then ""Days to Death"" is required",SRRSClinicalDataTier2 +Days to Progression,Days to Progression,DaystoProgression,Number of days between the date used for index and the date the patient's disease progressed.,False,True,," If Progression or Recurrence is ""Yes - Progression or Recurrence"" then ""Days to Progression"" is required",SRRSClinicalDataTier2 +Progression or Recurrence Type,Progression or Recurrence Type,ProgressionorRecurrenceType,The text term used to describe the type of progressive or recurrent disease or relapsed disease.,False,True,"['Distant', 'Not Reported', 'Unknown', 'Biochemical', 'Regional', 'Local', '']"," If Progression or Recurrence is ""Yes - Progression or Recurrence"" then ""Progression or Recurrence Type"" is required",SRRSClinicalDataTier2 +Progression or Recurrence Anatomic Site,Progression or Recurrence Anatomic Site,ProgressionorRecurrenceAnatomicSite,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,False,True,"['Paraurethral gland', 'Colon NOS', 'Frontal sinus', 'Overlapping lesion of tongue', 'Overlapping lesion of palate', 'Scrotum NOS', 'Bone marrow', 'Axillary tail of breast', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'unknown primary site', 'Broad ligament', 'Lateral floor of mouth', 'Overlapping lesion of vulva', 'Trigone of bladder', 'Lacrimal gland', 'Thorax NOS', 'Ampulla of Vater', 'Myometrium', 'Penis NOS', 'Female genital tract NOS', 'Submandibular gland', 'Anterior 2/3 of tongue NOS', 'Posterior wall of bladder', 'Thymus', 'Endocrine gland NOS', 'Stomach NOS', 'Unknown', 'Cerebrum', 'Splenic flexure of colon', 'Urachus', 'Skin of lip NOS', 'Mucosa of lip NOS', 'Accessory sinus NOS', 'Cortex of adrenal gland', 'Other ill-defined sites', 'Middle lobe lung', 'Pelvis NOS', 'Anus NOS', 'Upper-inner quadrant of breast', 'Posterior mediastinum', 'Esophagus NOS', 'Duodenum', 'Cervical esophagus', 'Optic nerve', 'Long bones of lower limb and associated joints', 'Middle ear', 'Breast NOS', 'Dorsal surface of tongue NOS', 'Lesser curvature of stomach NOS', 'Overlapping lesion of floor of mouth', 'Overlapping lesion of heart mediastinum and pleura', 'Eye NOS', 'Overlapping lesion of esophagus', 'Ciliary body', 'Ureteric orifice', 'Postcricoid region', 'External ear', 'Base of tongue NOS', 'Liver', 'Commissure of lip', 'Cloacogenic zone', 'Lower lobe lung', 'Transverse colon', 'Acoustic nerve', 'Supraglottis', 'Fallopian tube', 'Upper third of esophagus', 'Skin of scalp and neck', 'Choroid', 'Long bones of upper limb scapula and associated joints', 'Overlapping lesion of brain', 'Upper gum', 'Skin NOS', 'Hard palate', 'Ileum', 'Overlapping lesion of colon', 'Ascending colon', 'Lower gum', 'Pelvic bones sacrum coccyx and associated joints', 'Hepatic flexure of colon', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Vestibule of mouth', 'Cervix uteri', 'Bones of skull and face and associated joints', 'Overlapping lesion of lip oral cavity and pharynx', 'Endometrium', 'Sphenoid sinus', 'Overlapping lesion of ill-defined sites', 'Sigmoid colon', 'Peritoneum NOS', 'Specified parts of peritoneum', 'Meckel diverticulum', 'Rectosigmoid junction', 'Kidney NOS', 'Reticuloendothelial system NOS', 'Rectum NOS', 'Pylorus', 'Overlapping lesion of tonsil', 'Pleura NOS', 'Jejunum', 'Vallecula', 'Skin of lower limb and hip', 'Pelvic lymph nodes', 'External lower lip', 'Overlapping lesion of skin', 'Mucosa of upper lip', 'Ovary', 'Cauda equina', 'Lower limb NOS', 'Body of stomach', 'Overlapping lesion of larynx', 'Pancreas NOS', 'Overlapping lesion of lung', 'Overlapping lesion of major salivary glands', 'Uvula', 'Overlapping lesion of hypopharynx', 'Round ligament', 'Corpus uteri', 'Biliary tract NOS', 'Male genital organs NOS', 'Parametrium', 'External lip NOS', 'Overlapping lesion of accessory sinuses', 'Cardia NOS', 'Islets of Langerhans', 'Carotid body', 'Ventral surface of tongue NOS', 'Autonomic nervous system NOS', 'Overlapping lesion of corpus uteri', 'Spinal meninges', 'Posterior wall of nasopharynx', 'Placenta', 'Intrahepatic bile duct', 'Overlapping lesion of digestive system', 'Mediastinum NOS', 'Hematopoietic system NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Major salivary gland NOS', 'Cerebellum NOS', 'Overlapping lesion of stomach', 'Vulva NOS', 'Craniopharyngeal duct', 'Lung NOS', 'Greater curvature of stomach NOS', 'Upper-outer quadrant of breast', 'Gallbladder', 'Thoracic esophagus', 'Lymph nodes of axilla or arm', 'Ventricle NOS', 'Overlapping lesion of biliary tract', 'Hypopharynx NOS', 'Clitoris', 'Exocervix', 'Parietal lobe', 'Waldeyer ring', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Head face or neck NOS', 'Anterior wall of nasopharynx', 'Urethra', 'Overlapping lesion of nasopharynx', 'Maxillary sinus', 'Lymph nodes of inguinal region or leg', 'Ureter', 'Tonsillar pillar', 'Sublingual gland', 'Pituitary gland', 'Gastrointestinal tract NOS', 'Pineal gland', 'Meninges NOS', 'Lingual tonsil', 'Trachea', 'Pyriform sinus', 'Mucosa of lower lip', 'Not Reported', 'Posterior wall of hypopharynx', 'Urinary system NOS', 'Orbit NOS', 'Short bones of lower limb and associated joints', 'Connective subcutaneous and other soft tissues of thorax', 'Upper limb NOS', 'Gastric antrum', 'Lymph node NOS', 'Peripheral nerves and autonomic nervous system of thorax', 'Ill-defined sites within respiratory system', 'Other specified parts of male genital organs', 'Rib sternum clavicle and associated joints', 'Overlapping lesion of bladder', 'Appendix', 'Prostate gland', 'Lymph nodes of multiple regions', 'Lateral wall of nasopharynx', 'Branchial cleft', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Floor of mouth NOS', 'Connective subcutaneous and other soft tissues NOS', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Bladder neck', 'Border of tongue', 'Connective subcutaneous and other soft tissues of abdomen', 'Overlapping lesion of small intestine', 'Lateral wall of bladder', 'Soft palate NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Isthmus uteri', 'Nasal cavity', 'Endocervix', 'Tonsil NOS', 'Glottis', 'Retroperitoneum', 'Peripheral nerves and autonomic nervous system of pelvis', 'Frontal lobe', 'Vagina NOS', 'Undescended testis', 'Laryngeal cartilage', 'Eyelid', 'Hypopharyngeal aspect of aryepiglottic fold', 'Overlapping lesion of other and unspecified parts of mouth', 'Upper lobe lung', 'Lip NOS', 'Lymph nodes of head face and neck', 'Overlapping lesion of brain and central nervous system', 'Overlapping lesion of penis', 'Overlapping lesion of retroperitoneum and peritoneum', 'Parotid gland', 'Dome of bladder', 'Bone of limb NOS', 'Descended testis', 'Vertebral column', 'Fundus uteri', 'Connective subcutaneous and other soft tissues of pelvis', 'Epididymis', 'Intra-abdominal lymph nodes', 'Prepuce', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Pharynx NOS', 'Overlapping lesion of endocrine glands and related structures', 'Gum NOS', 'Spinal cord', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Skin of upper limb and shoulder', 'Nasopharynx NOS', 'Parathyroid gland', 'Bone NOS', 'Mouth NOS', 'Abdomen NOS', 'Conjunctiva', 'Spermatic cord', 'External upper lip', 'Labium minus', 'Renal pelvis', 'Overlapping lesion of lip', 'Short bones of upper limb and associated joints', 'Main bronchus', 'Upper respiratory tract NOS', 'Body of penis', 'Small intestine NOS', 'Central portion of breast', 'Lower-inner quadrant of breast', 'Labium majus', 'Tonsillar fossa', 'Cecum', 'Glans penis', 'Tail of pancreas', 'Lower third of esophagus', 'Body of pancreas', 'Intestinal tract NOS', 'Brain stem', 'Overlapping lesion of rectum anus and anal canal', 'Posterior wall of oropharynx', 'Pancreatic duct', 'Blood', 'Temporal lobe', 'Anterior floor of mouth', 'Nervous system NOS', 'Cornea NOS', 'Palate NOS', 'Occipital lobe', 'Abdominal esophagus', 'Overlapping lesion of pancreas', 'Overlapping lesion of female genital organs', 'Cheek mucosa', 'Retina', 'Overlapping lesion of male genital organs', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Larynx NOS', 'Skin of other and unspecified parts of face', 'Spleen', 'Oropharynx NOS', 'Anal canal', 'Subglottis', 'Cerebral meninges', 'Lateral wall of oropharynx', 'Middle third of esophagus', 'Nipple', 'Medulla of adrenal gland', 'Overlapping lesion of eye and adnexa', 'Olfactory nerve', 'Ethmoid sinus', 'Overlapping lesion of cervix uteri', 'Descending colon', 'Brain NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Anterior wall of bladder', 'Mandible', 'Other specified parts of pancreas', 'Skin of trunk', 'Other specified parts of female genital organs', 'Uterus NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Intrathoracic lymph nodes', 'Heart', 'Adrenal gland NOS', 'Aortic body and other paraganglia', 'Extrahepatic bile duct', 'Overlapping lesion of breast', 'Superior wall of nasopharynx', 'Fundus of stomach', 'Anterior mediastinum', 'Tongue NOS', 'Cranial nerve NOS', 'Head of pancreas', 'Overlapping lesions of oropharynx', 'Overlapping lesion of bones joints and articular cartilage', 'Retromolar area', 'Testis NOS', 'Connective subcutaneous and other soft tissues of head face and neck', 'Bladder NOS', 'Overlapping lesion of urinary organs', 'Lower-outer quadrant of breast', 'Thyroid gland', 'Anterior surface of epiglottis', 'Uterine adnexa', '']"," If Progression or Recurrence is ""Yes - Progression or Recurrence"" then ""Progression or Recurrence Anatomic Site"" is required",SRRSClinicalDataTier2 +Days to Progression Free,Days to Progression Free,DaystoProgressionFree,Number of days between the date used for index and the date the patient's disease was formally confirmed as progression-free.,False,True,," If Progression or Recurrence is ""Yes - Progression or Recurrence"" then ""Days to Progression Free"" is required",SRRSClinicalDataTier2 +Medically Underserved Score,Medically Underserved Score,MedicallyUnderservedScore,"Index of Medical Underservice (IMU) score, a number between 0 and 100, where 0 represents completely underserved and 100 represents best served or least underserved. Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the asociated county on the right side of the result field. Go to data.hrsa.gov website and select Query Data. Pick the Medically Underserved Areas/Populations (MUA/P) data source in the step 1 menu and select View Data. Enter the name of the county (______ county) in the first ""Service Area"" column, adding the state in the 5th column may help direct you to the data. Enter the Index of Medical Underservice Score in the fourth column to one decimal place as the value.",False,True,," If Medically Underserved Area is ""Medically Underserved Area - Yes"" then ""Medically Underserved Score"" is required",SRRSClinicalDataTier2 +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,LungCancerTier3 +Lung Tumor Location Anatomic Site,Lung Tumor Location Anatomic Site,LungTumorLocationAnatomicSite,Anatomic location of the tumor inside the lung,False,,"['Not Reported', 'Main carina', 'Unknown', 'Left', 'Right', '']",,LungCancerTier3 +Lung Cancer Harboring Genomic Aberrations,Lung Cancer Harboring Genomic Aberrations,LungCancerHarboringGenomicAberrations,Genomic aberrations in participants with lung cancer (specific lung cancer associated gene mutations not covered in Tiers 1 and 2),False,,"['D963 splice MET mutation', 'A146T KRAS mutation', 'G12A KRAS mutation', 'G12D KRAS mutation', 'EML4-ALK translocation-variant 5', 'L858R EGFR mutation', 'G13C KRAS mutation', 'Intron 13 mutation', 'G13V KRAS mutation', 'EML4-ALK translocation-variant 2', 'Exon 20 insertion', 'EML4-ALK translocation-variant 1', 'D1010 splice MET mutation', 'Unknown', 'G12C KRAS mutation', 'G12V KRAS mutation', 'Q61H KRAS mutation', 'G719X EGFR mutation', 'C797S EGFR mutation', 'G13R KRAS mutation', 'G13D KRAS mutation', 'G13A KRAS mutation', 'G12S KRAS mutation', 'Exon 14 deletion', 'Not Reported', 'T790M EGFR mutation', 'L861Q EGFR mutation', 'V600K BRAF mutation', 'Q61L KRAS mutation', 'V600E BRAF mutation', 'Exon 19 deletion', 'K601E BRAF mutation', 'EML4-ALK translocation-variant 3', 'Intron 14 mutation', 'V600R BRAF mutation', 'G12R KRAS mutation', 'Other', 'Exon 14 mutation', 'EML4-ALK translocation-variant 4', 'D1010N MET mutation', 'V600D BRAF mutation', '']",,LungCancerTier3 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,LungCancerTier3 +Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,LungCancerTier3 +Stop Days from Index,Stop Days from Index,StopDaysfromIndex,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'",False,,,,LungCancerTier3 +Lung Adjacent Histology Type,Lung Adjacent Histology Type,LungAdjacentHistologyType,The type of morphologic characteristics observed by microscope in the tissue next to a benign or malignant tissue growth,False,,"['Sarcomatoid carcinoma', 'Squamous cell lung carcinoma', 'Thoracic NUT carcinoma', 'Large cell lung carcinoma', 'Not Reported', 'Carcinoid tumor and lung atypical carcinoid tumor', 'Bronchioalveolar carcinoma', 'Other', 'Lung adenocarcinoma', 'Small cell lung carcinoma', 'Unknown', 'Adenosquamous carcinoma', 'Lung squamous cell carcinoma in situ', 'Large cell neuroendocrine carcinoma', 'Lung lymphoepithelioma-like carcinoma', 'Lung adenocarcinoma in situ', '']",,LungCancerTier3 +Lung Tumor Lobe Bronchial Location,Lung Tumor Lobe Bronchial Location,LungTumorLobeBronchialLocation,Anatomic lobe and bronchial location of the tumor inside the lung,False,,"['Not Reported', 'Stump', 'Lower lobe', 'Bronchus', 'Upper lobe', 'Unknown', 'Middle lobe', '']",,LungCancerTier3 +Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,LungCancerTier3 +Current Lung Cancer Symptoms,Current Lung Cancer Symptoms,CurrentLungCancerSymptoms,Reported lung cancer related symptoms person is currently experiencing,False,,"['no evidence of lung cancer recurrence', 'asbestosis', 'Dysphagia', 'dullness to percussion', 'non-productive cough', 'unlabored/normal breathing', 'abnormal breath sounds', 'unexplained weight loss', 'fair/poor aeration', 'Pneumonia', 'breath sounds coarse/diminished', 'prolonged expiration-long/forced expiratory phase', 'clear lungs to auscultation or percussion', 'Wheezing', 'unexplained loss of energy/fatigue', 'Unknown', 'crackles', 'air entry decreased/fair/poor/diminished', 'chest pain or discomfort', 'finger clubbing', 'Not Reported', 'patient is NED', 'hoarseness/laryngitis/vocal cord inflammation', 'shallow inspiration', 'cold symptoms/flu/sinus/nasal congestion', 'rhonci', 'Dyspnea', 'sinus pain/infection', 'Other', 'oxygen supplemental-portable O2 at night or continuous', 'productive cough', 'hemoptysis', '']",,LungCancerTier3 +Lung Topography,Lung Topography,LungTopography,Lung PCA specific topography (not covered in previous tiers),False,,"['LL NOS (Left lung not otherwise specified)', 'LB10A/B Carina between the apical and lateral subsegments of the posterior segment of the LLL', 'RB5A/B - Carina between the medial and lateral subsegments of the medial segment of the right middle lobe', 'RB10B/C - Carina between medial and lateral subsegments posterior segment RLL', 'RB7 Medial basal segment right lower lobe (Carina at RB7 orifice takeoff from RLL orifice)', 'LB4/5 Carina between superior and inferior segment lingula (Carina between LB4 orifice and LB5 orifice)', 'RB6 - Carina of superior segment RLL (Carina between RB6 orifice and lower portion of RLL orifice)', 'LB5A/B Carina between the medial and lateral subsegments inferior segment lingula', 'LB9 orifice Lateral segment left lower lobe(airway wall between LB9 and LB9A/B carinae)', 'LB1/2 Carina between apical and posterior segment left upper lobe (Carina between LB1 orifice and LB2 orifice)', 'RB6A/B - Carina between apical and lateral subsegments superior segment RLL', 'LB2A/C Carina between the apical and medial subsegments of the posterior segment of the left upper lobe', 'RB7 orifice Airway wall between RB7 and RB7A/B carinae', 'LB10A/C Carina between the apical and medial segments of the posterior segment of the LLL', 'RML orifice Airway wall between RML and RB4/5', 'Not Reported', 'LUL orifice Airway wall between LUL and LUDB', 'RB7A/B - Carina between medial and lateral subsegments medial basal segment RLL', 'TR -Trachea (airway wall between tracheo-esophageal bifurcation and main carina)', 'RB4 orifice Lateral segment right middle lobe (airway wall between RB4 and RB4A/B carinae)', 'RB10A/C - Carina between medial and apical subsegments posterior segment RLL', 'Other', 'LUL Carina between the LUL orifice and LLL orifice (airways)', 'RB5 orifice Medial segment right middle lobe (airway wall between RB5 and RB5A/B carinae)', 'RB4/5 - Carina between the lateral and medial segments right middle lobe (Carina between RB4 orifice and RB5 orifice)', 'LB10 orifice Posterior segment left lower lobe(airway wall between LB10 and LB10A/B carinae)', 'LB3A/B Carina between the apical and lateral subsegments of the anterior segment of the left upper lobe', 'RB10A/B - Carina between medial and lateral subsegments posterior segment RLL', 'LB8A/B Carina between the medial and lateral subsegments of the anterior segment LLL', 'RLL orifice Airway wall between RML and RB6-10 carinae', 'RB10 Posterior segment right lower lobe (Carina at RB10 orifice takeoff from RLL orifice)', 'LB6 The superior segment of the left lower lobe (Carina between LB6 orifice and lower portion of LLL orifice)', 'MC-Carina between right and left lungs (main carina)', 'Unknown', 'RB6 orifice Airway wall between RB6 and RB6A/B/C carinae', 'LB6 orifice Airway wall between LB6 and LB6A/B carinae', 'LB9A/B Carina between the medial and lateral subsegments of the lateral segment LLL', 'LB6B/C Carina between the medial and lateral subsegments of the superior segment LLL', 'RB1/3 - Carina between apical and anterior segments RUL (Carina between RB1 orifice and RB3 orifice)', 'RB4A/B - Carina between the medial and lateral subsegments of the lateral segment of the right middle lobe', 'LB4 orifice Superior segment lingula(airway wall between LB4 and LB4A/B carinae)', 'RB1A/B - Carina between medial and lateral subsegments apical segment RUL', 'RB8A/B - Carina between medial and lateral subsegments anterior segment RLL', 'LLL orifice Airway wall between LUL carina and LB6-10 carinae', 'RB1/2 - Carina between apical and posterior segments right upper lobe (Carina between RB1 orifice and RB2 orifice)', 'RB3A/B - Carina between the medial and lateral subsegments of the anterior segment RUL', 'RB10 orifice Airway wall between RB10 and RB10A/B carinae', 'LUDB-Carina between the lingula and upper division left upper lobe', 'RB1 orifice Apical segment - right upper lobe(airway wall between RB1 and RB1A/B carinae)', 'LB5 orifice Inferior segment lingula(airway wall between LB5 and LB5A/B carinae)', 'LB6A/B Carina between the superior and lateral subsegments superior segment LLL', 'RB2 orifice Posterior segment - right upper lobe(airway wall between RB2 and RB2A/B carinae)', 'RUL Carinae between RUL orifice and bronchus intermedius', 'LB2A/B Carina between the apical and lateral subsegments of the posterior segment of the left upper lobe', 'RB9A/B - Carina between medial and lateral subsegments lateral segment RLL', 'RB8/9 - Carina between anterior and lateral segments RLL (Carina between RB8 orifice and RB9 orifice)', 'RB9 orifice Lateral segment right lower lobe(airway wall between RB9 and RB9A/B carinae)', 'Bronchus Intermedius Bronchus (airway wall) between right upper and right middle lobes', 'RB3 orifice Anterior segment - right upper lobe(airway wall between RB3 and RB3A/B carinae)', 'LB1A/B Carina between the lateral and medial subsegments of the apical segment of the LUL', 'LB4A/B Carina between medial and lateral subsegments superior segment lingula', 'Carina NOS (Carina not otherwise specified)', 'LB8 orifice Anterior segment left lower lobe(airway wall between LB8 and LB8A/B carinae)', 'LUDB-orifice airway wall between LUDB and LB3(LB1+2 carinae)', 'Carina between LUDB orifice and lingula orifice', 'LB1+2/3 Carina between the apico-posterior and anterior segments of the left upper lobe (Carina between LB1+2 orifice and LB3 orifice)', 'LMB-Left mainstem bronchus(airway wall between MC & LUL carina)', 'RB9/10 - Carina between lateral and posterior segments RLL', 'RB6A/C - Carina between apical and medial subsegments superior segment RLL', 'RB2/3 - Carina between anterior and posterior segments RUL (Carina between RB2 orifice and RB3 orifice)', 'LB1A/C Carina between the apical and lateral subsegments of the apical segment left upper lobe', 'LB1B/C Carina between the medial and lateral subsegments of the apical segment of the left upper lobe', 'RMB-Right mainstem bronchus(airway wall between MC & RUL carina)', 'RB2A/B - Carina between the medial and lateral subsegments of the posterior segment (RUL)', 'LB8/9 Carina between the anterior and lateral segments LLL (Carina between LB8 orifice and LB9 orifice)', 'LB6A/C Carina between the superior and medial subsegments of superior segment LLL', 'LB10B/C Carina between the medial and lateral subsegments of the posterior segment of the LLL', 'RUL orifice Airway wall between RUL and RB1/RB2/RB3', 'LB9/10 Carina between the lateral and posterior segments LLL (Carina between LB9 orifice and LB10 orifice)', 'LB2B/C Carina between the medial and lateral subsegments of the posterior segment left upper lobe', 'LB3 orifice Anterior segment left upper lobe(airway wall between LB3 and LB3A/B carinae)', 'LB1+2 orifice The apico-posterior segment of the left upper lobe (airway wall between LB1+2/3 carina and LB1 or LB2)', 'RB8 orifice Anterior segment right lower lobe(airway wall between RB8 and RB8A/B carinae)', 'Lingula orifice airway wall between LUDB and LB4/5 carinae', 'RML - Carina between RML orifice and RLL orifice', 'RB6B/C - Carina between medial and lateral subsegments superior segment RLL', 'RL NOS (Right lung not otherwise specified)', '']",,LungCancerTier3 +Lung Cancer Detection Method Type,Lung Cancer Detection Method Type,LungCancerDetectionMethodType,"The means, manner of procedure, or systematic course of actions performed in order to discover or identify lung cancer",False,,"['Data not available', 'Chest CT', 'Low Dose Computed Tomography (LDCT)', 'Other', 'Unknown', 'Chest X-ray', '']",,LungCancerTier3 +Lung Cancer Participant Procedure History,Lung Cancer Participant Procedure History,LungCancerParticipantProcedureHistory,Text name of a surgical or operative procedure used in a natural history protocol of a lung cancer participant.,False,,"['Lung Wedge Resection Bilateral', 'Lobectomy Right', 'Lung Wedge Resection Left', 'Pneumonectomy Left', 'Lung Wedge Resection Multiple', 'Endobronchial biopsy', 'Mediastinoscopy', 'Not Reported', 'Lobectomy Left', 'Other', 'Unknown', 'Lung Wedge Resection Right', 'VATS Sclerosis', 'Segmentectomy', 'Lobectomy Bilateral', 'Brain resection', 'Pneumonectomy Right', '']",,LungCancerTier3 +Colorectal Polyp Type,Colorectal Polyp Type,ColorectalPolypType,Type of polyp found in the participant,False,,"['Adenoma', 'Hyperplastic', 'Other', 'Unknown', 'Normal', 'Mixed', 'Papillomatous', 'Cancer', '']",,ColorectalCancerTier3 +Colorectal Cancer Detection Method Type,Colorectal Cancer Detection Method Type,ColorectalCancerDetectionMethodType,"The means, manner of procedure, or systematic course of actions performed in order to discover or identify colorectal cancer",False,,"['Data not available', 'DNA stool test', 'Sigmoidoscopy', 'Virtual colonoscopy', 'Other', 'Unknown', 'Fecal occult blood test', 'Colonoscopy', '']",,ColorectalCancerTier3 +Patient Inflammatory Bowel Disease Personal Medica History,Patient Inflammatory Bowel Disease Personal Medica History,PatientInflammatoryBowelDiseasePersonalMedicaHistory,"The indicator for patient's personal medical history of inflammatory bowel disease (chronic, non-specific disorders of unknown etiology, including Crohn disease and ulcerative colitis).",False,,"['Yes - Ulcerative colitis', 'No', 'Not Applicable', ""Yes - Crohn's disease"", 'Unknown', '']",,ColorectalCancerTier3 +History of Prior Colon Polyps,History of Prior Colon Polyps,HistoryofPriorColonPolyps,Yes/No indicator to describe if the subject had a previous history of colon polyps as noted in the history/physical or previous endoscopic report (s).,False,,"['No', 'Not Applicable', 'Unknown', 'Yes', '']",,ColorectalCancerTier3 +Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,ColorectalCancerTier3 +Colorectal Polyp Shape,Colorectal Polyp Shape,ColorectalPolypShape,Shape of polyp identified in the participant,False,,"['Pedunculated', 'Sessile', 'Not Applicable', 'Not stated', 'Flat', '']",,ColorectalCancerTier3 +Colorectal Cancer KRAS Indicator,Colorectal Cancer KRAS Indicator,ColorectalCancerKRASIndicator,The yes/no/not applicable indicator that describes if patient has diagnosis of colorectal cancer with known KRAS.,False,,"['Not Applicable', 'No', 'Unknown', 'Yes', '']",,ColorectalCancerTier3 +MLH1 Promoter Methylation Status,MLH1 Promoter Methylation Status,MLH1PromoterMethylationStatus,Text term to define the status of promoter methylation for the MLH1 gene. Note: MLH1 gene is commonly associated with hereditary nonpolyposis colorectal cancer. Testing for methylation of the MLH1 promoter can help distinguish sporadic from inherited cancers.,False,,"['Absent', 'Indeterminate', 'Not Assessed', 'Present', '']",,ColorectalCancerTier3 +Colon Polyp Occurence Indicator,Colon Polyp Occurence Indicator,ColonPolypOccurenceIndicator,Yes/No indicator to describe if the subject had a previous history of colon polyps as noted in the history/physical or previous endoscopic report (s).,False,,"['Not Applicable', 'No', 'Unknown', 'Yes', '']",,ColorectalCancerTier3 +Stop Days from Index,Stop Days from Index,StopDaysfromIndex,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'",False,,,,ColorectalCancerTier3 +Family Medical History Colorectal Polyp Diagnosis,Family Medical History Colorectal Polyp Diagnosis,FamilyMedicalHistoryColorectalPolypDiagnosis,A yes/no/unknown/not applicable indicator related to family medical history diagnosis of polypoid lesion that arises from the colon or rectum and protrudes into the lumen.,False,,"['No', 'Not Applicable', 'Unknown', 'Yes', '']",,ColorectalCancerTier3 +Colorectal Polyp Count,Colorectal Polyp Count,ColorectalPolypCount,The total number of polyps detected,False,,,,ColorectalCancerTier3 +Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,ColorectalCancerTier3 +Immediate Family History Ovarian Cancer,Immediate Family History Ovarian Cancer,ImmediateFamilyHistoryOvarianCancer,Text that describes the age at which the family member was diagnosed with ovarian cancer in relationship to their 50th birthday.,False,,"['Not Applicable', 'Unknown', 'Not before age 50', 'Before age 50', '']",,ColorectalCancerTier3 +Colorectal Cancer Tumor Border Configuration,Colorectal Cancer Tumor Border Configuration,ColorectalCancerTumorBorderConfiguration,The description of the border configuration of a colorectal tumor at pathologic assessment.,False,,"['Not Applicable', 'Other', 'Infiltrating', 'Pushing', 'Indeterminate', '']",,ColorectalCancerTier3 +Family Colon Cancer History Indicator,Family Colon Cancer History Indicator,FamilyColonCancerHistoryIndicator,The indicator to designate if any first degree relative has a history of colorectal cancer.,False,,"['No', 'Not Applicable', 'Unknown', 'Yes', '']",,ColorectalCancerTier3 +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,ColorectalCancerTier3 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ColorectalCancerTier3 +Size of Polyp Removed,Size of Polyp Removed,SizeofPolypRemoved,Size of the polyp removed in cm,False,,,,ColorectalCancerTier3 +Colorectal Polyp New Indicator,Colorectal Polyp New Indicator,ColorectalPolypNewIndicator,A yes/no response to a question that asks whether any new polyps greater or equal to two millimeter were identified.,False,,"['Not Applicable', 'No', 'Unknown', 'Yes', '']",,ColorectalCancerTier3 +Colorectal Polyp Adenoma Type,Colorectal Polyp Adenoma Type,ColorectalPolypAdenomaType,Type of adenoma associated with the polyp,False,,"['Serrated not specified', 'Tubulovillous', 'Villous', 'Not Applicable', 'Tubular', 'Sessile serrated', 'Not stated', 'Traditional serrated', '']",,ColorectalCancerTier3 +Immediate Family History Endometrial Cancer,Immediate Family History Endometrial Cancer,ImmediateFamilyHistoryEndometrialCancer,Text that describes the age at which the family member was diagnosed with endometrial or uterine cancer in relationship to their 50th birthday.,False,,"['Not Applicable', 'Unknown', 'Not before age 50', 'Before age 50', '']",,ColorectalCancerTier3 +Family History Colorectal Polyp,Family History Colorectal Polyp,FamilyHistoryColorectalPolyp,A yes/no/unknown/not applicable indicator related to family medical history diagnosis of polypoid lesion that arises from the colon or rectum and protrudes into the lumen.,False,,"['Not Applicable', 'No', 'Unknown', 'Yes', '']",,ColorectalCancerTier3 +Patient Colonoscopy Performed Indicator,Patient Colonoscopy Performed Indicator,PatientColonoscopyPerformedIndicator,The yes/no indicator that records if the subject has undergone a previous colonoscopy.,False,,"['No', 'Not Applicable', 'Unknown', 'Yes', '']",,ColorectalCancerTier3 +Breast Carcinoma Detection Method Type,Breast Carcinoma Detection Method Type,BreastCarcinomaDetectionMethodType,"The means, manner of procedure, or systematic course of actions performed in order to discover or identify breast cancer.",False,,"['Clinical Exam', 'Data not available', 'Screening Mammography', 'Other', 'Unknown', 'Self exam', 'Nipple Discharge', 'Screening MRI', '']",,BreastCancerTier3 +Breast Carcinoma HER2 Centromere17 Copynumber Total,Breast Carcinoma HER2 Centromere17 Copynumber Total,BreastCarcinomaHER2Centromere17CopynumberTotal,Number of Cells Counted for HER2 & Centromere 17 Copy Numbers in a participant with breast cancer,False,,,,BreastCancerTier3 +Breast Carcinoma HER2 Status,Breast Carcinoma HER2 Status,BreastCarcinomaHER2Status,Text term to signify the result of the medical procedure that involves testing a sample of blood or tissue for HER2 in a participant with breast cancer,False,,"['Non-amplified', 'Equivocal', 'Not Performed', 'Positive', 'Unknown', 'Amplified', 'Indeterminate', 'Negative', '']",,BreastCancerTier3 +Prior Invasive Breast Disease,Prior Invasive Breast Disease,PriorInvasiveBreastDisease,Text term to indicate prior invasive breast condition in the participant,False,,"['Data not available', 'Other', 'DCIS', 'Unknown', 'LCIS', 'Invasive breast cancer (unrelated to the current cancer)', '']",,BreastCancerTier3 +Breast Imaging Performed Type,Breast Imaging Performed Type,BreastImagingPerformedType,"The kind of technology or method performed for screening, diagnosis, surgical procedures or therapy that aids in the visualization of the breast(s).",False,,"['Ultrasound', 'Data not available', 'MRI', 'Mammogram', 'Unknown', 'CT', 'Multiple imaging modalities', 'PET/CT', '']",,BreastCancerTier3 +Mammaprint Risk Group,Mammaprint Risk Group,MammaprintRiskGroup,Text term that represents the risk group for breast cancer as determined by assessment of the MammaPrint test.,False,,"['High risk', 'Data not available', 'Unknown', 'Low risk', 'Intermediate risk', '']",,BreastCancerTier3 +Hormone Therapy Breast Cancer Prevention Indicator,Hormone Therapy Breast Cancer Prevention Indicator,HormoneTherapyBreastCancerPreventionIndicator,Did the patient receive hormonal therapy for prevention of breast cancer?,False,,"['Not Applicable', 'No', 'Unknown', 'Yes', '']",,BreastCancerTier3 +Breast Carcinoma ER Status Percentage Value,Breast Carcinoma ER Status Percentage Value,BreastCarcinomaERStatusPercentageValue,A numerical quantity measured or assigned or computed which captures the estrogen receptor level measured in a participant with breast cancer,False,,,,BreastCancerTier3 +Breast Carcinoma Surgical Procedure Name,Breast Carcinoma Surgical Procedure Name,BreastCarcinomaSurgicalProcedureName,Text name of a surgical procedure performed for a person with a diagnosis of breast cancer,False,,"['Modified radical mastectomy', 'Simple mastectomy', 'Surgery not performed', 'Radical mastectomy', 'Other', 'Unknown', 'Partial mastectomy', 'Re-excision', 'Lumpectomy', '']",,BreastCancerTier3 +Multifocal Breast Carcinoma Present Indicator,Multifocal Breast Carcinoma Present Indicator,MultifocalBreastCarcinomaPresentIndicator,A response to indicate if there is breast cancer characterized by the presence of multiple cancerous tumors that originate from the same clone and usually located in the same quadrant of the breast.,False,,"['No', 'Unknown', 'Data not available', 'Yes', '']",,BreastCancerTier3 +Breast Biopsy Procedure Finding Type,Breast Biopsy Procedure Finding Type,BreastBiopsyProcedureFindingType,Text term to describe the result of the examination of the breast tissue specimen or fluid as related to the presence and nature of disease.,False,,"['Atypical hyperplasia', 'No cancer', 'Other', 'DCIS', 'LCIS', 'Cancer', '']",,BreastCancerTier3 +Invasive Ductal Breast Carcinoma Histologic Category,Invasive Ductal Breast Carcinoma Histologic Category,InvasiveDuctalBreastCarcinomaHistologicCategory,The histologic subtype for the most common type of invasive breast carcinoma.,False,,"['Tubulolobular carcinoma', 'Classical type', 'Invasive micropapillary carcinoma', 'Data not available', 'Invasive papillary carcinoma', 'Invasive tubular carcinoma', 'Other', 'Medullary carcinoma', 'Unknown', 'Mucinous carcinoma', 'Invasive carcinoma-type cannot be determined', 'Invasive cribriform carcinoma', '']",,BreastCancerTier3 +Breast Carcinoma Progesteroner Receptor Status,Breast Carcinoma Progesteroner Receptor Status,BreastCarcinomaProgesteronerReceptorStatus,Text term to represent the overall result of Progresterone Receptor (PR) testing in a participant with breast cancer,False,,"['Equivocal', 'Performed but Not Available', 'Not Performed', 'Positive', 'Unknown', 'Indeterminate', 'Negative', 'Borderline', '']",,BreastCancerTier3 +Breast Carcinoma PR Staining Intensity,Breast Carcinoma PR Staining Intensity,BreastCarcinomaPRStainingIntensity,Text term to indicate the PR staining intensity on pathology assessment in a participant with breast cancer,False,,"['Weak-Moderate', 'Weak-Strong', 'Strong', 'Other', 'Unknown', 'Moderate', 'Moderate-Strong', 'Weak', '']",,BreastCancerTier3 +Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,BreastCancerTier3 +Breast Carcinoma Centromere 17 Copy Number,Breast Carcinoma Centromere 17 Copy Number,BreastCarcinomaCentromere17CopyNumber,"Result of Centromere 17 testing in a sample or specimen of metastatic breast carcinoma, expressed as a range of values.",False,,,,BreastCancerTier3 +Breast Carcinoma HER2 Ratio Diagnosis,Breast Carcinoma HER2 Ratio Diagnosis,BreastCarcinomaHER2RatioDiagnosis,HER2 ratio of the participant at diagnosis,False,,,,BreastCancerTier3 +Breast Quadrant Site,Breast Quadrant Site,BreastQuadrantSite,The breast quadrant or structure from which the breast tissue specimen was removed for microscopic examination.,False,,"['Upper inner quadrant', 'Lower outer quadrant', 'Data not available', 'Upper outer quadrant', 'Central', 'Lower inner quadrant', 'Unknown', 'Nipple', '']",,BreastCancerTier3 +Breast Carcinoma HER2 Chromosome17 Ratio,Breast Carcinoma HER2 Chromosome17 Ratio,BreastCarcinomaHER2Chromosome17Ratio,HER2 chromosome 17 ratio in participants with breast cancer,False,,,,BreastCancerTier3 +Breast Cancer Genomic Test Performed,Breast Cancer Genomic Test Performed,BreastCancerGenomicTestPerformed,Text term that represents the name of the genomic test performed for breast cancer.,False,,"['Data not available', 'Oncotype', 'Other', 'Not performed', 'Unknown', 'MammaPrint', '']",,BreastCancerTier3 +Breast Carcinoma Estrogen Receptor Status,Breast Carcinoma Estrogen Receptor Status,BreastCarcinomaEstrogenReceptorStatus,Text term to represent the overall result of Estrogen Receptor (ER) testing in a participant with breast cancer,False,,"['Equivocal', 'Performed but Not Available', 'Not Performed', 'Positive', 'Unknown', 'Indeterminate', 'Negative', 'Borderline', '']",,BreastCancerTier3 +Breast Carcinoma Histology Category,Breast Carcinoma Histology Category,BreastCarcinomaHistologyCategory,Classification of the type of invasive breast carcinoma diagnosed based on histologic attributes.,False,,"['Invasive mammary carcinoma NOS', 'Infiltrating ductal carcinoma', 'Other', 'Invasive mixed ductal and lobular carcinoma', 'Infiltrating lobular carcinoma', '']",,BreastCancerTier3 +BIRADS Mammography Breast Density Category,BIRADS Mammography Breast Density Category,BIRADSMammographyBreastDensityCategory,The category that describes the relative amount of different tissues present in the breast on a mammogram based on the updated 2015 edition of the American College of Radiology's Breast Imaging Reporting and Data System (BI-RADS) reporting guidelines.,False,,"['Extremely dense', 'Data not available', 'Heterogeneously dense', 'Unknown', 'Predominantly fatty', 'Scattered fibroglandular densities', '']",,BreastCancerTier3 +Stop Days from Index,Stop Days from Index,StopDaysfromIndex,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'",False,,,,BreastCancerTier3 +Breast Carcinoma PR Status Percentage Value,Breast Carcinoma PR Status Percentage Value,BreastCarcinomaPRStatusPercentageValue,A numerical quantity measured or assigned or computed which captures the progesterone receptor level measured in a participant with breast cancer,False,,,,BreastCancerTier3 +Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,BreastCancerTier3 +HER2 Breast Carcinoma Copy Number Total,HER2 Breast Carcinoma Copy Number Total,HER2BreastCarcinomaCopyNumberTotal,"Result of HER2 Copy Number testing (in a participant with breast cancer), expressed as a range of values.",False,,,,BreastCancerTier3 +Breast Carcinoma ER Staining Intensity,Breast Carcinoma ER Staining Intensity,BreastCarcinomaERStainingIntensity,Text term to indicate the ER staining intensity on pathology assessment in a participant with breast cancer,False,,"['Weak-Moderate', 'Weak-Strong', 'Strong', 'Other', 'Unknown', 'Moderate', 'Moderate-Strong', 'Weak', '']",,BreastCancerTier3 +Oncotype Risk Group,Oncotype Risk Group,OncotypeRiskGroup,Text term that represents the risk group for breast cancer as determined by assessment of the Oncotype recurrence score.,False,,"['High risk', 'Data not available', 'Unknown', 'Low risk', 'Intermediate risk', '']",,BreastCancerTier3 +Oncotype Score,Oncotype Score,OncotypeScore,OncotypeDX recurrence score,False,,,,BreastCancerTier3 +Multicentric Breast Carcinoma Present Indicator,Multicentric Breast Carcinoma Present Indicator,MulticentricBreastCarcinomaPresentIndicator,A response to indicate if there is breast cancer characterized by the presence of multiple cancerous tumors that originate from different clones and usually located in different quadrants of the breast.,False,,"['No', 'Unknown', 'Data not available', 'Yes', '']",,BreastCancerTier3 +Breast Cancer Allred Estrogen Receptor Score,Breast Cancer Allred Estrogen Receptor Score,BreastCancerAllredEstrogenReceptorScore,"The numeric Allred score, that is cell staining percentage plus intensity, to determine estrogen receptor status.",False,,"['4', '1', '5', '6', 'Unknown', '2', '7', '10', '3', '8', '0', '']",,BreastCancerTier3 +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,BreastCancerTier3 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BreastCancerTier3 +Breast Cancer Assessment Tests,Breast Cancer Assessment Tests,BreastCancerAssessmentTests,Text term to identify assessment tests done in participants during diagnosis,False,,"['HER2 IHC', 'Data not available', 'HER2 FISH-CISH', 'Estrogen receptor IHC', 'Other', 'HER2 FISH', 'Unknown', 'Progesterone receptor IHC', '']",,BreastCancerTier3 +Invasive Lobular Breast Carcinoma Histologic Category,Invasive Lobular Breast Carcinoma Histologic Category,InvasiveLobularBreastCarcinomaHistologicCategory,The histologic subtype for an infiltrating lobular carcinoma of the breast.,False,,"['Data not available', 'Classical type', 'Pleomorphic type', 'Alveolar type', 'Unknown', '']",,BreastCancerTier3 +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,NeuroblastomaandGliomaTier3 +Glioma Specific Metastasis Sites,Glioma Specific Metastasis Sites,GliomaSpecificMetastasisSites,Evidence of active brain metastasis including leptomeningeal involvement,False,,"['Leptomeningeal', 'Bone marrow', 'Other', 'Not Applicable', 'CSF', 'Brain', 'Spine', '']",,NeuroblastomaandGliomaTier3 +Supra Tentorial Ependymoma Molecular Subgroup,Supra Tentorial Ependymoma Molecular Subgroup,SupraTentorialEpendymomaMolecularSubgroup,Text term to identify the molecular subgroup in a supra tentorial ependymoma,False,,"['Unknown', 'ST-EPN-RELA', 'Not Applicable', 'ST-EPN-YAP1', '']",,NeuroblastomaandGliomaTier3 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,NeuroblastomaandGliomaTier3 +Glioma Specific Radiation Field,Glioma Specific Radiation Field,GliomaSpecificRadiationField,A description of the location on or within the CNS where radiation was administered in a partcipant with glioma,False,,"['Focal-tumor bed', 'Unknown', 'Not Applicable', 'Craniospinal', '']",,NeuroblastomaandGliomaTier3 +Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,NeuroblastomaandGliomaTier3 +Stop Days from Index,Stop Days from Index,StopDaysfromIndex,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'",False,,,,NeuroblastomaandGliomaTier3 +Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,NeuroblastomaandGliomaTier3 +Neuroblastoma MYCN Gene Amplification Status,Neuroblastoma MYCN Gene Amplification Status,NeuroblastomaMYCNGeneAmplificationStatus,Neuroblastoma MYCN amplification or over-expression status,False,,"['Unknown', 'Amplified', 'Not done', 'Not amplified', '']",,NeuroblastomaandGliomaTier3 +CNS Tumor Primary Anatomic Site,CNS Tumor Primary Anatomic Site,CNSTumorPrimaryAnatomicSite,Primary tumor location in the central nervous system that comprise the tissues of the central nervous system (brain and spinal cord)-not covered in Tiers 1 and 2,False,,"['Ventricles', 'Spinal cord-Cervical', 'Spinal cord-Lumbar', 'Optic pathway', 'Other locations NOS', 'Meninges/Dura', 'Other lymph nodes', 'Spinal cord-Thoracic', 'Paraspinal ganglion', 'Basal ganglia', 'Hippocampus', 'Thalamus', 'Suprasellar/Hypothalamic/Pituitary', 'Brain stem-Midbrain/Tectum', 'Cerebellar/Posterior fossa', 'Intracranial/Leptomeningeal', 'Brainstem-Pons', 'Brain stem-Medulla', '']",,NeuroblastomaandGliomaTier3 +Infra Tentorial Ependymoma Molecular Subgroup,Infra Tentorial Ependymoma Molecular Subgroup,InfraTentorialEpendymomaMolecularSubgroup,Text term to identify the molecular subgroup in a infra tentorial ependymoma,False,,"['PF-EPN-A', 'Not Applicable', 'PF-EPN-B', 'Unknown', 'Myxopapillary ependymoma', '']",,NeuroblastomaandGliomaTier3 +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,AcuteLymphoblasticLeukemiaTier3 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,AcuteLymphoblasticLeukemiaTier3 +NCI ALL Risk Group,NCI ALL Risk Group,NCIALLRiskGroup,The NCI risk group assigned to a patient at initial diagnosis with Acute Lymphoblastic Leukemia.,False,,"['Unknown', 'NCI Standard Risk', 'NCI High Risk', '']",,AcuteLymphoblasticLeukemiaTier3 +Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,AcuteLymphoblasticLeukemiaTier3 +Stop Days from Index,Stop Days from Index,StopDaysfromIndex,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'",False,,,,AcuteLymphoblasticLeukemiaTier3 +MRD ALL Diagnostic Sensitivity,MRD ALL Diagnostic Sensitivity,MRDALLDiagnosticSensitivity,The assay sensitivity results of a diagnostic assessment of Minimal Residual Disease in patients diagnosed with Acute Lymphoblastic Leukemia.,False,,"['Unknown', 'Indeterminate', 'Optimal', 'Suboptimal', '']",,AcuteLymphoblasticLeukemiaTier3 +CNS Leukemia Status,CNS Leukemia Status,CNSLeukemiaStatus,The status of central nervous system leukemia at the time of diagnosis.,False,,"['CNS 2c', 'CNS 2', 'CNS 1', 'Unknown', 'CNS 3b', 'CNS 2a', 'CNS 2b', 'CNS 3c', 'Not evaluated', 'CNS 3a', 'CNS 3', '']",,AcuteLymphoblasticLeukemiaTier3 +Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,AcuteLymphoblasticLeukemiaTier3 +Specimen Blast Count Percentage Value,Specimen Blast Count Percentage Value,SpecimenBlastCountPercentageValue,"The value, in percent(%) of the medical procedure that involves testing a sample of blood for blast cells, immature (undifferentiated) cells during diagnosis",False,,,,AcuteLymphoblasticLeukemiaTier3 +Ovarian Cancer Platinum Status,Ovarian Cancer Platinum Status,OvarianCancerPlatinumStatus,Text term to indicate the status of treatment with platinum in participant with ovarian cancer,False,,"['Platinum-sensitive', 'Platinum-resistant', 'Data not available', 'Platinum-refractory', 'Unknown', '']",,OvarianCancerTier3 +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,OvarianCancerTier3 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,OvarianCancerTier3 +Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,OvarianCancerTier3 +Stop Days from Index,Stop Days from Index,StopDaysfromIndex,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'",False,,,,OvarianCancerTier3 +Ovarian Cancer Surgical Outcome,Ovarian Cancer Surgical Outcome,OvarianCancerSurgicalOutcome,Text term that describes the kind of surgical treatment administered.,False,,"['Data not available', 'R0 resection', 'Optimal cytoreduction', 'Other', 'Unknown', 'Sub-optimal cytoreduction', '']",,OvarianCancerTier3 +Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,OvarianCancerTier3 +Ovarian Cancer Histologic Subtype,Ovarian Cancer Histologic Subtype,OvarianCancerHistologicSubtype,Text term to describe the histological subtype of ovarian cancer in the participant,False,,"['Low-grade serous', 'Germ cell', 'High-grade endometrioid', 'Mucinous', 'Data not available', 'Other', 'Clear cell', 'Unknown', 'Sex-cord stromal', 'Low-grade endometrioid', 'High-grade serous', '']",,OvarianCancerTier3 +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,ProstateCancerTier3 +Seminal Vesicle Invasion,Seminal Vesicle Invasion,SeminalVesicleInvasion,An anatomic position identifying a side of the body where local spread of malignant neoplasm is found to infiltrate tissue in the saclike glandular diverticulum on the ductus deferens in a male.,False,,"['None', 'Both sides', 'Not Reported', 'Unknown', 'Left', 'Right', '']",,ProstateCancerTier3 +Location Nature Positive Margins,Location Nature Positive Margins,LocationNaturePositiveMargins,Location and nature of positive margins,False,,"['Left Positive in an area of intraprostatic incision (II)', 'Right Positive where it is difficult to distinguish EPE vs II', 'Vas deferens', 'Right Anterior', 'Left Lateral', 'Right Lateral', 'Left Focal', 'Right Apex', 'Left Apex', 'Right Focal', 'Right Positive in an area of intraprostatic incision (II)', 'Unknown', 'Left Positive in an area of extraprostatic extension (EPE)', 'Right Positive in an area of extraprostatic extension (EPE)', 'Bladder neck (block PUM)', 'Left Posterior', 'Left Extensive', 'Not Reported', 'Left Posterolateral', 'Left Anterior', 'Apical margin (block DUM)', 'Left Positive where it is difficult to distinguish EPE vs II', 'Right Posterior', 'Right Mid', 'Left Mid', 'Right Posterolateral', 'Right Base', 'Left Base', 'Right Extensive', '']",,ProstateCancerTier3 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ProstateCancerTier3 +Prostate Carcinoma Histologic Type,Prostate Carcinoma Histologic Type,ProstateCarcinomaHistologicType,The diagnostic subclassification of an invasive prostate carcinoma.,False,,"['Undifferentiated carcinoma NOS', 'Acinar prostate adenocarcinoma-signet-ring variant', 'Prostatic small cell carcinoma', 'Acinar prostate mucinous adenocarcinoma', 'Other', 'Prostatic duct adenocarcinoma', 'Prostatic adenosquamous carcinoma', 'Prostatic adenocarcinoma (conventional NOS)', 'Acinar prostate mucinous (colloid) adenocarcinoma', 'Acinar prostate adenocarcinoma-sarcomatoid variant', '']",,ProstateCancerTier3 +Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,ProstateCancerTier3 +Stop Days from Index,Stop Days from Index,StopDaysfromIndex,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'",False,,,,ProstateCancerTier3 +Prostate Cancer Cytologic Morphologic Subtypes,Prostate Cancer Cytologic Morphologic Subtypes,ProstateCancerCytologicMorphologicSubtypes,Text term that describes various morphological and cytological subtypes in protate tumors.,False,,"['Not Reported', 'prostatic atypical adenomatous hyperplasia (adenosis or AAH)', 'prostatic clear cell cribiform hyperplasia', 'High grade prostatic intraepithelial neoplasia (HGPIN)/ (PIN II & PIN III)', 'Other', 'Low grade prostatic intraepithelial neoplasia (PIN)/(PIN I)', 'Unknown', 'prostatic basal cell hyperplasia', '']",,ProstateCancerTier3 +Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,ProstateCancerTier3 +Prostate Cancer Local Extent,Prostate Cancer Local Extent,ProstateCancerLocalExtent,The response used to categorize the local extent of disease for prostate cancer.,False,,"['Extraprostatic extension', 'Unknown', 'Organ Confined', 'Not Reported', '']",,ProstateCancerTier3 +Location Extent Extraprostatic Extension,Location Extent Extraprostatic Extension,LocationExtentExtraprostaticExtension,Location and extent of extraprostatic extension,False,,"['Right Anterior', 'Left Lateral', 'Right Lateral', 'Left Focal', 'Right Apex', 'Left Apex', 'Right Focal', 'Unknown', 'Right Non-focal (established)', 'Left Non-focal (established)', 'Not Reported', 'Left Posterior', 'Left Posterolateral', 'Left Anterior', 'Right Posterior', 'Right Mid', 'Left Mid', 'Right Posterolateral', 'Right Base', 'Left Base', '']",,ProstateCancerTier3 +Additonal Findings Uninvolved Prostate,Additonal Findings Uninvolved Prostate,AdditonalFindingsUninvolvedProstate,"Additional findings, uninvolved prostate",False,,"['High-grade prostatic intraepithelial neoplasia (PIN)', 'Not Reported', 'Inflammation', 'Benign prostatic hyperplasia (BPH)', 'Other', 'Unknown', 'Prostatic Intraductal adenocarcinoma', '']",,ProstateCancerTier3 +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,SarcomaTier3 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,SarcomaTier3 +Sarcoma Tumor Extension Type,Sarcoma Tumor Extension Type,SarcomaTumorExtensionType,The field to indicate the organs and structures to which the tumor has become adherent or has invaded.,False,,"['Extraosseous', 'Not Reported', 'Intracranial', 'Thoracic cavity', 'Other', 'Parameningeal', 'Unknown', 'Lymph nodes', '']",,SarcomaTier3 +Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,SarcomaTier3 +Stop Days from Index,Stop Days from Index,StopDaysfromIndex,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'",False,,,,SarcomaTier3 +Sarcoma Subtype,Sarcoma Subtype,SarcomaSubtype,"The subtype related to the scientific determination and investigation, analysis and recognition of the presence and nature of disease, condition, or injury from expressed signs and symptoms of tissue growth resulting from uncontrolled cell proliferation.",False,,"['Other Synovial Sarcoma Or Malignant Peripheral Nerve Sheath Tumor Sarcoma', 'Gastrointestinal Stromal Tumor', 'Not Reported', 'Undifferentiated pleomorphic sarcoma', 'Other', 'Unknown', 'Liposarcoma', 'Leiomyosarcoma (uterine or extra-uterine)', 'undifferentiated pleomorphic sarcoma or malignant fibrous histiosarcoma', '']",,SarcomaTier3 +Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,SarcomaTier3 +Sarcoma Diagnosis Classification Category,Sarcoma Diagnosis Classification Category,SarcomaDiagnosisClassificationCategory,"High level grouping to describe a diagnostic grouping or category for sarcoma, a malignant mesenchymal cell tumor most commonly arising from muscle, fat, fibrous tissue, bone, cartilage, and blood vessels.",False,,"['Not Reported', 'Unknown', 'Soft Tissue Sarcoma', 'Musculoskeletal Sarcoma', 'Bone Sarcoma', '']",,SarcomaTier3 +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,PancreaticCancerTier3 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,PancreaticCancerTier3 +Pancreatic IPMN Pathology Epithelial Subtype,Pancreatic IPMN Pathology Epithelial Subtype,PancreaticIPMNPathologyEpithelialSubtype,The Intraductal Papillary Mucinous Neoplasm (IPMN) epithelial cell subtype based on the gross and microscopic examination of a pancreatic neoplasm specimen,False,,"['Intestinal', 'Not Reported', 'Intraductal Tubopapillary', 'Pancreatobiliary', 'Oncocytic', 'Other', 'Unknown', 'Gastric Foveolar', '']",,PancreaticCancerTier3 +Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,PancreaticCancerTier3 +Stop Days from Index,Stop Days from Index,StopDaysfromIndex,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'",False,,,,PancreaticCancerTier3 +Pancreatic Duct Final Pathology Type,Pancreatic Duct Final Pathology Type,PancreaticDuctFinalPathologyType,The final pathology result of the pancreatic duct communication type.,False,,"['None', 'Not Reported', 'Not Specified', 'Side-Branch', 'Main Duct', 'Mixed', '']",,PancreaticCancerTier3 +Pancreas Precancer Histopathologic Grade,Pancreas Precancer Histopathologic Grade,PancreasPrecancerHistopathologicGrade,The grade of precancerous pancreatic tissue based on microscopic study of characteristic tissue abnormalities by employing various cytochemical and immunocytochemical stains.,False,,"['PanIN 1', 'IPMN-Borderline', 'PanIN 1A', 'IPMN-Invasive carcinoma', 'Not Reported', 'PanIN 1B', 'PanIN 3', 'PanIN 2', 'Unknown', 'IPMN-Carcinoma in situ', 'IPMN-Adenoma', '']",,PancreaticCancerTier3 +Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,PancreaticCancerTier3 +Melanoma Lesion Size,Melanoma Lesion Size,MelanomaLesionSize,"Diameter of lesion determined on skin examination (pre-bx), in mm",False,,,,MelanomaTier3 +Cutaneous Melanoma Ulceration,Cutaneous Melanoma Ulceration,CutaneousMelanomaUlceration,Description of extent of disruption to the surface of the skin caused by the cutaneous melanoma.,False,,"['Absent', 'Unknown', 'Not Reported', 'Present', '']",,MelanomaTier3 +History of Atypical Nevi,History of Atypical Nevi,HistoryofAtypicalNevi,Patient has a history of atypical nevi,False,,"['Yes (less than 50)', 'Yes (more than 50)', 'Not Reported', 'No', 'Unknown', '']",,MelanomaTier3 +Cutaneous Melanoma Tumor Infiltrating Lymphocytes,Cutaneous Melanoma Tumor Infiltrating Lymphocytes,CutaneousMelanomaTumorInfiltratingLymphocytes,Description of degree of lymphocytic infiltration surrounding and disrupting tumor cells of the vertical growth phase in a cutaneous melanoma.,False,,"['Brisk', 'Absent', 'Unknown', 'Nonbrisk', '']",,MelanomaTier3 +Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,MelanomaTier3 +History of Tanning Bed Use,History of Tanning Bed Use,HistoryofTanningBedUse,History of tanning bed use of the patient,False,,"['Not Reported', 'Never', 'Less than 10 times', '50-100 times', '10-50 times', 'More than 100 times', '']",,MelanomaTier3 +Cutaneous Melanoma Surgical Margins,Cutaneous Melanoma Surgical Margins,CutaneousMelanomaSurgicalMargins,Text term to indicate presence of tumor at resection margins,False,,"['Positive', 'Unknown', 'Not Reported', 'Negative', '']",,MelanomaTier3 +Stop Days from Index,Stop Days from Index,StopDaysfromIndex,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'",False,,,,MelanomaTier3 +Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,MelanomaTier3 +Cutaneous Melanoma Additional Findings,Cutaneous Melanoma Additional Findings,CutaneousMelanomaAdditionalFindings,Significant pathologic finding present in addition to the cutaneous melanoma.,False,,"['Solar Elastosis', 'Nevus Remnant', 'Vascular Proliferation', 'Not Applicable', 'Other', 'Actinic Keratosis', 'Nesting Melanoma', 'Unknown', 'Fibrosing Regression', 'Pagetoid Spread', '']",,MelanomaTier3 +Immediate Family History Melanoma,Immediate Family History Melanoma,ImmediateFamilyHistoryMelanoma,Text that describes the age at which the family member was diagnosed with melanoma skin cancer in relationship to their 50th birthday.,False,,"['Unknown', 'Not before age 50', 'Before age 50', '']",,MelanomaTier3 +Melanoma Biopsy Resection Sites,Melanoma Biopsy Resection Sites,MelanomaBiopsyResectionSites,Biopsy resection sites specific to melanoma (not covered in Tiers 1 and 2),False,,"['Skin of scrotum', 'Skin of ear', 'Skin of lower limb and hip', 'Skin of breast', 'skin of trunk-other', 'Skin of scalp', 'Skin of penis', 'Not Reported', 'Skin NOS', 'Skin of neck', 'Skin of lip', 'Skin of back', 'Skin of upper limb and shoulder', 'Skin of sole', 'Skin of vulva', 'Skin of chest', 'Skin of other parts of face', 'Skin of abdomen', 'Skin of palm', 'Skin of nose', 'Skin of eye lid', 'skin other', '']",,MelanomaTier3 +History of Chronic UV Exposure,History of Chronic UV Exposure,HistoryofChronicUVExposure,History of chronic UV exposure,False,,"['None', 'Not Reported', 'Outdoor occupational', 'Outdoor recreational', 'Therapeutic', '']",,MelanomaTier3 +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,MelanomaTier3 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MelanomaTier3 +Cutaneous Melanoma Tumor Regression Range,Cutaneous Melanoma Tumor Regression Range,CutaneousMelanomaTumorRegressionRange,Description of the degree to which tumor cells are replaced by lymphocytic inflammation with or without dermal melanophages and fibrosis._Range; the difference between the lowest and highest numerical values.,False,,"['Present involving 75% or more', 'Absent', 'Present involving less than 75%', 'Unknown', '']",,MelanomaTier3 +Fitzpatrick Skin Tone,Fitzpatrick Skin Tone,FitzpatrickSkinTone,The Fitzpatrick classification of skin phototype,False,,"['Not Reported', 'III', 'V', 'Unknown', 'I', 'VI', 'II', 'IV', '']",,MelanomaTier3 +History of Blistering Sunburn,History of Blistering Sunburn,HistoryofBlisteringSunburn,Patient has history of blistering sunburn,False,,"['No', 'Unknown', 'Not Reported', 'Yes', '']",,MelanomaTier3 +Melanoma Specimen Clark Level Value,Melanoma Specimen Clark Level Value,MelanomaSpecimenClarkLevelValue,Definition of the Clark level or depth of involvement of a melanoma in the skin or a specimen.,False,,"['III', 'V', 'Unknown', 'I', 'No Source Documentation', 'II', 'IV', '']",,MelanomaTier3 +Ischemic Temperature,Ischemic Temperature,IschemicTemperature,Specify whether specimen experienced warm or cold ischemia.,False,,"['4C wet ice', 'Ambient air', 'Cold Ischemia', 'Warm Ischemia', 'Unknown', 'Liquid Nitrogen', 'Negative -20C', 'Dry Ice', '']",,SRRSBiospecimen +Additional Topography,Additional Topography,AdditionalTopography,Topography not included in the ICD-O-3 Topography codes.,False,,"['Hilar Airway', 'Skin of scrotum', 'Skin of ear', 'Skin of lower limb and hip', 'Skin of breast', 'Skin of scalp', 'Skin of penis', 'Not Reported', 'Skin NOS', 'Skin of neck', 'Skin of lip', 'Skin of back', 'Skin of trunk', 'Skin of upper limb and shoulder', 'Skin of sole', 'Skin of vulva', 'Skin of chest', 'Skin of other parts of face', 'Skin of abdomen', 'Peri-tumoral Airway', 'Skin of palm', 'Skin of nose', 'Skin of eye lid', '']",,SRRSBiospecimen +Fixative Type,Fixative Type,FixativeType,Text term to identify the type of fixative used to preserve a tissue specimen,True,,"['95% Ethanol', 'Dimidoester', 'Acetone', 'RNAlater', 'Polaxamer', 'Glutaraldehyde', 'Cryo-store', 'Carbodiimide', 'OCT media', 'None', 'Formalin', 'Methacarn', 'Unknown', 'NP40 lysis buffer', 'PAXgene tissue', 'Para-benzoquinone', 'Alcohol', 'TCL lysis buffer', 'Dimethylacetamide', 'Saline', 'Other', ""Carnoy's Fixative""]",,SRRSBiospecimen +Biospecimen Type,Biospecimen Type,BiospecimenType,Biospecimen Type,True,,"['Bone Marrow Biospecimen Type', 'Tissue Biospecimen Type', 'Stool Biospecimen Type', 'Fluids Biospecimen Type', 'Cells Biospecimen Type', 'Urine Biospecimen Type', 'Blood Biospecimen Type', 'Ascites Biospecimen Type', 'Analyte Biospecimen Type', 'Mouth Rinse Biospecimen Type', 'Sputum Biospecimen Type']",,SRRSBiospecimen +Preservation Method,Preservation Method,PreservationMethod,Text term that represents the method used to preserve the sample.,True,,"['Negative 80 Deg C', 'Formalin fixed-unbuffered', 'Formalin fixed-buffered', 'Formalin fixed paraffin embedded - FFPE', 'Fresh dissociated and single cell sorted', 'Fresh', 'Frozen', 'Cryopreservation in liquid nitrogen - dead tissue', 'Unknown', 'Liquid Nitrogen', 'OCT', 'Cryopreserved', 'Methacarn fixed paraffin embedded - MFPE', 'Not Reported', 'Cryopreservation in dry ice - dead tissue', 'Snap Frozen', 'Fresh dissociated and single cell sorted into plates', 'Fresh dissociated and single cell sorted into plates in NP40 buffer', 'Fresh dissociated', 'Cryopreservation in liquid nitrogen - live cells']",,SRRSBiospecimen +Histologic Morphology Code,Histologic Morphology Code,HistologicMorphologyCode,"Histologic Morphology Code, based on ICD-O-3. Any valid ICD-O-3 morphology code. See https://seer.cancer.gov/icd-o-3/ and https://seer.cancer.gov/icd-o-3/sitetype.icdo3.20200629.xlsx. Examples: 80510",True,,,,SRRSBiospecimen +HTAN Parent ID,HTAN Parent ID,HTANParentID,HTAN ID of parent from which the biospecimen was obtained. Parent could be another biospecimen or a research participant.,True,,,,SRRSBiospecimen +Source HTAN Biospecimen ID,Source HTAN Biospecimen ID,SourceHTANBiospecimenID,This is the HTAN ID that may have been assigned to the biospecimen at the site of biospecimen origin (e.g. BU).,False,,,,SRRSBiospecimen +HTAN Biospecimen ID,HTAN Biospecimen ID,HTANBiospecimenID,HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,SRRSBiospecimen +Collection Days from Index,Collection Days from Index,CollectionDaysfromIndex,Number of days from the research participant's index date that the biospecimen was obtained.,True,,,,SRRSBiospecimen +Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,SRRSBiospecimen +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,SRRSBiospecimen +Storage Method,Storage Method,StorageMethod,The method by which a biomaterial was stored after preservation or before another protocol was used.,True,,"['RNAlater at 25C', '4C in vacuum chamber', 'RNAlater at 4C', 'Frozen at -80C', 'Cut slide', 'Frozen at -70C', 'Fresh', 'Frozen in vapor phase', 'Not Applicable', 'Ambient temperature', 'Refrigerated at 4 degrees', 'Unknown', 'Paraffin block', 'Refrigerated vacuum chamber', 'Frozen in liquid nitrogen', 'Desiccant at 4C', 'RNAlater at -20C', 'Frozen at -150C']",,SRRSBiospecimen +Processing Days from Index,Processing Days from Index,ProcessingDaysfromIndex,Number of days from the research participant's index date that the biospecimen was processed,True,,,,SRRSBiospecimen +Ischemic Time,Ischemic Time,IschemicTime,"Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value.",False,,,,SRRSBiospecimen +Acquisition Method Type,Acquisition Method Type,AcquisitionMethodType,Records the method of acquisition or source for the specimen under consideration.,True,,"['Blood draw', 'Core needle biopsy', 'Lymphadenectomy - Regional Nodes', 'Biopsy', 'Endoscopic biopsy', 'Shave Biopsy', 'Other Acquisition Method', 'Re-excision', 'BAL (bronchial alveolar lavage)', 'Not specified', 'Induced sputum', 'Cytobrush', 'Sentinel Node Biopsy', 'Surgical Resection', 'Excision', 'Fine Needle Aspirate', 'Punch Biopsy', 'Non induced sputum', 'Fluid collection', 'Forceps biopsy', 'Autopsy']",,SRRSBiospecimen +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,SRRSBiospecimen +Adjacent Biospecimen IDs,Adjacent Biospecimen IDs,AdjacentBiospecimenIDs,"List of HTAN Identifiers (separated by commas) of adjacent biospecimens cut from the same sample; for example HTA3_3000_3, HTA3_3000_4, ...",False,,,,SRRSBiospecimen +Collection Media,Collection Media,CollectionMedia,Material Specimen is collected into post procedure,False,,"['None', 'PBS', 'PBS+Serum', 'RPMI', 'DMEM+Serum', 'RPMI+Serum', 'DMEM', '']",,SRRSBiospecimen +Preinvasive Morphology,Preinvasive Morphology,PreinvasiveMorphology,"Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the HTAN",False,,"['Melanoma in situ - superficial spreading', 'Invasive melanoma - other', 'Benign tumor NOS', 'No diagnosis possible', 'Melanoma in situ - lentigo maligna type', 'Normal WDA', 'Persistent melanoma in situ', 'Atypical adenomatous hyperplasia', 'Squamous Carcinoma in situ', 'Invasive melanoma - nevoid', 'Invasive melanoma - nodular type', 'Severe dysplasia', 'Reserve cell hyperplasia', 'Melanocytic hyperplasia', 'Squamous metaplasia - immature', 'Melanoma in situ - acral-lentiginous', 'Melanoma in situ - arising in a giant congenital nevus', 'Atypical melanocytic proliferation', 'Carcinoma NOS', 'Mild dysplasia', 'Squamous metaplasia - mature', 'Moderate dysplasia', 'Invasive melanoma - acral lentiginous', 'Melanoma in situ - not otherwise classified', 'Adenocarcinoma in situ - mucinous', 'Invasive melanoma - desmoplastic', 'Hamartoma', 'Scar - no residual melanoma', 'Invasive melanoma - superficial spreading', 'Adenocarcinoma in situ - non mucinous', 'Invasive melanoma - lentigo maligna', '']",,SRRSBiospecimen +Topography Code,Topography Code,TopographyCode,"Topography Code, indicating site within the body, based on ICD-O-3.",False,,"['8140/3', '9571/3', '9063/3', '9194/3', '9261/3', '8280/0', '8315/3', '9442/1', '8072/3', '8221/0', '8540/3', '9840/3', '8453/0', '8631/3', '9502/0', '8912/3', '8723/0', '8741/2', '9728/3', '8761/0', '8802/3', '8098/3', '9042/3', '8052/3', '8835/1', '9103/0', '8905/0', '8004/3', '8480/0', '8841/1', '9174/1', '9659/3', '9807/3', '8121/0', '8588/3', '8380/0', '8392/0', '8472/1', '9812/3', '8830/3', '8390/3', '9130/3', '9242/3', '9301/0', '8453/3', '9302/3', '9837/3', '8091/3', '8980/3', '9680/3', '8970/3', '8408/3', '8508/3', '8936/1', '8576/3', '8584/3', '8711/0', '8589/3', '9170/3', '8650/0', '8622/1', '8011/3', '9054/0', '8012/3', '9350/1', '9719/3', '9508/3', '9752/1', '9833/3', '8094/3', '8163/2', '9504/3', '9140/3', '8551/3', '9490/3', '8806/3', '9450/3', '8681/1', '8152/3', '8592/1', '9741/1', '8880/0', '8174/3', '8721/3', '8800/3', '8500/2', '8693/3', '8080/2', '8803/3', '8381/1', '8902/3', '9766/1', '8842/3', '8441/2', '8001/3', '8503/3', '8930/0', '8150/0', '9051/0', '9250/3', '8806/6', '8220/3', '9390/1', '9431/1', '9476/3', '9871/3', '8340/3', 'Unknown', '9120/0', '8720/6', '8280/3', '8336/0', '8504/2', '8714/3', '9542/3', '8904/0', '9654/3', '9755/3', '9065/3', '8521/3', '9911/3', '8121/3', '8981/3', '9655/3', '9391/3', '9590/3', '8815/1', '8290/0', '8973/3', '9051/3', '9423/3', '9767/1', '9735/3', '9898/3', '8723/3', '8350/3', '8311/1', '9989/3', '8583/1', '8172/3', '8580/0', '9071/3', '8634/1', '9013/0', '8375/0', '8230/2', '8850/3', '9740/1', '8052/2', '8210/2', '8247/3', '8800/9', '8031/3', '8051/0', '9805/3', '9987/3', '8281/0', '9174/0', '8660/0', '8010/2', '9320/0', '9717/3', '8405/0', '9945/3', '9530/1', '9733/3', '8402/3', '9432/1', '8210/3', '8339/3', '8332/3', '8163/3', '9764/3', '9984/3', '8270/3', '8831/0', '9311/0', '8085/3', '8102/0', '8250/1', '8092/3', '8854/3', '8076/2', '9501/0', '8931/3', '8650/1', '8770/0', '9872/3', '8050/3', '9000/3', '8594/1', '9041/3', '8810/1', '9441/3', '9020/3', '8960/3', '9827/3', '8130/2', '8173/3', '8801/6', '8920/3', '8728/1', '9760/3', '9460/3', '8814/3', '8220/0', '8852/3', '9200/0', '8170/3', '8641/0', '8812/0', '8824/1', '8780/3', '9836/3', '8474/3', '9150/3', '8471/0', '8896/3', '8261/3', '9826/3', '8041/3', '8310/0', '8140/2', '9161/1', '8103/0', '9670/3', '8155/1', '9820/3', '8856/0', '9424/3', '8073/3', '8936/0', '8720/3', '8441/6', '8102/3', '9122/0', '8692/1', '8460/0', '8522/3', '9182/3', '9351/1', '9664/3', '8210/0', '8966/0', '8825/0', '9832/3', '8740/0', '8149/0', '9540/0', '8010/0', '8081/2', '8982/0', '9290/3', '8272/0', '9302/0', '8330/0', '9754/3', '8463/1', '8582/3', '8347/3', '9186/3', '9341/3', '9064/2', '9712/3', '9083/3', '8231/3', '9085/3', '8580/3', '8811/1', '9962/3', '8201/2', '9531/0', '8147/3', '8840/0', '8722/0', '9173/0', '8090/3', '9091/1', '8900/0', '9421/1', '9530/0', '9982/3', '8346/3', '8374/0', '8200/3', '8761/3', '8940/3', '9580/3', '9651/3', '9875/3', '9110/3', '8257/3', '9230/3', '9946/3', '8690/1', '8160/0', '9086/3', '9395/3', '9055/0', '9965/3', '9252/3', '8982/3', '8242/3', '8713/0', '8000/3', '8512/3', '9040/0', '9520/3', '8070/2', '8965/0', '9270/0', '8254/3', '9474/3', '9110/1', '8571/3', '8312/3', '9691/3', '8213/3', '8371/0', '8100/0', '8601/0', '9015/1', '9385/3', '9503/3', '9180/0', '9831/3', '8245/3', '9430/3', '9975/3', '9121/0', '8241/3', '8550/1', '9420/3', '9191/0', '9870/3', '8380/1', '9980/3', '8161/0', '8043/3', '8246/3', '8642/1', '8156/1', '9014/3', '8310/6', '9130/1', '8190/0', '8561/0', '9220/1', '9865/3', '8319/3', '8408/0', '9992/3', '8900/3', '9101/3', '8345/3', '8712/0', '8842/0', '9753/1', '9372/3', '9352/1', '9661/3', '8086/3', '8240/1', '9475/3', '8881/0', '8474/1', '8959/1', '8990/1', '8313/3', '8409/0', '9251/3', '9410/3', '9716/3', '9180/6', '9141/0', '8380/3', '9801/3', '8602/0', '9653/3', '9053/3', '8590/1', '9440/3', '8078/3', '8381/3', '8046/6', '8893/0', '9532/0', '9665/3', '9690/3', '8093/3', '8451/1', '8890/0', '8730/3', '8983/3', '9000/0', '9541/0', '8634/3', '8772/0', '9310/0', '9726/3', '8333/3', '8967/0', '9490/0', '8935/1', '9971/3', '9105/3', '8314/3', '8610/0', '8853/3', '9132/0', '8507/2', '8391/0', '8593/1', '8077/0', '8935/3', '9401/3', '8824/0', '8633/1', '8892/0', '8311/3', '8857/0', '8521/1', '9150/1', '9195/3', '8040/0', '8740/3', '8245/1', '8265/3', '8407/3', '9762/3', '8390/0', '8325/0', '8870/0', '8045/3', '8810/0', '8272/3', '9718/3', '8076/3', '8263/0', '9684/3', '9275/0', '9330/3', '9142/0', '9866/3', '8041/6', '8680/1', '8840/3', '9835/3', '8246/6', '8890/1', '8161/3', '8805/3', '9731/3', '8021/3', '8250/3', '8162/3', '8334/0', '8250/2', '9597/3', '9535/0', '9705/3', '8140/33', '9250/1', '9273/0', '9231/3', '8200/0', '8825/1', '8631/1', '9650/3', '9400/3', '8525/3', '9596/3', '8920/6', '8827/1', '8013/3', '8373/0', '8897/1', '8011/0', '9102/3', '9698/3', '8801/3', '9506/1', '8823/0', '9050/0', '8420/0', '8935/0', '9170/0', '9732/3', '9510/0', '8746/3', '9948/3', '8320/3', '8895/3', '8144/3', '8502/3', '8972/3', '8964/3', '8519/2', '8895/0', '9185/3', '9560/1', '8473/1', '9724/3', '8140/0', '9442/3', '9161/0', '9741/3', '9382/3', '8407/0', '8300/0', '8573/3', '8800/0', '9440/6', '8725/0', '9702/3', '8150/1', '8826/0', '9052/0', '8974/1', '9814/3', '9210/1', '8131/3', '8204/0', '9758/3', '9131/0', '8052/0', '8410/0', '8700/3', '8120/2', '8158/1', '8936/3', '8750/0', '9811/3', '9876/3', '8010/9', '8372/0', '8450/0', '8523/3', '8550/3', '9813/3', '8581/1', '8053/0', '8140/1', '8821/1', '9570/0', '8153/3', '8001/1', '8252/3', '8620/1', '9687/3', '8682/1', '9860/3', '8313/1', '8400/1', '8452/3', '9084/0', '9062/3', '9480/3', '8862/0', '8600/0', '8152/1', '8190/3', '8120/3', '8271/0', '8462/1', '8560/3', '9100/1', '9390/3', '9580/0', '9817/3', '9689/3', '8441/0', '8830/1', '8959/0', '9970/1', '8213/0', '9110/0', '8097/3', '8023/3', '9014/1', '8000/1', '8811/3', '8383/3', '9136/1', '8461/0', '9171/0', '8513/3', '8323/3', '8921/3', 'Not Reported', '9241/0', '8950/3', '8249/3', '9365/3', '9342/3', '8256/3', '8261/0', '8040/1', '8408/1', '8522/6', '9370/3', '9514/1', '9679/3', '8772/3', '9560/0', '8322/3', '9040/3', '9384/1', '9015/0', '8005/3', '9510/3', '9561/3', '8744/3', '9708/3', '9740/3', '9874/3', '9701/3', '9363/0', '8560/0', '8077/2', '8120/1', '9180/3', '9090/3', '8728/0', '8442/1', '8580/1', '8480/3', '8631/0', '8894/3', '9090/0', '9160/0', '8450/3', '8249/6', '8770/3', '9800/3', '8344/3', '8722/3', '8504/3', '8774/3', '8481/3', '8022/3', '8000/9', '8384/3', '9125/0', '8263/3', '9221/3', '9220/0', '8215/3', '8852/0', '9493/0', '9920/3', '8461/6', '8330/3', '9727/3', '8003/3', '8951/3', '8010/3', '8820/0', '8148/2', '8514/3', '8140/6', '9963/3', '8010/6', '8773/3', '9675/3', '8482/6', '9472/3', '8522/2', '9072/3', '9015/3', '8581/3', '8983/0', '8822/1', '9084/3', '8180/3', '9910/3', '9582/0', '9678/3', '8074/3', '9873/3', '8240/6', '9193/3', '8260/0', '8623/1', '8311/6', '8584/1', '8825/3', '8343/2', '8861/0', '8480/1', '8500/3', '8501/2', '8000/0', '8211/0', '8582/1', '9012/0', '8402/0', '9502/3', '9806/3', '9507/0', '8142/3', '8401/3', '9073/1', '8453/2', '9280/0', '9512/3', '9699/3', '9940/3', '9742/3', '8123/3', '8380/2', '8342/3', '8990/0', '8243/3', '9192/3', '8452/1', '8600/3', '8720/0', '8154/3', '8240/3', '8400/0', '9364/3', '9412/1', '8490/3', '8550/0', '9270/3', '8155/3', '8110/0', '8130/3', '8860/0', '9540/3', '9175/0', '9282/0', '8317/3', '9150/0', '9260/3', '8251/0', '8461/3', '8910/3', '9445/3', '9834/3', '8991/3', '8762/1', '9272/0', '9700/3', '9172/0', '9863/3', '8855/3', '9221/0', '8480/6', '8850/1', '9360/1', '8934/3', '8804/6', '8460/3', '8813/0', '8335/3', '8630/0', '9187/3', '9986/3', '8071/2', '8810/3', '9538/1', '9030/0', '9133/1', '8370/3', '8141/3', '8323/0', '8095/3', '9991/3', '8401/0', '8051/3', '9184/3', '9281/0', '9390/0', '8381/0', '8790/0', '9509/1', '9230/0', '9539/1', '8261/2', '8321/0', '8290/3', '9124/3', '9765/1', '9540/1', '9759/3', '8000/6', '9930/3', '9010/0', '8409/3', '8507/3', '8130/1', '8260/3', '8971/3', '8804/3', '9373/0', '8670/0', '9534/0', '8620/3', '9688/3', '8727/0', '8585/3', '8891/0', '8510/3', '8046/3', '9591/3', '8153/1', '8574/3', '8726/0', '8122/3', '8160/3', '9050/3', '8940/0', '9020/1', '8505/0', '8430/3', '9274/0', '9394/1', '8101/0', '9271/0', '8262/3', '8440/3', '8403/3', '9312/0', '9060/3', '9725/3', '9768/1', '8251/3', '9869/3', '8146/0', '9523/3', '9897/3', '8771/0', '9505/3', '8963/3', '8901/3', '9043/3', '9340/0', '9560/3', '8509/3', '8331/3', '8587/0', '9000/1', '9310/3', '9738/3', '8444/1', '8503/2', '8075/3', '9413/0', '9262/0', '9044/3', '9756/3', '8832/3', '8854/0', '8156/3', '8380/6', '9322/0', '9971/1', '8470/0', '8471/3', '8728/3', '8281/3', '8815/3', '8834/1', '9011/0', '9181/3', '8410/3', '9581/3', '8720/2', '8894/0', '8761/1', '8454/0', '9895/3', '8640/1', '8145/3', '8691/1', '9383/1', '8171/3', '8020/6', '8430/1', '9020/0', '9451/3', '9521/3', '8124/3', '8680/0', '9751/1', '8083/3', '8333/0', '8742/2', '8800/6', '9729/3', '8975/1', '9931/3', '8932/0', '8221/3', '9014/0', '9380/3', '8543/3', '8413/3', '8671/0', '9321/0', '8343/3', '8850/0', '9381/3', '9444/1', '8175/3', '9330/0', '8403/0', '9673/3', '8316/3', '9045/3', '9960/3', '8591/1', '8002/3', '9070/3', '8255/3', '8120/0', '8562/3', '8933/3', '8264/0', '9709/3', '8440/0', '8811/0', '8191/0', '9361/1', '8700/0', '9750/3', '8903/0', '8032/3', '9539/3', '9411/3', '8830/0', '9243/3', '9761/3', '9513/3', '8084/3', '9983/3', '9695/3', '9016/0', '8891/3', '8930/3', '9473/3', '8324/0', '8530/3', '8370/1', '8680/3', '8096/0', '8163/0', '9898/1', '9961/3', '9815/3', '8263/2', '8242/1', '9425/3', '8244/3', '8382/3', '8060/0', '8857/3', '9392/3', '8337/3', '9120/3', '9470/3', '8501/3', '9966/3', '9550/0', '9867/3', '9757/3', '8858/3', '9183/3', '9562/0', '8034/3', '9137/3', '8959/3', '9252/0', '8248/1', '8836/1', '9300/0', '9505/1', '9751/3', '8040/3', '8211/3', '8148/0', '8070/3', '8710/3', '9240/3', '9769/1', '8683/0', '8050/2', '8780/0', '9530/3', '9662/3', '8745/3', '8121/1', '8890/3', '8504/0', '9100/0', '8851/0', '8230/3', '8520/3', '8035/3', '9737/3', '8771/3', '8404/0', '8898/1', '9064/3', '8313/0', '8015/3', '8851/3', '9667/3', '8370/0', '8482/3', '8170/0', '8760/0', '8812/3', '8318/3', '9818/3', '9210/0', '9538/3', '8202/0', '9130/0', '8151/0', '8630/3', '9251/1', '9270/1', '9080/1', '8420/3', '8110/3', '8300/3', '9511/3', '9816/3', '8524/3', '8509/2', '8042/3', '9861/3', '8071/3', '8082/3', '8090/1', '8360/1', '9522/3', '9985/3', '8500/6', '8813/3', '8583/3', '8743/3', '9571/0', '8310/3', '8650/3', '9220/3', '8212/0', '9967/3', '8050/0', '8044/3', '8005/0', '9964/3', '8201/3', '8832/0', '8214/3', '9477/3', '9950/3', '8070/33', '8490/6', '9823/3', '9080/3', '9135/1', '8506/0', '8960/1', '9290/0', '9671/3', '9200/1', '8041/34', '8742/3', '9501/3', '9537/0', '9061/3', '8020/3', '9341/1', '9478/3', '8270/0', '8520/2', '9080/0', '8575/3', '9663/3', '8586/3', '8621/1', '8361/0', '9734/3', '8670/3', '8322/0', '8572/3', '9714/3', '8730/0', '8471/1', '8406/0', '8143/3', '8443/0', '8470/3', '8503/0', '8400/3', '8741/3', '9808/3', '8630/1', '8541/3', '9362/3', '8833/3', '8990/3', '8001/0', '8253/3', '8585/1', '9652/3', '9052/3', '9104/1', '9396/3', '8033/3', '8570/3', '8950/6', '9533/0', '9393/3', '8632/1', '8542/3', '8460/2', '8693/1', '9896/3', '8070/6', '8711/3', '9100/3', '8150/3', '9491/0', '9371/3', '8341/3', '8441/3', '8640/3', '9500/3', '9123/0', '8030/3', '9082/3', '8014/3', '8330/1', '8151/3', '9055/1', '9133/3', '8941/3', '8522/1', '8552/3', '9081/3', '9809/3', '8470/2', '9492/0', '8147/0', '9471/3', '8815/0', '9891/3', '']",,SRRSBiospecimen +Biospecimen Dimension 3,Biospecimen Dimension 3,BiospecimenDimension3,"Third dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,," If Biospecimen is ""Bone"" OR ""Tissue"" then ""Biospecimen Dimension 3"" is required",SRRSBiospecimen +Portion Weight,Portion Weight,PortionWeight,"Numeric value that represents the sample portion weight, measured in milligrams.",False,True,," If Biospecimen is ""Bone"" OR ""Tissue"" OR ""Urine"" then ""Portion Weight"" is required",SRRSBiospecimen +Site of Resection or Biopsy,Site of Resection or Biopsy,SiteofResectionorBiopsy,"The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",False,True,"['Paraurethral gland', 'Colon NOS', 'Frontal sinus', 'Overlapping lesion of tongue', 'Overlapping lesion of palate', 'Scrotum NOS', 'Bone marrow', 'Axillary tail of breast', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'unknown primary site', 'Broad ligament', 'Lateral floor of mouth', 'Overlapping lesion of vulva', 'Trigone of bladder', 'Lacrimal gland', 'Thorax NOS', 'Ampulla of Vater', 'Myometrium', 'Penis NOS', 'Female genital tract NOS', 'Submandibular gland', 'Anterior 2/3 of tongue NOS', 'Posterior wall of bladder', 'Thymus', 'Endocrine gland NOS', 'Stomach NOS', 'Unknown', 'Cerebrum', 'Splenic flexure of colon', 'Urachus', 'Skin of lip NOS', 'Mucosa of lip NOS', 'Accessory sinus NOS', 'Cortex of adrenal gland', 'Other ill-defined sites', 'Middle lobe lung', 'Pelvis NOS', 'Anus NOS', 'Upper-inner quadrant of breast', 'Posterior mediastinum', 'Esophagus NOS', 'Duodenum', 'Cervical esophagus', 'Optic nerve', 'Long bones of lower limb and associated joints', 'Middle ear', 'Breast NOS', 'Dorsal surface of tongue NOS', 'Lesser curvature of stomach NOS', 'Overlapping lesion of floor of mouth', 'Overlapping lesion of heart mediastinum and pleura', 'Eye NOS', 'Overlapping lesion of esophagus', 'Ciliary body', 'Ureteric orifice', 'Postcricoid region', 'External ear', 'Base of tongue NOS', 'Liver', 'Commissure of lip', 'Cloacogenic zone', 'Lower lobe lung', 'Transverse colon', 'Acoustic nerve', 'Supraglottis', 'Fallopian tube', 'Upper third of esophagus', 'Skin of scalp and neck', 'Choroid', 'Long bones of upper limb scapula and associated joints', 'Overlapping lesion of brain', 'Upper gum', 'Skin NOS', 'Hard palate', 'Ileum', 'Overlapping lesion of colon', 'Ascending colon', 'Lower gum', 'Pelvic bones sacrum coccyx and associated joints', 'Hepatic flexure of colon', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Vestibule of mouth', 'Cervix uteri', 'Bones of skull and face and associated joints', 'Overlapping lesion of lip oral cavity and pharynx', 'Endometrium', 'Sphenoid sinus', 'Overlapping lesion of ill-defined sites', 'Sigmoid colon', 'Peritoneum NOS', 'Specified parts of peritoneum', 'Meckel diverticulum', 'Rectosigmoid junction', 'Kidney NOS', 'Reticuloendothelial system NOS', 'Rectum NOS', 'Pylorus', 'Overlapping lesion of tonsil', 'Pleura NOS', 'Jejunum', 'Vallecula', 'Skin of lower limb and hip', 'Pelvic lymph nodes', 'External lower lip', 'Overlapping lesion of skin', 'Mucosa of upper lip', 'Ovary', 'Cauda equina', 'Lower limb NOS', 'Body of stomach', 'Overlapping lesion of larynx', 'Pancreas NOS', 'Overlapping lesion of lung', 'Overlapping lesion of major salivary glands', 'Uvula', 'Overlapping lesion of hypopharynx', 'Round ligament', 'Corpus uteri', 'Biliary tract NOS', 'Male genital organs NOS', 'Parametrium', 'External lip NOS', 'Overlapping lesion of accessory sinuses', 'Cardia NOS', 'Islets of Langerhans', 'Carotid body', 'Ventral surface of tongue NOS', 'Autonomic nervous system NOS', 'Overlapping lesion of corpus uteri', 'Spinal meninges', 'Posterior wall of nasopharynx', 'Placenta', 'Intrahepatic bile duct', 'Overlapping lesion of digestive system', 'Mediastinum NOS', 'Hematopoietic system NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Major salivary gland NOS', 'Cerebellum NOS', 'Overlapping lesion of stomach', 'Vulva NOS', 'Craniopharyngeal duct', 'Lung NOS', 'Greater curvature of stomach NOS', 'Upper-outer quadrant of breast', 'Gallbladder', 'Thoracic esophagus', 'Lymph nodes of axilla or arm', 'Ventricle NOS', 'Overlapping lesion of biliary tract', 'Hypopharynx NOS', 'Clitoris', 'Exocervix', 'Parietal lobe', 'Waldeyer ring', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Head face or neck NOS', 'Anterior wall of nasopharynx', 'Urethra', 'Overlapping lesion of nasopharynx', 'Maxillary sinus', 'Lymph nodes of inguinal region or leg', 'Ureter', 'Tonsillar pillar', 'Sublingual gland', 'Pituitary gland', 'Gastrointestinal tract NOS', 'Pineal gland', 'Meninges NOS', 'Lingual tonsil', 'Trachea', 'Pyriform sinus', 'Mucosa of lower lip', 'Not Reported', 'Posterior wall of hypopharynx', 'Urinary system NOS', 'Orbit NOS', 'Short bones of lower limb and associated joints', 'Connective subcutaneous and other soft tissues of thorax', 'Upper limb NOS', 'Gastric antrum', 'Lymph node NOS', 'Peripheral nerves and autonomic nervous system of thorax', 'Ill-defined sites within respiratory system', 'Other specified parts of male genital organs', 'Rib sternum clavicle and associated joints', 'Overlapping lesion of bladder', 'Appendix', 'Prostate gland', 'Lymph nodes of multiple regions', 'Lateral wall of nasopharynx', 'Branchial cleft', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Floor of mouth NOS', 'Connective subcutaneous and other soft tissues NOS', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Bladder neck', 'Border of tongue', 'Connective subcutaneous and other soft tissues of abdomen', 'Overlapping lesion of small intestine', 'Lateral wall of bladder', 'Soft palate NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Isthmus uteri', 'Nasal cavity', 'Endocervix', 'Tonsil NOS', 'Glottis', 'Retroperitoneum', 'Peripheral nerves and autonomic nervous system of pelvis', 'Frontal lobe', 'Vagina NOS', 'Undescended testis', 'Laryngeal cartilage', 'Eyelid', 'Hypopharyngeal aspect of aryepiglottic fold', 'Overlapping lesion of other and unspecified parts of mouth', 'Upper lobe lung', 'Lip NOS', 'Lymph nodes of head face and neck', 'Overlapping lesion of brain and central nervous system', 'Overlapping lesion of penis', 'Overlapping lesion of retroperitoneum and peritoneum', 'Parotid gland', 'Dome of bladder', 'Bone of limb NOS', 'Descended testis', 'Vertebral column', 'Fundus uteri', 'Connective subcutaneous and other soft tissues of pelvis', 'Epididymis', 'Intra-abdominal lymph nodes', 'Paraspinal', 'Prepuce', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Pharynx NOS', 'Overlapping lesion of endocrine glands and related structures', 'Gum NOS', 'Spinal cord', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Skin of upper limb and shoulder', 'Nasopharynx NOS', 'Parathyroid gland', 'Bone NOS', 'Mouth NOS', 'Abdomen NOS', 'Conjunctiva', 'Spermatic cord', 'External upper lip', 'Labium minus', 'Renal pelvis', 'Overlapping lesion of lip', 'Short bones of upper limb and associated joints', 'Main bronchus', 'Upper respiratory tract NOS', 'Body of penis', 'Small intestine NOS', 'Central portion of breast', 'Lower-inner quadrant of breast', 'Labium majus', 'Tonsillar fossa', 'Cecum', 'Glans penis', 'Tail of pancreas', 'Lower third of esophagus', 'Body of pancreas', 'Intestinal tract NOS', 'Brain stem', 'Overlapping lesion of rectum anus and anal canal', 'Posterior wall of oropharynx', 'Pancreatic duct', 'Blood', 'Temporal lobe', 'Anterior floor of mouth', 'Nervous system NOS', 'Cornea NOS', 'Palate NOS', 'Occipital lobe', 'Abdominal esophagus', 'Overlapping lesion of pancreas', 'Overlapping lesion of female genital organs', 'Cheek mucosa', 'Retina', 'Overlapping lesion of male genital organs', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Larynx NOS', 'Skin of other and unspecified parts of face', 'Spleen', 'Oropharynx NOS', 'Anal canal', 'Subglottis', 'Cerebral meninges', 'Lateral wall of oropharynx', 'Middle third of esophagus', 'Nipple', 'Medulla of adrenal gland', 'Overlapping lesion of eye and adnexa', 'Olfactory nerve', 'Ethmoid sinus', 'Overlapping lesion of cervix uteri', 'Descending colon', 'Brain NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Anterior wall of bladder', 'Mandible', 'Other specified parts of pancreas', 'Skin of trunk', 'Other specified parts of female genital organs', 'Uterus NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Intrathoracic lymph nodes', 'Heart', 'Adrenal gland NOS', 'Aortic body and other paraganglia', 'Extrahepatic bile duct', 'Overlapping lesion of breast', 'Superior wall of nasopharynx', 'Fundus of stomach', 'Anterior mediastinum', 'Tongue NOS', 'Cranial nerve NOS', 'Head of pancreas', 'Overlapping lesions of oropharynx', 'Overlapping lesion of bones joints and articular cartilage', 'Retromolar area', 'Testis NOS', 'Connective subcutaneous and other soft tissues of head face and neck', 'Bladder NOS', 'Overlapping lesion of urinary organs', 'Lower-outer quadrant of breast', 'Thyroid gland', 'Anterior surface of epiglottis', 'Uterine adnexa', '']"," If Biospecimen is ""Bone"" OR ""Tissue"" OR ""Urine"" then ""Site of Resection or Biopsy"" is required",SRRSBiospecimen +Specimen Laterality,Specimen Laterality,SpecimenLaterality,"For tumors in paired organs, designates the side on which the specimen was obtained.",False,True,"['Not Reported', 'Bilateral', 'Not Applicable', 'Unknown', 'Left', 'Right', '']"," If Biospecimen is ""Bone"" OR ""Tissue"" OR ""Urine"" then ""Specimen Laterality"" is required",SRRSBiospecimen +Tumor Tissue Type,Tumor Tissue Type,TumorTissueType,Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint (add rows to select multiple values along with timepoints),False,True,"['Not analyzed', 'Local recurrence', 'Metastatic', 'Premalignant - in situ', 'primary', 'Post therapy neoadjuvant', 'Normal adjacent', 'Post therapy', 'Normal', 'Recurrent', 'Not Otherwise Specified', 'Premalignant', 'Normal distant', 'Additional Primary', 'Post therapy adjuvant', 'Atypia - hyperplasia', '']"," If Biospecimen is ""Bone"" OR ""Tissue"" OR ""Urine"" then ""Tumor Tissue Type"" is required",SRRSBiospecimen +Biospecimen Dimension 1,Biospecimen Dimension 1,BiospecimenDimension1,"First dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,," If Biospecimen is ""Bone"" OR ""Tissue"" then ""Biospecimen Dimension 1"" is required",SRRSBiospecimen +Total Volume,Total Volume,TotalVolume,Numeric value for the total amount of sample or specimen,False,True,," If Biospecimen is ""Bone"" OR ""Tissue"" OR ""Urine"" then ""Total Volume"" is required",SRRSBiospecimen +Section Number in Sequence,Section Number in Sequence,SectionNumberinSequence,"Numeric value (integer, including ranges) provided to a sample in a series of sections (list all adjacent sections in the Adjacent Biospecimen IDs field)",False,True,," If Biospecimen is ""Bone"" OR ""Tissue"" then ""Section Number in Sequence"" is required",SRRSBiospecimen +Biospecimen Dimension 2,Biospecimen Dimension 2,BiospecimenDimension2,"Second dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,," If Biospecimen is ""Bone"" OR ""Tissue"" then ""Biospecimen Dimension 2"" is required",SRRSBiospecimen +Shipping Condition Type,Shipping Condition Type,ShippingConditionType,Text descriptor of the shipping environment of a biospecimen.,False,True,"['Ambient Pack', 'Other Shipping Environment', 'Ice Pack', 'Cold Pack', 'Liquid Nitrogen', 'Not Shipped', 'Dry Ice', 'Specimen at Room Temperature', '']"," If Biospecimen is ""Blood"" OR ""Analyte"" then ""Shipping Condition Type"" is required",SRRSBiospecimen +Slide Charge Type,Slide Charge Type,SlideChargeType,A description of the charge on the glass slide.,False,True,"['Not applicable', 'Uncharged', 'Charged', 'Other', 'Coverslip', '']"," If Biospecimen is ""Analyte"" then ""Slide Charge Type"" is required",SRRSBiospecimen +Fixation Duration,Fixation Duration,FixationDuration,"The length of time, from beginning to end, required to process or preserve biospecimens in fixative (measured in minutes)",False,True,," If Biospecimen is ""Analyte"" then ""Fixation Duration"" is required",SRRSBiospecimen +Section Thickness Value,Section Thickness Value,SectionThicknessValue,"Numeric value to describe the thickness of a slice to tissue taken from a biospecimen, measured in microns (um).",False,True,," If Biospecimen is ""Analyte"" then ""Section Thickness Value"" is required",SRRSBiospecimen +Sectioning Days from Index,Sectioning Days from Index,SectioningDaysfromIndex,Number of days from the research participant's index date that the biospecimen was sectioned after collection,False,True,," If Biospecimen is ""Analyte"" then ""Sectioning Days from Index"" is required",SRRSBiospecimen +Analyte Type,Analyte Type,AnalyteType,The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen,False,True,"['cfDNA Analyte', 'RNA Analyte', 'PBMCs or Plasma or Serum Analyte', 'PBMCs', 'Plasma', 'DNA Analyte', 'cDNA Libraries Analyte', 'Total RNA Analyte', 'Serum Analyte', 'Tissue Section Analyte', 'Tissue Block Analyte', '']"," If Biospecimen is ""Analyte"" then ""Analyte Type"" is required",SRRSBiospecimen +Acquisition Method Other Specify,Acquisition Method Other Specify,AcquisitionMethodOtherSpecify,A custom acquisition method [Text - max length 100 characters],False,True,," If Acquisition is ""Other Acquisition Method"" then ""Acquisition Method Other Specify"" is required",SRRSBiospecimen +Dimensions Unit,Dimensions Unit,DimensionsUnit,"Unit of measurement used for dimension CDEs in metric system (i.e. cm, mm, etc)",False,,"['cm', 'mm', '']",,SRRSBiospecimen +Total Volume Unit,Total Volume Unit,TotalVolumeUnit,Unit of measurement used for the total amount of sample or specimen,False,,"['mL', 'cubic millimeter', 'square centimeter', '']",,SRRSBiospecimen +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,OtherAssay +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,OtherAssay +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,OtherAssay +File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,OtherAssay +Assay Type,Assay Type,AssayType,"The type and level of assay this metadata applies to (e.g. RPPA, Nanostring DSP, etc.)",True,,,,OtherAssay +Filename,Filename,filename,Name of a file ,True,,,,OtherAssay +Technical Replicate Group,Technical Replicate Group,TechnicalReplicateGroup,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),False,,,,ScRNA-seqLevel1 +End Bias,End Bias,EndBias,"The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript",True,,"['Full Length Transcript', '5 Prime', '3 Prime']",,ScRNA-seqLevel1 +Single Cell Dissociation Days from Index,Single Cell Dissociation Days from Index,SingleCellDissociationDaysfromIndex,Number of days between sample for single cell assay was received in lab and when the sample was dissociated and cells were isolated [number],True,,,,ScRNA-seqLevel1 +Read2,Read2,Read2,Read 2 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,ScRNA-seqLevel1 +File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,ScRNA-seqLevel1 +Dissociation Method,Dissociation Method,DissociationMethod,The tissue dissociation method used for scRNASeq or scATAC-seq assays,True,,"['Enzymatic Digestion', 'Not Applicable', 'Dounce', 'gentleMACS']",,ScRNA-seqLevel1 +Read1,Read1,Read1,Read 1 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,ScRNA-seqLevel1 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScRNA-seqLevel1 +Read Indicator,Read Indicator,ReadIndicator,Indicate if this is Read 1 (R1) or Read 2 (R2),True,,"['R1', 'R1&R2', 'R2']",,ScRNA-seqLevel1 +Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number],False,,,,ScRNA-seqLevel1 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ScRNA-seqLevel1 +Single Cell Isolation Method,Single Cell Isolation Method,SingleCellIsolationMethod,"The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)",True,,"['Nuclei Isolation', 'Droplets', 'Plates', '10x', 'Microfluidics Chip', 'FACS']",,ScRNA-seqLevel1 +Nucleic Acid Capture Days from Index,Nucleic Acid Capture Days from Index,NucleicAcidCaptureDaysfromIndex,Number of days between sample for single cell assay was received in lab and day of nucleic acid capture part of library construction (in number of days since sample received in lab) [number],True,,,,ScRNA-seqLevel1 +Input Cells and Nuclei,Input Cells and Nuclei,InputCellsandNuclei,"Number of cells and number of nuclei input; entry format: number, number",True,,,,ScRNA-seqLevel1 +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ScRNA-seqLevel1 +Library Construction Method,Library Construction Method,LibraryConstructionMethod,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],True,,"['10xV1.1', 'inDropsV2', 'Drop-seq', '10xV1.0', '10xV2', '10xV3', 'TruDrop', 'Smart-SeqV4', 'inDropsV3', '10xV3.1', 'sci-ATAC-seq', 'Smart-seq2', 'CEL-seq2']",,ScRNA-seqLevel1 +Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Single Cell', 'Bulk Nuclei', 'Bulk Whole Cell']",,ScRNA-seqLevel1 +Cryopreserved Cells in Sample,Cryopreserved Cells in Sample,CryopreservedCellsinSample,Indicate if library preparation was based on revived frozen cells.,True,,"['No', 'Yes']",,ScRNA-seqLevel1 +Sequencing Library Construction Days from Index,Sequencing Library Construction Days from Index,SequencingLibraryConstructionDaysfromIndex,Number of days between sample for assay was received in lab and day of sequencing library construction [number],True,,,,ScRNA-seqLevel1 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScRNA-seqLevel1 +Total Number of Input Cells,Total Number of Input Cells,TotalNumberofInputCells,Number of cells loaded/placed on plates,True,,,,ScRNA-seqLevel1 +Spike In,Spike In,SpikeIn,A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix,True,,"['No Spike In', 'ERCC', 'Other Spike In', 'PhiX']",,ScRNA-seqLevel1 +Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Genome Analyzer II', 'Illumina Genome Analyzer IIx', 'Illumina Next Seq 2500', 'Illumina NextSeq', 'PacBio RS', 'Illumina HiSeq X Five', 'AB SOLiD 3', 'Illumina HiSeq 2000', 'Illumina HiSeq 4000', 'Unknown', 'Complete Genomics', 'Ion Torrent S5', 'Not Reported', 'Illumina HiSeq X Ten', '454 GS FLX Titanium', 'Ion Torrent Proton', 'Illumina Next Seq 500', 'NovaSeqS4', 'Illumina MiSeq', 'AB SOLiD 4 AB SOLiD 2', 'Illumina NovaSeq 6000', 'NovaSeq 6000', 'Illumina HiSeq 2500', 'Other', 'Illumina Next Seq 550', 'Ion Torrent PGM']",,ScRNA-seqLevel1 +Reverse Transcription Primer,Reverse Transcription Primer,ReverseTranscriptionPrimer,"An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA",True,,"['Poly-dT', 'Feature barcoding', 'Random', 'Oligo-dT']",,ScRNA-seqLevel1 +Filename,Filename,filename,Name of a file ,True,,,,ScRNA-seqLevel1 +Median UMIs per Cell Number,Median UMIs per Cell Number,MedianUMIsperCellNumber,Number,False,True,," If Read1 is ""Cell Barcode and UMI"" then ""Median UMIs per Cell Number"" is required",ScRNA-seqLevel1 +Cell Barcode Length,Cell Barcode Length,CellBarcodeLength,Length of cell barcode read (in bp): number,False,True,," If Read1 is ""Cell Barcode and UMI"" then ""Cell Barcode Length"" is required",ScRNA-seqLevel1 +Valid Barcodes Cell Number,Valid Barcodes Cell Number,ValidBarcodesCellNumber,Number,False,True,," If Read1 is ""Cell Barcode and UMI"" then ""Valid Barcodes Cell Number"" is required",ScRNA-seqLevel1 +Cell Barcode Offset,Cell Barcode Offset,CellBarcodeOffset,Offset in sequence for cell barcode read (in bp): number,False,True,," If Read1 is ""Cell Barcode and UMI"" then ""Cell Barcode Offset"" is required",ScRNA-seqLevel1 +UMI Barcode Length,UMI Barcode Length,UMIBarcodeLength,Length of UMI barcode read (in bp): number,False,True,," If Read1 is ""Cell Barcode and UMI"" then ""UMI Barcode Length"" is required",ScRNA-seqLevel1 +UMI Barcode Offset,UMI Barcode Offset,UMIBarcodeOffset,"Start position of UMI barcode in the sequence. Values: number, 0 for start of read",False,True,," If Read1 is ""Cell Barcode and UMI"" then ""UMI Barcode Offset"" is required",ScRNA-seqLevel1 +cDNA Offset,cDNA Offset,CDNAOffset,Offset in sequence for cDNA read (in bp): number,False,True,," If Read1 is ""cDNA"" then ""cDNA Offset"" is required",ScRNA-seqLevel1 +cDNA Length,cDNA Length,CDNALength,Length of cDNA read (in bp): number,False,True,," If Read1 is ""cDNA"" then ""cDNA Length"" is required",ScRNA-seqLevel1 +Well Index,Well Index,WellIndex,Indicate if protein expression (EPCAM/CD45) positive/negative data is available for each cell in CEL-seq2 assays,False,True,"['No', 'Yes', '']"," If Library Construction Method is ""CEL-seq2"" then ""Well Index"" is required",ScRNA-seqLevel1 +Empty Well Barcode,Empty Well Barcode,EmptyWellBarcode,Unique cell barcode assigned to empty cells used as controls in CEL-seq2 assays.,False,True,," If Library Construction Method is ""CEL-seq2"" then ""Empty Well Barcode"" is required",ScRNA-seqLevel1 +Spike In Concentration,Spike In Concentration,SpikeInConcentration,The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910],False,True,," If Spike In is ""ERCC"" then ""Spike In Concentration"" is required",ScRNA-seqLevel1 +Feature Reference Id,Feature Reference Id,FeatureReferenceId,"Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]",False,True,," If Reverse Transcription Primer is ""Feature barcoding"" then ""Feature Reference Id"" is required",ScRNA-seqLevel1 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScRNA-seqLevel2 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScRNA-seqLevel2 +Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/),True,,,,ScRNA-seqLevel2 +scRNAseq Workflow Parameters Description,scRNAseq Workflow Parameters Description,ScRNAseqWorkflowParametersDescription,"Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion",True,,,,ScRNA-seqLevel2 +Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,ScRNA-seqLevel2 +Genome Annotation URL,Genome Annotation URL,GenomeAnnotationURL,Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz),True,,,,ScRNA-seqLevel2 +Whitelist Cell Barcode File Link,Whitelist Cell Barcode File Link,WhitelistCellBarcodeFileLink,Link to file listing all possible cell barcodes. URL,True,,,,ScRNA-seqLevel2 +Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz) [URL],True,,,,ScRNA-seqLevel2 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScRNA-seqLevel2 +UMI Tag,UMI Tag,UMITag,"SAM tag for UMI field; please provide a valid UB, UMI",True,,,,ScRNA-seqLevel2 +scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['Cell annotation', 'Cufflinks', 'STARsolo', 'CellRanger', 'SEQC', 'DEXSeq', 'dropEST', 'HTSeq - FPKM', 'Differentiation trajectory analysis', 'Other', 'HCA Optimus']",,ScRNA-seqLevel2 +Checksum,Checksum,Checksum,MD5 checksum of the BAM file,True,,,,ScRNA-seqLevel2 +Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,ScRNA-seqLevel2 +File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,ScRNA-seqLevel2 +Applied Hard Trimming,Applied Hard Trimming,AppliedHardTrimming,TBD,True,,"['No', 'Yes - Applied Hard Trimming']",,ScRNA-seqLevel2 +Cell Barcode Tag,Cell Barcode Tag,CellBarcodeTag,SAM tag for cell barcode field; please provide a valid cell barcode tag,True,,,,ScRNA-seqLevel2 +Filename,Filename,filename,Name of a file ,True,,,,ScRNA-seqLevel2 +Aligned Read Length,Aligned Read Length,AlignedReadLength,Read length used for alignment if hard trimming was applied,False,True,," If Applied Hard Trimming is ""Yes - Applied Hard Trimming"" then ""Aligned Read Length"" is required",ScRNA-seqLevel2 +Linked Matrices,Linked Matrices,LinkedMatrices,All matrices associated with every part of a SingleCellExperiment object. Comma-delimited list of filenames,False,,,,ScRNA-seqLevel3 +Cell Total,Cell Total,CellTotal,Number of sequenced cells. Applies to raw counts matrix only.,True,,,,ScRNA-seqLevel3 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScRNA-seqLevel3 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScRNA-seqLevel3 +Cell Median Number Reads,Cell Median Number Reads,CellMedianNumberReads,Median number of reads per cell. Number,True,,,,ScRNA-seqLevel3 +scRNAseq Workflow Parameters Description,scRNAseq Workflow Parameters Description,ScRNAseqWorkflowParametersDescription,"Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion",True,,,,ScRNA-seqLevel3 +Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,ScRNA-seqLevel3 +Cell Median Number Genes,Cell Median Number Genes,CellMedianNumberGenes,Median number of genes detected per cell. Number,True,,,,ScRNA-seqLevel3 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScRNA-seqLevel3 +scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['Cell annotation', 'Cufflinks', 'STARsolo', 'CellRanger', 'SEQC', 'DEXSeq', 'dropEST', 'HTSeq - FPKM', 'Differentiation trajectory analysis', 'Other', 'HCA Optimus']",,ScRNA-seqLevel3 +Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,ScRNA-seqLevel3 +File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,ScRNA-seqLevel3 +Data Category,Data Category,DataCategory,Specific content type of the data file.,True,,"['Splice Junction Quantification', 'Gene Expression Quantification', 'Isoform Expression Quantification', 'Exon Expression Quantification', 'Gene Expression', 'Other', 'Transcript Expression']",,ScRNA-seqLevel3 +Filename,Filename,filename,Name of a file ,True,,,,ScRNA-seqLevel3 +Matrix Type,Matrix Type,MatrixType,Type of data stored in matrix.,True,,"['Batch Corrected Counts', 'Raw Counts', 'Scaled Counts', 'Normalized Counts']",,ScRNA-seqLevel3 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScRNA-seqLevel4 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScRNA-seqLevel4 +scRNAseq Workflow Parameters Description,scRNAseq Workflow Parameters Description,ScRNAseqWorkflowParametersDescription,"Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion",True,,,,ScRNA-seqLevel4 +Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,ScRNA-seqLevel4 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScRNA-seqLevel4 +scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['Cell annotation', 'Cufflinks', 'STARsolo', 'CellRanger', 'SEQC', 'DEXSeq', 'dropEST', 'HTSeq - FPKM', 'Differentiation trajectory analysis', 'Other', 'HCA Optimus']",,ScRNA-seqLevel4 +Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,ScRNA-seqLevel4 +File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,ScRNA-seqLevel4 +Filename,Filename,filename,Name of a file ,True,,,,ScRNA-seqLevel4 +Kmer Content,Kmer Content,KmerContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkRNA-seqLevel1 +Per Base N Content,Per Base N Content,PerBaseNContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkRNA-seqLevel1 +Library Strand,Library Strand,LibraryStrand,Library stranded-ness.,False,,"['Unstranded', 'Second Stranded', 'Not Applicable', 'First Stranded', '']",,BulkRNA-seqLevel1 +Sequencing Batch ID,Sequencing Batch ID,SequencingBatchID,Links samples to a specific local sequencer run. Can be string or 'null',True,,,,BulkRNA-seqLevel1 +Per Sequence GC Content,Per Sequence GC Content,PerSequenceGCContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkRNA-seqLevel1 +Fragment Mean Length,Fragment Mean Length,FragmentMeanLength,"Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number",False,,,,BulkRNA-seqLevel1 +Adapter Content,Adapter Content,AdapterContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkRNA-seqLevel1 +Library Preparation Kit Vendor,Library Preparation Kit Vendor,LibraryPreparationKitVendor,Vendor of Library Preparation Kit. String,True,,,,BulkRNA-seqLevel1 +To Trim Adapter Sequence,To Trim Adapter Sequence,ToTrimAdapterSequence,Does the user suggest adapter trimming?,False,,"['No', 'Yes - Trim Adapter Sequence', '']",,BulkRNA-seqLevel1 +File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,BulkRNA-seqLevel1 +Adapter Name,Adapter Name,AdapterName,Name of the sequencing adapter. String,False,,,,BulkRNA-seqLevel1 +Fragment Minimum Length,Fragment Minimum Length,FragmentMinimumLength,"Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,BulkRNA-seqLevel1 +RIN,RIN,RIN,A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products. Number,False,,,,BulkRNA-seqLevel1 +Encoding,Encoding,Encoding,Version of ASCII encoding of quality values found in the file. String,False,,,,BulkRNA-seqLevel1 +QC Workflow Version,QC Workflow Version,QCWorkflowVersion,Major version for a workflow. String,False,,,,BulkRNA-seqLevel1 +Basic Statistics,Basic Statistics,BasicStatistics,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkRNA-seqLevel1 +Sequence Length Distribution,Sequence Length Distribution,SequenceLengthDistribution,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkRNA-seqLevel1 +QC Workflow Link,QC Workflow Link,QCWorkflowLink,Link to workflow used. String,False,,,,BulkRNA-seqLevel1 +DV200,DV200,DV200,Represents the percentage of RNA fragments that are >200 nucleotides in size. Number,False,,,,BulkRNA-seqLevel1 +Cell Barcode,Cell Barcode,CellBarcode,TBD,False,,,,BulkRNA-seqLevel1 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkRNA-seqLevel1 +Library Selection Method,Library Selection Method,LibrarySelectionMethod,How RNA molecules are isolated.,True,,"['rRNA Depletion', 'miRNA Size Fractionation', 'Other', 'Random', 'Affinity Enrichment', 'PCR', 'Poly-T Enrichment', 'Hybrid Selection']",,BulkRNA-seqLevel1 +Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,BulkRNA-seqLevel1 +Base Caller Name,Base Caller Name,BaseCallerName,Name of the base caller. String,False,,,,BulkRNA-seqLevel1 +QC Workflow Type,QC Workflow Type,QCWorkflowType,Generic name for the workflow used to analyze a data set. String,False,,,,BulkRNA-seqLevel1 +Per Base Sequence Quality,Per Base Sequence Quality,PerBaseSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkRNA-seqLevel1 +Sequence Duplication Levels,Sequence Duplication Levels,SequenceDuplicationLevels,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkRNA-seqLevel1 +Read Indicator,Read Indicator,ReadIndicator,Indicate if this is Read 1 (R1) or Read 2 (R2),True,,"['R1', 'R1&R2', 'R2']",,BulkRNA-seqLevel1 +Library Preparation Kit Version,Library Preparation Kit Version,LibraryPreparationKitVersion,Version of Library Preparation Kit. String,True,,,,BulkRNA-seqLevel1 +Per Tile Sequence Quality,Per Tile Sequence Quality,PerTileSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkRNA-seqLevel1 +Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number],False,,,,BulkRNA-seqLevel1 +Base Caller Version,Base Caller Version,BaseCallerVersion,Version of the base caller. String,False,,,,BulkRNA-seqLevel1 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,BulkRNA-seqLevel1 +Read Length,Read Length,ReadLength,"The length of the sequencing reads. Can be integer, null",True,,,,BulkRNA-seqLevel1 +Flow,Flow,Flow,TBD,False,,,,BulkRNA-seqLevel1 +Overrepresented Sequences,Overrepresented Sequences,OverrepresentedSequences,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkRNA-seqLevel1 +Per Sequence Quality Score,Per Sequence Quality Score,PerSequenceQualityScore,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkRNA-seqLevel1 +Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Paired End', 'Single Read']",,BulkRNA-seqLevel1 +Transcript Integrity Number,Transcript Integrity Number,TranscriptIntegrityNumber,"Used to describe the quality of the starting material, esp. in regards to FFPE samples. Number",False,,,,BulkRNA-seqLevel1 +Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Single Cell', 'Bulk Nuclei', 'Bulk Whole Cell']",,BulkRNA-seqLevel1 +Percent GC Content,Percent GC Content,PercentGCContent,The overall %GC of all bases in all sequences. Integer,False,,,,BulkRNA-seqLevel1 +Lane Number,Lane Number,LaneNumber,"The basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer",False,,,,BulkRNA-seqLevel1 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkRNA-seqLevel1 +Fragment Standard Deviation Length,Fragment Standard Deviation Length,FragmentStandardDeviationLength,"Standard deviation of the sequenced fragments length (e.g., as predicted by Agilent Bioanalyzer). Number",False,,,,BulkRNA-seqLevel1 +Multiplex Barcode,Multiplex Barcode,MultiplexBarcode,The barcode/index sequence used. Wrong or missing information may affect analysis results. String,False,,,,BulkRNA-seqLevel1 +Per Base Sequence Content,Per Base Sequence Content,PerBaseSequenceContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkRNA-seqLevel1 +Adapter Sequence,Adapter Sequence,AdapterSequence,Base sequence of the sequencing adapter. String,False,,,,BulkRNA-seqLevel1 +Spike In,Spike In,SpikeIn,A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix,True,,"['No Spike In', 'ERCC', 'Other Spike In', 'PhiX']",,BulkRNA-seqLevel1 +Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Genome Analyzer II', 'Illumina Genome Analyzer IIx', 'Illumina Next Seq 2500', 'Illumina NextSeq', 'PacBio RS', 'Illumina HiSeq X Five', 'AB SOLiD 3', 'Illumina HiSeq 2000', 'Illumina HiSeq 4000', 'Unknown', 'Complete Genomics', 'Ion Torrent S5', 'Not Reported', 'Illumina HiSeq X Ten', '454 GS FLX Titanium', 'Ion Torrent Proton', 'Illumina Next Seq 500', 'NovaSeqS4', 'Illumina MiSeq', 'AB SOLiD 4 AB SOLiD 2', 'Illumina NovaSeq 6000', 'NovaSeq 6000', 'Illumina HiSeq 2500', 'Other', 'Illumina Next Seq 550', 'Ion Torrent PGM']",,BulkRNA-seqLevel1 +Library Preparation Kit Name,Library Preparation Kit Name,LibraryPreparationKitName,Name of Library Preparation Kit. String,True,,,,BulkRNA-seqLevel1 +Target Depth,Target Depth,TargetDepth,The targeted read depth prior to sequencing. Integer,False,,,,BulkRNA-seqLevel1 +Fragment Maximum Length,Fragment Maximum Length,FragmentMaximumLength,"Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,BulkRNA-seqLevel1 +Size Selection Range,Size Selection Range,SizeSelectionRange,Range of size selection. String,False,,,,BulkRNA-seqLevel1 +Filename,Filename,filename,Name of a file ,True,,,,BulkRNA-seqLevel1 +Spike In Concentration,Spike In Concentration,SpikeInConcentration,The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910],False,True,," If Spike In is ""ERCC"" then ""Spike In Concentration"" is required",BulkRNA-seqLevel1 +Total Unmapped reads,Total Unmapped reads,TotalUnmappedreads,Number of reads that did not map to genome. Integer,False,,,,BulkRNA-seqLevel2 +Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz) [URL],True,,,,BulkRNA-seqLevel2 +Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,BulkRNA-seqLevel2 +File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,BulkRNA-seqLevel2 +Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,BulkRNA-seqLevel2 +Proportion Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,BulkRNA-seqLevel2 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkRNA-seqLevel2 +Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,BulkRNA-seqLevel2 +Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,BulkRNA-seqLevel2 +Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,BulkRNA-seqLevel2 +Proportion,Proportion,Proportion,TBD,False,,,,BulkRNA-seqLevel2 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkRNA-seqLevel2 +Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,BulkRNA-seqLevel2 +Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,BulkRNA-seqLevel2 +Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,BulkRNA-seqLevel2 +Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/),True,,,,BulkRNA-seqLevel2 +MSI Workflow Link,MSI Workflow Link,MSIWorkflowLink,Link to method workflow (or command) used in estimating the MSI. URL,False,,,,BulkRNA-seqLevel2 +MSI Status,MSI Status,MSIStatus,MSIsensor determination of either microsatellite stability or instability.,False,,"['MSI', 'MSS', 'MSI-low', 'MSI-high', '']",,BulkRNA-seqLevel2 +Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['None', 'STAR 2-Pass Genome', 'Other Alignment Workflow', 'BWA', 'STAR 2-Pass', 'BWA with Mark Duplicates and BQSR', 'BWA-aln', 'STAR 2-Pass Chimeric', 'BWA-mem', 'BWA with BQSR', 'STAR 2-Pass Transcriptome']",,BulkRNA-seqLevel2 +Targets No Coverage,Targets No Coverage,TargetsNoCoverage,TBD,False,,,,BulkRNA-seqLevel2 +Pairs On Diff CHR,Pairs On Diff CHR,PairsOnDiffCHR,Pairs on different chromosomes collected from samtools. Integer,False,,,,BulkRNA-seqLevel2 +Contamination Error,Contamination Error,ContaminationError,Estimation error of cross-sample contamination collected from GATK4. Number,False,,,,BulkRNA-seqLevel2 +Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,BulkRNA-seqLevel2 +Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,BulkRNA-seqLevel2 +MSI Score,MSI Score,MSIScore,Numeric score denoting the aligned reads file's MSI score from MSIsensor. Number,False,,,,BulkRNA-seqLevel2 +Alignment Workflow Url,Alignment Workflow Url,AlignmentWorkflowUrl,Link to workflow used for read alignment. DockStore.org recommended. String,True,,,,BulkRNA-seqLevel2 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkRNA-seqLevel2 +Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,BulkRNA-seqLevel2 +Filename,Filename,filename,Name of a file ,True,,,,BulkRNA-seqLevel2 +Custom Alignment Workflow,Custom Alignment Workflow,CustomAlignmentWorkflow,Specify the name of a custom alignment workflow,False,True,," If Alignment is ""Other Alignment Workflow"" then ""Custom Alignment Workflow"" is required",BulkRNA-seqLevel2 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkRNA-seqLevel3 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkRNA-seqLevel3 +Pseudo Alignment Used,Pseudo Alignment Used,PseudoAlignmentUsed,Pseudo aligners such as Kallisto or Salmon do not produce aligned reads BAM files. True indicates pseudoalignment was used.,True,,"['No', 'Yes - Pseudo Alignment Used']",,BulkRNA-seqLevel3 +Fusion Gene Identity,Fusion Gene Identity,FusionGeneIdentity,The gene symbols of fused genes.,False,,,,BulkRNA-seqLevel3 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkRNA-seqLevel3 +Expression Units,Expression Units,ExpressionUnits,How quantities are corrected for gene length,True,,"['FPKM', 'TPM', 'RPKM', 'NA', 'Other', 'Counts']",,BulkRNA-seqLevel3 +Fusion Gene Detected,Fusion Gene Detected,FusionGeneDetected,Was a fusion gene identified?,False,,"['No', 'Unknown', 'Yes - Fusion Gene Detected', '']",,BulkRNA-seqLevel3 +File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,BulkRNA-seqLevel3 +Data Category,Data Category,DataCategory,Specific content type of the data file.,True,,"['Splice Junction Quantification', 'Gene Expression Quantification', 'Isoform Expression Quantification', 'Exon Expression Quantification', 'Gene Expression', 'Other', 'Transcript Expression']",,BulkRNA-seqLevel3 +Filename,Filename,filename,Name of a file ,True,,,,BulkRNA-seqLevel3 +Matrix Type,Matrix Type,MatrixType,Type of data stored in matrix.,True,,"['Batch Corrected Counts', 'Raw Counts', 'Scaled Counts', 'Normalized Counts']",,BulkRNA-seqLevel3 +Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,False,True,," If Pseudo Alignment Used is ""Yes - Pseudo Alignment Used"" then ""Workflow Link"" is required",BulkRNA-seqLevel3 +Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz) [URL],False,True,," If Pseudo Alignment Used is ""Yes - Pseudo Alignment Used"" then ""Genomic Reference URL"" is required",BulkRNA-seqLevel3 +Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,False,True,," If Pseudo Alignment Used is ""Yes - Pseudo Alignment Used"" then ""Software and Version"" is required",BulkRNA-seqLevel3 +Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/),False,True,," If Pseudo Alignment Used is ""Yes - Pseudo Alignment Used"" then ""Genomic Reference"" is required",BulkRNA-seqLevel3 +Specify Other Fusion Gene,Specify Other Fusion Gene,SpecifyOtherFusionGene,"Specify fusion gene detected, if not in list",False,True,," If Fusion Gene Identity is ""Other Fusion Gene"" then ""Specify Other Fusion Gene"" is required",BulkRNA-seqLevel3 +Sequencing Batch ID,Sequencing Batch ID,SequencingBatchID,Links samples to a specific local sequencer run. Can be string or 'null',True,,,,BulkWESLevel1 +Fragment Mean Length,Fragment Mean Length,FragmentMeanLength,"Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number",False,,,,BulkWESLevel1 +Library Preparation Kit Vendor,Library Preparation Kit Vendor,LibraryPreparationKitVendor,Vendor of Library Preparation Kit. String,True,,,,BulkWESLevel1 +To Trim Adapter Sequence,To Trim Adapter Sequence,ToTrimAdapterSequence,Does the user suggest adapter trimming?,False,,"['No', 'Yes - Trim Adapter Sequence', '']",,BulkWESLevel1 +File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,BulkWESLevel1 +Adapter Name,Adapter Name,AdapterName,Name of the sequencing adapter. String,False,,,,BulkWESLevel1 +Target Capture Kit,Target Capture Kit,TargetCaptureKit,"Description that can uniquely identify a target capture kit. Suggested value is a combination of vendor, kit name, and kit version.",True,,"['SeqCap EZ HGSC VCRome v2.1', 'Custom AmpliSeq Cancer Hotspot GENIE-MDA Augmented Panel v1 - 46 Genes', 'Custom GENIE-DFCI OncoPanel - 275 Genes', 'Custom SeqCap EZ TARGET-OS Panel - 7.0 Mb', 'Not Applicable', 'TruSeq RNA Exome', 'Custom Twist Broad PanCancer Panel - 396 Genes', 'xGen Exome Research Panel v1.0', 'Custom MSK IMPACT Panel - 341 Genes', 'Custom Large Construct Capture TARGET-OS Panel - 8 Genes', 'TruSight Myeloid Sequencing Panel', 'Custom Solid Tumor GENIE-VICC Panel - 34 Genes', 'SureSelect Human All Exon v3', 'SureSelect Human All Exon v5', 'Custom SureSelect CGCI-HTMCP-CC Panel - 19.7 Mb', 'Custom SureSelect CGCI-BLGSP Panel - 4.6 Mb', 'Unknown', 'Custom SeqCap EZ HGSC VCRome v2.1 ER Augmented v1', 'SeqCap EZ Human Exome v2.0', 'Foundation Medicine T7 Panel - 429 Genes', 'Custom GENIE-DFCI Oncopanel - 300 Genes', 'Custom MSK IMPACT Panel - 468 Genes', 'Custom Targets File Provided', 'TruSeq Exome Enrichment - 62 Mb', 'Nextera DNA Exome', 'Custom PGDX SureSelect CancerSelect VAREPOP-APOLLO Panel - 88 Genes', 'Custom Ion AmpliSeq Hotspot GENIE-MOSC3 Augmented Panel - 74 Genes', 'Custom SureSelect CGCI-HTMCP-CC KMT2D And Hotspot Panel - 37.0 Kb', 'Custom Twist Broad Exome v1.0 - 35.0 Mb', 'SureSelect Human All Exon v5 + UTR', 'Custom GENIE-DFCI Oncopanel - 447 Genes', 'Nextera Rapid Capture Exome v1.2', 'Custom HaloPlex DLBCL Panel - 370 Genes', 'Custom SureSelect Human All Exon v1.1 Plus 3 Boosters', 'Custom Myeloid GENIE-VICC Panel - 37 Genes', 'Custom SureSelect TARGET-AML_NBL_WT Panel - 2.8 Mb', 'TruSeq Amplicon Cancer Panel', 'Custom SeqCap EZ HGSC VCRome v2.1 ER Augmented v2', 'Custom SureSelect GENIE-UHN Panel - 555 Genes', 'Custom MSK IMPACT Panel - 410 Genes', 'Foundation Medicine T5a Panel - 322 Genes', 'Ion AmpliSeq Cancer Hotspot Panel v2', 'SureSelect Human All Exon v4', 'SeqCap EZ Human Exome v3.0', 'Custom PGDX SureSelect CancerSelect VAREPOP-APOLLO Panel - 203 Genes', 'Ion AmpliSeq Comprehensive Cancer Panel', 'Custom Personalis ACEcp VAREPOP-APOLLO Panel v2']",,BulkWESLevel1 +Fragment Minimum Length,Fragment Minimum Length,FragmentMinimumLength,"Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,BulkWESLevel1 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkWESLevel1 +Library Selection Method,Library Selection Method,LibrarySelectionMethod,How RNA molecules are isolated.,True,,"['rRNA Depletion', 'miRNA Size Fractionation', 'Other', 'Random', 'Affinity Enrichment', 'PCR', 'Poly-T Enrichment', 'Hybrid Selection']",,BulkWESLevel1 +Base Caller Name,Base Caller Name,BaseCallerName,Name of the base caller. String,False,,,,BulkWESLevel1 +Read Indicator,Read Indicator,ReadIndicator,Indicate if this is Read 1 (R1) or Read 2 (R2),True,,"['R1', 'R1&R2', 'R2']",,BulkWESLevel1 +Library Preparation Kit Version,Library Preparation Kit Version,LibraryPreparationKitVersion,Version of Library Preparation Kit. String,True,,,,BulkWESLevel1 +Base Caller Version,Base Caller Version,BaseCallerVersion,Version of the base caller. String,False,,,,BulkWESLevel1 +Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number],False,,,,BulkWESLevel1 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,BulkWESLevel1 +Read Length,Read Length,ReadLength,"The length of the sequencing reads. Can be integer, null",True,,,,BulkWESLevel1 +Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Paired End', 'Single Read']",,BulkWESLevel1 +Lane Number,Lane Number,LaneNumber,"The basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer",False,,,,BulkWESLevel1 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkWESLevel1 +Fragment Standard Deviation Length,Fragment Standard Deviation Length,FragmentStandardDeviationLength,"Standard deviation of the sequenced fragments length (e.g., as predicted by Agilent Bioanalyzer). Number",False,,,,BulkWESLevel1 +Multiplex Barcode,Multiplex Barcode,MultiplexBarcode,The barcode/index sequence used. Wrong or missing information may affect analysis results. String,False,,,,BulkWESLevel1 +Adapter Sequence,Adapter Sequence,AdapterSequence,Base sequence of the sequencing adapter. String,False,,,,BulkWESLevel1 +Library Preparation Kit Name,Library Preparation Kit Name,LibraryPreparationKitName,Name of Library Preparation Kit. String,True,,,,BulkWESLevel1 +Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Genome Analyzer II', 'Illumina Genome Analyzer IIx', 'Illumina Next Seq 2500', 'Illumina NextSeq', 'PacBio RS', 'Illumina HiSeq X Five', 'AB SOLiD 3', 'Illumina HiSeq 2000', 'Illumina HiSeq 4000', 'Unknown', 'Complete Genomics', 'Ion Torrent S5', 'Not Reported', 'Illumina HiSeq X Ten', '454 GS FLX Titanium', 'Ion Torrent Proton', 'Illumina Next Seq 500', 'NovaSeqS4', 'Illumina MiSeq', 'AB SOLiD 4 AB SOLiD 2', 'Illumina NovaSeq 6000', 'NovaSeq 6000', 'Illumina HiSeq 2500', 'Other', 'Illumina Next Seq 550', 'Ion Torrent PGM']",,BulkWESLevel1 +Flow Cell Barcode,Flow Cell Barcode,FlowCellBarcode,Flow cell barcode. Wrong or missing information may affect analysis results. String,False,,,,BulkWESLevel1 +Target Depth,Target Depth,TargetDepth,The targeted read depth prior to sequencing. Integer,False,,,,BulkWESLevel1 +Fragment Maximum Length,Fragment Maximum Length,FragmentMaximumLength,"Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,BulkWESLevel1 +Size Selection Range,Size Selection Range,SizeSelectionRange,Range of size selection. String,False,,,,BulkWESLevel1 +Filename,Filename,filename,Name of a file ,True,,,,BulkWESLevel1 +Per Base N Content,Per Base N Content,PerBaseNContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkWESLevel2 +Per Sequence GC Content,Per Sequence GC Content,PerSequenceGCContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkWESLevel2 +Total Unmapped reads,Total Unmapped reads,TotalUnmappedreads,Number of reads that did not map to genome. Integer,False,,,,BulkWESLevel2 +Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz) [URL],True,,,,BulkWESLevel2 +Adapter Content,Adapter Content,AdapterContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkWESLevel2 +Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,BulkWESLevel2 +File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,BulkWESLevel2 +Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,BulkWESLevel2 +Encoding,Encoding,Encoding,Version of ASCII encoding of quality values found in the file. String,False,,,,BulkWESLevel2 +QC Workflow Version,QC Workflow Version,QCWorkflowVersion,Major version for a workflow. String,False,,,,BulkWESLevel2 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkWESLevel2 +Proportion Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,BulkWESLevel2 +Basic Statistics,Basic Statistics,BasicStatistics,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkWESLevel2 +Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,BulkWESLevel2 +Proportion Targets No Coverage,Proportion Targets No Coverage,ProportionTargetsNoCoverage,Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number,False,,,,BulkWESLevel2 +Sequence Length Distribution,Sequence Length Distribution,SequenceLengthDistribution,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkWESLevel2 +QC Workflow Link,QC Workflow Link,QCWorkflowLink,Link to workflow used. String,False,,,,BulkWESLevel2 +Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,BulkWESLevel2 +Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,BulkWESLevel2 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkWESLevel2 +Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,BulkWESLevel2 +Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,BulkWESLevel2 +QC Workflow Type,QC Workflow Type,QCWorkflowType,Generic name for the workflow used to analyze a data set. String,False,,,,BulkWESLevel2 +Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,BulkWESLevel2 +Per Base Sequence Quality,Per Base Sequence Quality,PerBaseSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkWESLevel2 +Sequence Duplication Levels,Sequence Duplication Levels,SequenceDuplicationLevels,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkWESLevel2 +Per Tile Sequence Quality,Per Tile Sequence Quality,PerTileSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkWESLevel2 +Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/),True,,,,BulkWESLevel2 +MSI Workflow Link,MSI Workflow Link,MSIWorkflowLink,Link to method workflow (or command) used in estimating the MSI. URL,False,,,,BulkWESLevel2 +MSI Status,MSI Status,MSIStatus,MSIsensor determination of either microsatellite stability or instability.,False,,"['MSI', 'MSS', 'MSI-low', 'MSI-high', '']",,BulkWESLevel2 +Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['None', 'STAR 2-Pass Genome', 'Other Alignment Workflow', 'BWA', 'STAR 2-Pass', 'BWA with Mark Duplicates and BQSR', 'BWA-aln', 'STAR 2-Pass Chimeric', 'BWA-mem', 'BWA with BQSR', 'STAR 2-Pass Transcriptome']",,BulkWESLevel2 +Pairs On Diff CHR,Pairs On Diff CHR,PairsOnDiffCHR,Pairs on different chromosomes collected from samtools. Integer,False,,,,BulkWESLevel2 +Overrepresented Sequences,Overrepresented Sequences,OverrepresentedSequences,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkWESLevel2 +Per Sequence Quality Score,Per Sequence Quality Score,PerSequenceQualityScore,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkWESLevel2 +Contamination Error,Contamination Error,ContaminationError,Estimation error of cross-sample contamination collected from GATK4. Number,False,,,,BulkWESLevel2 +Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,BulkWESLevel2 +Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,BulkWESLevel2 +MSI Score,MSI Score,MSIScore,Numeric score denoting the aligned reads file's MSI score from MSIsensor. Number,False,,,,BulkWESLevel2 +Percent GC Content,Percent GC Content,PercentGCContent,The overall %GC of all bases in all sequences. Integer,False,,,,BulkWESLevel2 +Proportion Coverage 10x,Proportion Coverage 10x,ProportionCoverage10x,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools.",False,,,,BulkWESLevel2 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkWESLevel2 +Per Base Sequence Content,Per Base Sequence Content,PerBaseSequenceContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['WARN', 'Not Reported', 'FAIL', 'PASS', 'Unknown', '']",,BulkWESLevel2 +Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,BulkWESLevel2 +Proportion Coverage 30X,Proportion Coverage 30X,ProportionCoverage30X,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools.",False,,,,BulkWESLevel2 +Filename,Filename,filename,Name of a file ,True,,,,BulkWESLevel2 +Custom Alignment Workflow,Custom Alignment Workflow,CustomAlignmentWorkflow,Specify the name of a custom alignment workflow,False,True,," If Alignment is ""Other Alignment Workflow"" then ""Custom Alignment Workflow"" is required",BulkWESLevel2 +Structural Variant Workflow URL,Structural Variant Workflow URL,StructuralVariantWorkflowURL,Link to workflow document. DockStore.org recommended. URL,True,,,,BulkWESLevel3 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkWESLevel3 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkWESLevel3 +Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/),True,,,,BulkWESLevel3 +Somatic Variants Workflow URL,Somatic Variants Workflow URL,SomaticVariantsWorkflowURL,Generic name for the workflow used to analyze a data set.,True,,,,BulkWESLevel3 +Structural Variant Workflow Type,Structural Variant Workflow Type,StructuralVariantWorkflowType,Generic name for the workflow used to analyze a data set.,False,,"['None', 'Other Structural Variant Workflow Type', 'CNV', 'GATK4', 'BRASS', 'CNVkit', '']",,BulkWESLevel3 +Somatic Variants Workflow Type,Somatic Variants Workflow Type,SomaticVariantsWorkflowType,Generic name for the workflow used to analyze a data set.,False,,"['None', 'Other Somatic Variants Workflow Type', 'GATK4', 'SomaticSniper', 'MuSE', 'VarScan2', 'CaVEMan', 'MuTect2', 'Pindel', '']",,BulkWESLevel3 +Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz) [URL],True,,,,BulkWESLevel3 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkWESLevel3 +Somatic Variants Sample Type,Somatic Variants Sample Type,SomaticVariantsSampleType,Is the sample case or control in somatic variant analysis,True,,"['Case Sample', 'Control Sample', 'Not Applicable']",,BulkWESLevel3 +Germline Variants Workflow URL,Germline Variants Workflow URL,GermlineVariantsWorkflowURL,"Link to workflow document, e.g. Github, DockStore.org recommended",True,,,,BulkWESLevel3 +Germline Variants Workflow Type,Germline Variants Workflow Type,GermlineVariantsWorkflowType,Generic name for the workflow used to analyze a data set,False,,"['None', 'GATK4', 'Other Germline Variants Workflow Type', '']",,BulkWESLevel3 +File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,BulkWESLevel3 +Filename,Filename,filename,Name of a file ,True,,,,BulkWESLevel3 +Custom Structural Variant Workflow Type,Custom Structural Variant Workflow Type,CustomStructuralVariantWorkflowType,Specify the name of a custom workflow name,False,True,," If Structural is ""Other"" then ""Custom Structural Variant Workflow Type"" is required",BulkWESLevel3 +Custom Somatic Variants Workflow Type,Custom Somatic Variants Workflow Type,CustomSomaticVariantsWorkflowType,Specify the name of a custom workflow name,False,True,," If Somatic is ""Other"" then ""Custom Somatic Variants Workflow Type"" is required",BulkWESLevel3 +Custom Germline Variants Workflow Type,Custom Germline Variants Workflow Type,CustomGermlineVariantsWorkflowType,Specify the name of a custom alignment workflow,False,True,," If Germline is ""Other"" then ""Custom Germline Variants Workflow Type"" is required",BulkWESLevel3 +Technical Replicate Group,Technical Replicate Group,TechnicalReplicateGroup,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),False,,,,ScATAC-seqLevel1 +scATACseq Read3,scATACseq Read3,ScATACseqRead3,Read 3 content description,False,,"['DNA Insert', 'Sample Index', 'Cell Barcode and DNA Insert', 'Cell Barcode', 'Sample Index and DNA Insert', '']",,ScATAC-seqLevel1 +File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,ScATAC-seqLevel1 +Dissociation Method,Dissociation Method,DissociationMethod,The tissue dissociation method used for scRNASeq or scATAC-seq assays,True,,"['Enzymatic Digestion', 'Not Applicable', 'Dounce', 'gentleMACS']",,ScATAC-seqLevel1 +Median Fraction of Reads in Peaks,Median Fraction of Reads in Peaks,MedianFractionofReadsinPeaks,Median fraction of reads in peaks (FRIP),True,,,,ScATAC-seqLevel1 +Transposition Reaction,Transposition Reaction,TranspositionReaction,"Name of the transposase, transposon sequences",True,,"['EZ-Tn5', 'In-House', 'Tn5-059', 'Nextera Tn5', 'Tn5']",,ScATAC-seqLevel1 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScATAC-seqLevel1 +Median Percentage of Mitochondrial Reads per Nucleus,Median Percentage of Mitochondrial Reads per Nucleus,MedianPercentageofMitochondrialReadsperNucleus,Contamination from mitochondrial sequences,True,,,,ScATAC-seqLevel1 +scATACseq Read2,scATACseq Read2,ScATACseqRead2,Read 2 content description,True,,"['DNA Insert', 'Sample Index', 'Cell Barcode and DNA Insert', 'Cell Barcode', 'Sample Index and DNA Insert']",,ScATAC-seqLevel1 +Total Number of Passing Nuclei,Total Number of Passing Nuclei,TotalNumberofPassingNuclei,Number of nuclei sequenced,True,,,,ScATAC-seqLevel1 +Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,ScATAC-seqLevel1 +scATACseq Library Layout,scATACseq Library Layout,ScATACseqLibraryLayout,Sequencing read type,True,,['scATACseq Paired End'],,ScATAC-seqLevel1 +Single Nucleus Buffer,Single Nucleus Buffer,SingleNucleusBuffer,Nuclei isolation buffer,True,,"['Omni', 'NIB', '10x']",,ScATAC-seqLevel1 +Nucleus Identifier,Nucleus Identifier,NucleusIdentifier,Unique nuclei barcode; added at transposition step. Determines which nucleus the reads originated from,True,,['Nuclei Barcode'],,ScATAC-seqLevel1 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ScATAC-seqLevel1 +Median Passing Read Percentage,Median Passing Read Percentage,MedianPassingReadPercentage,Non-PCR duplicate nuclear genomic sequence reads not aligning to unanchored contigs out of total reads assigned to the nucleus barcode,True,,,,ScATAC-seqLevel1 +Single Cell Isolation Method,Single Cell Isolation Method,SingleCellIsolationMethod,"The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)",True,,"['Nuclei Isolation', 'Droplets', 'Plates', '10x', 'Microfluidics Chip', 'FACS']",,ScATAC-seqLevel1 +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ScATAC-seqLevel1 +Library Construction Method,Library Construction Method,LibraryConstructionMethod,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],True,,"['10xV1.1', 'inDropsV2', 'Drop-seq', '10xV1.0', '10xV2', '10xV3', 'TruDrop', 'Smart-SeqV4', 'inDropsV3', '10xV3.1', 'sci-ATAC-seq', 'Smart-seq2', 'CEL-seq2']",,ScATAC-seqLevel1 +Threshold for Minimum Passing Reads,Threshold for Minimum Passing Reads,ThresholdforMinimumPassingReads,Threshold for calling cells,True,,,,ScATAC-seqLevel1 +Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Single Cell', 'Bulk Nuclei', 'Bulk Whole Cell']",,ScATAC-seqLevel1 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScATAC-seqLevel1 +scATACseq Read1,scATACseq Read1,ScATACseqRead1,Read 1 content description,True,,"['DNA Insert', 'Sample Index', 'Cell Barcode and DNA Insert', 'Cell Barcode', 'Sample Index and DNA Insert']",,ScATAC-seqLevel1 +Nuclei Barcode Length,Nuclei Barcode Length,NucleiBarcodeLength,Nuclei Barcode Length,True,,,,ScATAC-seqLevel1 +Median Fraction of Reads in Annotated cis DNA Elements,Median Fraction of Reads in Annotated cis DNA Elements,MedianFractionofReadsinAnnotatedcisDNAElements,Median fraction of reads in annotated cis-DNA elements (FRIADE),True,,,,ScATAC-seqLevel1 +Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Genome Analyzer II', 'Illumina Genome Analyzer IIx', 'Illumina Next Seq 2500', 'Illumina NextSeq', 'PacBio RS', 'Illumina HiSeq X Five', 'AB SOLiD 3', 'Illumina HiSeq 2000', 'Illumina HiSeq 4000', 'Unknown', 'Complete Genomics', 'Ion Torrent S5', 'Not Reported', 'Illumina HiSeq X Ten', '454 GS FLX Titanium', 'Ion Torrent Proton', 'Illumina Next Seq 500', 'NovaSeqS4', 'Illumina MiSeq', 'AB SOLiD 4 AB SOLiD 2', 'Illumina NovaSeq 6000', 'NovaSeq 6000', 'Illumina HiSeq 2500', 'Other', 'Illumina Next Seq 550', 'Ion Torrent PGM']",,ScATAC-seqLevel1 +Nuclei Barcode Read,Nuclei Barcode Read,NucleiBarcodeRead,Nuclei Barcode Read,True,,,,ScATAC-seqLevel1 +Filename,Filename,filename,Name of a file ,True,,,,ScATAC-seqLevel1 +Peaks Calling Software,Peaks Calling Software,PeaksCallingSoftware,Generic name of peaks calling tool,False,,,,ScATAC-seqLevel1 +Well Index,Well Index,WellIndex,Indicate if protein expression (EPCAM/CD45) positive/negative data is available for each cell in CEL-seq2 assays,False,True,"['No', 'Yes', '']"," If Library Construction Method is ""CEL-seq2"" then ""Well Index"" is required",ScATAC-seqLevel1 +Empty Well Barcode,Empty Well Barcode,EmptyWellBarcode,Unique cell barcode assigned to empty cells used as controls in CEL-seq2 assays.,False,True,," If Library Construction Method is ""CEL-seq2"" then ""Empty Well Barcode"" is required",ScATAC-seqLevel1 +Total Unmapped reads,Total Unmapped reads,TotalUnmappedreads,Number of reads that did not map to genome. Integer,False,,,,ScATAC-seqLevel2 +Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,ScATAC-seqLevel2 +Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,ScATAC-seqLevel2 +Proportion Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,ScATAC-seqLevel2 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScATAC-seqLevel2 +MapQ30,MapQ30,MapQ30,Number of reads with Quality >= 30.,False,,,,ScATAC-seqLevel2 +Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,ScATAC-seqLevel2 +Proportion Targets No Coverage,Proportion Targets No Coverage,ProportionTargetsNoCoverage,Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number,False,,,,ScATAC-seqLevel2 +Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,ScATAC-seqLevel2 +Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,ScATAC-seqLevel2 +Median Percentage of Mitochondrial Reads per Nucleus,Median Percentage of Mitochondrial Reads per Nucleus,MedianPercentageofMitochondrialReadsperNucleus,Contamination from mitochondrial sequences,True,,,,ScATAC-seqLevel2 +Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,ScATAC-seqLevel2 +Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,ScATAC-seqLevel2 +Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,ScATAC-seqLevel2 +Reference URL,Reference URL,ReferenceURL,TBD,False,,,,ScATAC-seqLevel2 +Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/),True,,,,ScATAC-seqLevel2 +Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['None', 'STAR 2-Pass Genome', 'Other Alignment Workflow', 'BWA', 'STAR 2-Pass', 'BWA with Mark Duplicates and BQSR', 'BWA-aln', 'STAR 2-Pass Chimeric', 'BWA-mem', 'BWA with BQSR', 'STAR 2-Pass Transcriptome']",,ScATAC-seqLevel2 +HTAN Biospecimen ID,HTAN Biospecimen ID,HTANBiospecimenID,HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScATAC-seqLevel2 +Pairs On Diff CHR,Pairs On Diff CHR,PairsOnDiffCHR,Pairs on different chromosomes collected from samtools. Integer,False,,,,ScATAC-seqLevel2 +Contamination Error,Contamination Error,ContaminationError,Estimation error of cross-sample contamination collected from GATK4. Number,False,,,,ScATAC-seqLevel2 +Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,ScATAC-seqLevel2 +Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,ScATAC-seqLevel2 +Genomic,Genomic,Genomic,TBD,False,,,,ScATAC-seqLevel2 +Alignment Workflow Url,Alignment Workflow Url,AlignmentWorkflowUrl,Link to workflow used for read alignment. DockStore.org recommended. String,True,,,,ScATAC-seqLevel2 +Proportion Coverage 10x,Proportion Coverage 10x,ProportionCoverage10x,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools.",False,,,,ScATAC-seqLevel2 +Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,ScATAC-seqLevel2 +Proportion Coverage 30X,Proportion Coverage 30X,ProportionCoverage30X,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools.",False,,,,ScATAC-seqLevel2 +Custom Alignment Workflow,Custom Alignment Workflow,CustomAlignmentWorkflow,Specify the name of a custom alignment workflow,False,True,," If Alignment is ""Other Alignment Workflow"" then ""Custom Alignment Workflow"" is required",ScATAC-seqLevel2 +MACS2 Neg Log10 qvalue Summit,MACS2 Neg Log10 qvalue Summit,MACS2NegLog10qvalueSummit,Negative log10 q-value for the peak summit in MACS2,False,,,,ScATAC-seqLevel3 +Blacklist Ratio,Blacklist Ratio,BlacklistRatio,Ratio of reads in blacklist regions,False,,,,ScATAC-seqLevel3 +MACS2 Start,MACS2 Start,MACS2Start,Genomic starting position in MACS2,False,,,,ScATAC-seqLevel3 +Object ID,Object ID,ObjectID,TBD,False,,,,ScATAC-seqLevel3 +nFeature RNA,nFeature RNA,NFeatureRNA,Number of genes detected in cell,False,,,,ScATAC-seqLevel3 +Nucleosome Signal,Nucleosome Signal,NucleosomeSignal,"Nucleosome signal score (strength of the nucleosome signal per cell, computed as the ratio of fragments between 147 bp and 294 bp (mononucleosome) to fragments < 147 bp (nucleosome-free))",False,,,,ScATAC-seqLevel3 +Passed Filters,Passed Filters,PassedFilters,"Number of non-duplicate, usable read-pairs i.e. fragments",False,,,,ScATAC-seqLevel3 +TSS Percentile,TSS Percentile,TSSPercentile,Percentile rank of TSS score,False,,,,ScATAC-seqLevel3 +LowMapQ,LowMapQ,LowMapQ,Number of read-pairs with <30 mapq on at least one end,False,,,,ScATAC-seqLevel3 +MACS2 Strand,MACS2 Strand,MACS2Strand,DNA stand aligned with in MACS2,False,,,,ScATAC-seqLevel3 +Duplicate Read-Pairs,Duplicate Read-Pairs,DuplicateRead-Pairs,Number of duplicate read-pairs,False,,,,ScATAC-seqLevel3 +MACS2 Neg Log10 pvalue Summit,MACS2 Neg Log10 pvalue Summit,MACS2NegLog10pvalueSummit,Negative log10 p-value for the peak summit in MACS2,False,,,,ScATAC-seqLevel3 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScATAC-seqLevel3 +DNase Sensitive Region Fragments,DNase Sensitive Region Fragments,DNaseSensitiveRegionFragments,Number of fragments overlapping with DNase sensitive regions,False,,,,ScATAC-seqLevel3 +Blacklist Region Fragments,Blacklist Region Fragments,BlacklistRegionFragments,Number of fragments overlapping blacklisted regions,False,,,,ScATAC-seqLevel3 +Unmapped Read-Pairs,Unmapped Read-Pairs,UnmappedRead-Pairs,Number of read-pairs with at least one end not mapped,False,,,,ScATAC-seqLevel3 +Chimeric Read-Pairs,Chimeric Read-Pairs,ChimericRead-Pairs,Number of chimerically mapped read-pairs,False,,,,ScATAC-seqLevel3 +TSS Fragments,TSS Fragments,TSSFragments,Number of fragments overlapping with TSS regions,False,,,,ScATAC-seqLevel3 +Seurat Clusters,Seurat Clusters,SeuratClusters,Clusters of cells by a shared nearest neighbor (SNN) modularity optimization based clustering algorithm,False,,,,ScATAC-seqLevel3 +MACS2 Score,MACS2 Score,MACS2Score,Peak score (proportional to q-value) in MACS2,False,,,,ScATAC-seqLevel3 +Peak Region Cutsites,Peak Region Cutsites,PeakRegionCutsites,Number of ends of fragments in peak regions,False,,,,ScATAC-seqLevel3 +On Target Fragments,On Target Fragments,OnTargetFragments,"Number of fragments overlapping any of TSS, enhancer, promoter and DNase hypersensitivity sites (counted with multiplicity)",False,,,,ScATAC-seqLevel3 +Nucleosome Percentile,Nucleosome Percentile,NucleosomePercentile,Percentile rank of nucleosome score,False,,,,ScATAC-seqLevel3 +Pct Reads in Peaks,Pct Reads in Peaks,PctReadsinPeaks,Percentage of reads in peaks,False,,,,ScATAC-seqLevel3 +HTAN Biospecimen ID,HTAN Biospecimen ID,HTANBiospecimenID,HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScATAC-seqLevel3 +MACS2 End,MACS2 End,MACS2End,Genomic ending position in MACS2,False,,,,ScATAC-seqLevel3 +Peak Region Fragments,Peak Region Fragments,PeakRegionFragments,Number of fragments overlapping peaks,False,,,,ScATAC-seqLevel3 +MACS2 Seqnames,MACS2 Seqnames,MACS2Seqnames,Chromosome id,False,,,,ScATAC-seqLevel3 +MACS2 Relative Summit Position,MACS2 Relative Summit Position,MACS2RelativeSummitPosition,Position of the peak summit related to the start position in MACS2,False,,,,ScATAC-seqLevel3 +nCount Peaks,nCount Peaks,NCountPeaks,TBD,False,,,,ScATAC-seqLevel3 +MACS2 Fold Change,MACS2 Fold Change,MACS2FoldChange,Fold enrichment for this peak summit against random Poisson distribution with local lambda in MACS2,False,,,,ScATAC-seqLevel3 +TSS Enrichment,TSS Enrichment,TSSEnrichment,Transcription start site (TSS) enrichment score,False,,,,ScATAC-seqLevel3 +MACS2 Name,MACS2 Name,MACS2Name,Name of the peak in MACS2,False,,,,ScATAC-seqLevel3 +nFeature Peaks,nFeature Peaks,NFeaturePeaks,TBD,False,,,,ScATAC-seqLevel3 +Mitochondrial Read-Pairs,Mitochondrial Read-Pairs,MitochondrialRead-Pairs,Number of read-pairs mapping to mitochondria and non-nuclear contigs,False,,,,ScATAC-seqLevel3 +Enhancer Region Fragments,Enhancer Region Fragments,EnhancerRegionFragments,Number of fragments overlapping enhancer regions,False,,,,ScATAC-seqLevel3 +nCount RNA,nCount RNA,NCountRNA,Total number of fragments in genes,False,,,,ScATAC-seqLevel3 +MACS2 Width,MACS2 Width,MACS2Width,Width of the peak in bases in MACS2,False,,,,ScATAC-seqLevel3 +Total Read-Pairs,Total Read-Pairs,TotalRead-Pairs,Total read-pairs,False,,,,ScATAC-seqLevel3 +Promoter Region Fragments,Promoter Region Fragments,PromoterRegionFragments,Number of fragments overlapping promoter regions,False,,,,ScATAC-seqLevel3 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScATAC-seqLevel4 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScATAC-seqLevel4 +Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,ScATAC-seqLevel4 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScATAC-seqLevel4 +scATACseq Workflow Type,scATACseq Workflow Type,ScATACseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,,,ScATAC-seqLevel4 +Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,ScATAC-seqLevel4 +File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,ScATAC-seqLevel4 +scATACseq Workflow Parameters Description,scATACseq Workflow Parameters Description,ScATACseqWorkflowParametersDescription,Parameters used to run the scATAC-seq workflow. ,True,,,,ScATAC-seqLevel4 +Filename,Filename,filename,Name of a file ,True,,,,ScATAC-seqLevel4 +Imaging Assay Type,Imaging Assay Type,ImagingAssayType,Type of imaging assay,True,,"['CyCIF', 't-CyCIF', 'MxIF', 'MERFISH', 'IHC', 'MIBI', 'H&E', 'Not Applicable', 'GeoMX-DSP', 'IMC', 'CODEX', 'SABER', 'ExSeq', 'mIHC']",,ImagingLevel1 +Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ImagingLevel1 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ImagingLevel1 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ImagingLevel1 +Pre-processing Completed,Pre-processing Completed,Pre-processingCompleted,Pre-processing steps completed to convert level 1 raw data to a single level 2 image,True,,"['None', 'Illumination correction', 'Channel/Cycle Registration', 'Other', 'Tile Stitching', 'TMA de-arraying']",,ImagingLevel1 +Comment,Comment,Comment,Free text field (generally for QC comment),False,,,,ImagingLevel1 +Pre-processing Required,Pre-processing Required,Pre-processingRequired,Pre-processing steps required to convert level 1 raw data to a single level 2 image,True,,"['None', 'Illumination correction', 'Channel/Cycle Registration', 'Other', 'Tile Stitching', 'TMA de-arraying']",,ImagingLevel1 +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ImagingLevel1 +Commit SHA,Commit SHA,CommitSHA,"Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]",False,,,,ImagingLevel1 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel1 +File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,ImagingLevel1 +Filename,Filename,filename,Name of a file ,True,,,,ImagingLevel1 +WorkingDistance,WorkingDistance,WorkingDistance,"The working distance of the lens, expressed as a floating point number. Floating point > 0.",False,,,,ImagingLevel2 +Imaging Assay Type,Imaging Assay Type,ImagingAssayType,Type of imaging assay,True,,"['CyCIF', 't-CyCIF', 'MxIF', 'MERFISH', 'IHC', 'MIBI', 'H&E', 'Not Applicable', 'GeoMX-DSP', 'IMC', 'CODEX', 'SABER', 'ExSeq', 'mIHC']",,ImagingLevel2 +FOVX,FOVX,FOVX,Field of view X dimension. Floating point,False,,,,ImagingLevel2 +Image ID,Image ID,ImageID,"Unique internal image identifier. eg ""Image:0"". (To be extracted from OME-XML)",True,,,,ImagingLevel2 +PhysicalSizeZUnit,PhysicalSizeZUnit,PhysicalSizeZUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),True,,"['Å', 'cm', 'nm', 'mm', 'µm']",,ImagingLevel2 +PhysicalSizeYUnit,PhysicalSizeYUnit,PhysicalSizeYUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),True,,"['Å', 'cm', 'nm', 'mm', 'µm']",,ImagingLevel2 +PlaneCount,PlaneCount,PlaneCount,"Number of Z-planes (not to be confused with downsampled ""pyramid""). Integer >=1",True,,,,ImagingLevel2 +FOVYUnit,FOVYUnit,FOVYUnit,Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['Å', 'cm', 'nm', 'mm', 'µm', '']",,ImagingLevel2 +Frame Averaging,Frame Averaging,FrameAveraging,"Number of frames averaged together (if no averaging, set to 1). Integer >= 1",False,,,,ImagingLevel2 +Tseries,Tseries,Tseries,Does data file contain a time-series of images,True,,"['No', 'Yes']",,ImagingLevel2 +Objective,Objective,Objective,Objective,False,,,,ImagingLevel2 +File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,ImagingLevel2 +FOV number,FOV number,FOVnumber,Index of FOV (as it pertains to its sequence order). Integer >= 1,False,,,,ImagingLevel2 +Pixels BigEndian,Pixels BigEndian,PixelsBigEndian,Boolean (True/False),True,,"['False', 'True']",,ImagingLevel2 +FOVY,FOVY,FOVY,Field of view Y dimension. Floating point value,False,,,,ImagingLevel2 +SizeC,SizeC,SizeC,Number of channels. Integer >= 1,True,,,,ImagingLevel2 +PhysicalSizeX,PhysicalSizeX,PhysicalSizeX,Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.,True,,,,ImagingLevel2 +SizeY,SizeY,SizeY,Size of image: Y dimension (in pixels). Integer >= 1,True,,,,ImagingLevel2 +SizeT,SizeT,SizeT,Number of time points. Integer >= 1,True,,,,ImagingLevel2 +LensNA,LensNA,LensNA,The numerical aperture of the lens. Floating point value > 0.,False,,,,ImagingLevel2 +Comment,Comment,Comment,Free text field (generally for QC comment),False,,,,ImagingLevel2 +Microscope,Microscope,Microscope,"Microscope type (manufacturer, model, etc) used for this experiment",True,,,,ImagingLevel2 +WorkingDistanceUnit,WorkingDistanceUnit,WorkingDistanceUnit,The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['Å', 'cm', 'nm', 'mm', 'µm', '']",,ImagingLevel2 +Immersion,Immersion,Immersion,Immersion medium,False,,"['Air', 'Water', 'Other', 'Oil', '']",,ImagingLevel2 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel2 +Zstack,Zstack,Zstack,Does data file contain a Z-stack of images,True,,"['No', 'Yes']",,ImagingLevel2 +NominalMagnification,NominalMagnification,NominalMagnification,The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units),True,,,,ImagingLevel2 +Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ImagingLevel2 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ImagingLevel2 +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ImagingLevel2 +PixelType,PixelType,PixelType,"Data type for each pixel value. E.g. ""uint16""",True,,"['double', 'uint32', 'uint16', 'int16', 'float', 'int8', 'int32', 'uint8', 'bit']",,ImagingLevel2 +Channel Metadata Filename,Channel Metadata Filename,ChannelMetadataFilename,Full path within Synapse project of uploaded companion CSV file containing channel-level metadata details,True,,,,ImagingLevel2 +PhysicalSizeXUnit,PhysicalSizeXUnit,PhysicalSizeXUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['Å', 'cm', 'nm', 'mm', 'µm', '']",,ImagingLevel2 +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,ImagingLevel2 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ImagingLevel2 +FOVXUnit,FOVXUnit,FOVXUnit,Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['Å', 'cm', 'nm', 'mm', 'µm', '']",,ImagingLevel2 +DimensionOrder,DimensionOrder,DimensionOrder,The order in which the individual planes of data are interleaved.,True,,"['ZYX', 'XYCZT', 'XYTZC', 'XYZTC', 'XYZCT', 'XYCTZ']",,ImagingLevel2 +SizeX,SizeX,SizeX,Size of image: X dimension (in pixels). Integer >= 1,True,,,,ImagingLevel2 +SizeZ,SizeZ,SizeZ,Size of image: Z dimension (in pixels). Integer >= 1,True,,,,ImagingLevel2 +Passed QC,Passed QC,PassedQC,Did all channels pass QC (if not add free text Comment),True,,"['No - Channels QC', 'Yes']",,ImagingLevel2 +PhysicalSizeY,PhysicalSizeY,PhysicalSizeY,Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.,True,,,,ImagingLevel2 +Pyramid,Pyramid,Pyramid,Does data file contain pyramid of images,True,,"['No', 'Yes']",,ImagingLevel2 +PhysicalSizeZ,PhysicalSizeZ,PhysicalSizeZ,Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.,True,,,,ImagingLevel2 +Filename,Filename,filename,Name of a file ,True,,,,ImagingLevel2 +Parameter file,Parameter file,Parameterfile,Path in Syanpse to a text file listing algorithm version numbers and relevant parameters needed to reproduce the analysis,False,,,,ImagingLevel3Segmentation +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ImagingLevel3Segmentation +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ImagingLevel3Segmentation +Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ImagingLevel3Segmentation +Commit SHA,Commit SHA,CommitSHA,"Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]",False,,,,ImagingLevel3Segmentation +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel3Segmentation +Imaging Object Class,Imaging Object Class,ImagingObjectClass,Defines the structure that the mask delineates,True,,"['plasma membrane', 'cytoplasm', 'nucleus', 'Imaging Object Class Other', 'whole cell']",,ImagingLevel3Segmentation +Number of Objects,Number of Objects,NumberofObjects, The number of objects (eg cells) described,True,,,,ImagingLevel3Segmentation +File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,ImagingLevel3Segmentation +Filename,Filename,filename,Name of a file ,True,,,,ImagingLevel3Segmentation +Imaging Segmentation Data Type,Imaging Segmentation Data Type,ImagingSegmentationDataType,Specifies how the segmentation is stored,True,,"['Point', 'Polygon', 'Mask', 'Probability Map', 'Outline']",,ImagingLevel3Segmentation +Imaging Object Class Description,Imaging Object Class Description,ImagingObjectClassDescription,Free text description of object class [string],False,True,," If Imaging Object Class is ""Imaging Object Class Other"" then ""Imaging Object Class Description"" is required",ImagingLevel3Segmentation +WorkingDistance,WorkingDistance,WorkingDistance,"The working distance of the lens, expressed as a floating point number. Floating point > 0.",False,,,,ImagingLevel3Image +Imaging Assay Type,Imaging Assay Type,ImagingAssayType,Type of imaging assay,True,,"['CyCIF', 't-CyCIF', 'MxIF', 'MERFISH', 'IHC', 'MIBI', 'H&E', 'Not Applicable', 'GeoMX-DSP', 'IMC', 'CODEX', 'SABER', 'ExSeq', 'mIHC']",,ImagingLevel3Image +FOVX,FOVX,FOVX,Field of view X dimension. Floating point,False,,,,ImagingLevel3Image +Frame Averaging,Frame Averaging,FrameAveraging,"Number of frames averaged together (if no averaging, set to 1). Integer >= 1",False,,,,ImagingLevel3Image +Tseries,Tseries,Tseries,Does data file contain a time-series of images,True,,"['No', 'Yes']",,ImagingLevel3Image +Objective,Objective,Objective,Objective,False,,,,ImagingLevel3Image +File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,ImagingLevel3Image +FOV number,FOV number,FOVnumber,Index of FOV (as it pertains to its sequence order). Integer >= 1,False,,,,ImagingLevel3Image +FOVY,FOVY,FOVY,Field of view Y dimension. Floating point value,False,,,,ImagingLevel3Image +HTAN Parent Channel Metadata ID,HTAN Parent Channel Metadata ID,HTANParentChannelMetadataID,TBD,False,,,,ImagingLevel3Image +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ImagingLevel3Image +LensNA,LensNA,LensNA,The numerical aperture of the lens. Floating point value > 0.,False,,,,ImagingLevel3Image +Comment,Comment,Comment,Free text field (generally for QC comment),False,,,,ImagingLevel3Image +Microscope,Microscope,Microscope,"Microscope type (manufacturer, model, etc) used for this experiment",True,,,,ImagingLevel3Image +Immersion,Immersion,Immersion,Immersion medium,False,,"['Air', 'Water', 'Other', 'Oil', '']",,ImagingLevel3Image +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel3Image +Zstack,Zstack,Zstack,Does data file contain a Z-stack of images,True,,"['No', 'Yes']",,ImagingLevel3Image +NominalMagnification,NominalMagnification,NominalMagnification,The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units),True,,,,ImagingLevel3Image +Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ImagingLevel3Image +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ImagingLevel3Image +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ImagingLevel3Image +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ImagingLevel3Image +Passed QC,Passed QC,PassedQC,Did all channels pass QC (if not add free text Comment),True,,"['No - Channels QC', 'Yes']",,ImagingLevel3Image +Pyramid,Pyramid,Pyramid,Does data file contain pyramid of images,True,,"['No', 'Yes']",,ImagingLevel3Image +Filename,Filename,filename,Name of a file ,True,,,,ImagingLevel3Image +WorkingDistanceUnit,WorkingDistanceUnit,WorkingDistanceUnit,The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['Å', 'cm', 'nm', 'mm', 'µm', '']",,ImagingLevel3Image +FOVXUnit,FOVXUnit,FOVXUnit,Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['Å', 'cm', 'nm', 'mm', 'µm', '']",,ImagingLevel3Image +FOVYUnit,FOVYUnit,FOVYUnit,Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['Å', 'cm', 'nm', 'mm', 'µm', '']",,ImagingLevel3Image +Lot,Lot,Lot,Lot number from vendor,False,,,,ImagingLevel3Channels +Fluorophore,Fluorophore,Fluorophore,Fluorescent dye label (eg Alexa Fluor 488),False,,,,ImagingLevel3Channels +Catalog Number,Catalog Number,CatalogNumber,Catalog Number,False,,,,ImagingLevel3Channels +Metal Isotope Element,Metal Isotope Element,MetalIsotopeElement,Element abbreviation. eg “La” or “Nd”,False,,"['Rh', 'Pd', 'Fe', 'Nd', 'Sb', 'Zn', 'Ca', 'Ga', 'Au', 'B', 'Ti', 'Sr', 'Pm', 'Nb', 'Mt', 'Ge', 'Pr', 'Ce', 'Cd', 'Hf', 'Cu', 'Fr', 'In', 'Cr', 'H', 'Ar', 'Th', 'Rg', 'Ts', 'Pt', 'md', 'Lv', 'P', 'Li', 'Be', 'Cn', 'Eu', 'Nh', 'I', 'Y', 'Fm', 'Fl', 'Os', 'Ir', 'N', 'Db', 'Si', 'U', 'S', 'Mo', 'Dy', 'Cf', 'At', 'Tl', 'Ru', 'Sn', 'Yb', 'Se', 'Te', 'Mg', 'Ba', 'Ho', 'Hg', 'Pu', 'K', 'Xe', 'Lr', 'Ag', 'Zr', 'Ra', 'Kr', 'Re', 'Al', 'No', 'Bh', 'Er', 'Cs', 'Sm', 'Mc', 'Ni', 'Br', 'F', 'V', 'Rf', 'Pb', 'Gd', 'Na', 'Sc', 'He', 'La', 'W', 'O', 'Tb', 'As', 'Np', 'Co', 'Rb', 'Bi', 'Ac', 'Cl', 'am', 'Bk', 'Og', 'Mn', 'Po', 'Tm', 'Pa', 'Sg', 'Tc', 'Ne', 'Rn', 'Lu', 'Hs', 'Es', 'C', 'Ta', 'Ds', '']",,ImagingLevel3Channels +Cycle Number,Cycle Number,CycleNumber,The cycle # in which the co-listed reagent(s) was(were) used. Integer >= 1 (up to number of cycles),False,,,,ImagingLevel3Channels +Concentration,Concentration,Concentration,Concentration (eg 10ug/mL),False,,,,ImagingLevel3Channels +Channel Name,Channel Name,ChannelName,This must match the corresponding field in the OME-XML / TIFF header. (eg 'Blue' or 'CD45' or “E-cadherin”),True,,,,ImagingLevel3Channels +Clone,Clone,Clone,Clone,False,,,,ImagingLevel3Channels +Emission Bandwidth,Emission Bandwidth,EmissionBandwidth,Nominal width of emission spectrum (nm),False,,,,ImagingLevel3Channels +Vendor,Vendor,Vendor,Vendor,False,,,,ImagingLevel3Channels +Excitation Bandwidth,Excitation Bandwidth,ExcitationBandwidth,Nominal width of excitation spectrum (nm),False,,,,ImagingLevel3Channels +Channel Passed QC,Channel Passed QC,ChannelPassedQC,Identify stains that did not pass QC but are included in the dataset.,True,,"['No - Channel Failed QC', 'Yes']",,ImagingLevel3Channels +Dilution,Dilution,Dilution,Dilution (eg 1:1000),False,,,,ImagingLevel3Channels +Channel ID,Channel ID,ChannelID,This must match the corresponding field in the OME-XML / TIFF header. (eg 'Channel:0:1'),True,,,,ImagingLevel3Channels +Target Name,Target Name,TargetName,Short descriptive name (abbreviation) for this target (antigen),True,,,,ImagingLevel3Channels +Oligo Barcode Upper Strand,Oligo Barcode Upper Strand,OligoBarcodeUpperStrand,Oligo Barcode - Upper Strand,False,,,,ImagingLevel3Channels +Antibody Name,Antibody Name,AntibodyName,"Antibody Name (free text (eg “Keratin”, “CD163”, “DNA”))",True,,,,ImagingLevel3Channels +Emission Wavelength,Emission Wavelength,EmissionWavelength,Center/peak of the emission spectrum (nm),False,,,,ImagingLevel3Channels +Antibody Role,Antibody Role,AntibodyRole," ""Is this antibody acting as a primary or secondary antibody""",True,,"['secondary', 'primary']",,ImagingLevel3Channels +Oligo Barcode Lower Strand,Oligo Barcode Lower Strand,OligoBarcodeLowerStrand,Oligo Barcode - Lower Strand,False,,,,ImagingLevel3Channels +RRID identifier,RRID identifier,RRIDidentifier,Research Resource Identifier (eg “RRID: AB_394606”),True,,,,ImagingLevel3Channels +Excitation Wavelength,Excitation Wavelength,ExcitationWavelength,Center/peak of the excitation spectrum (nm),False,,,,ImagingLevel3Channels +HTAN Channel Metadata ID,HTAN Channel Metadata ID,HTANChannelMetadataID,HTAN ID for this channel metadata table (same for all rows),True,,,,ImagingLevel3Channels +Metal Isotope Mass,Metal Isotope Mass,MetalIsotopeMass,Element mass number,False,,,,ImagingLevel3Channels +Sub Cycle Number,Sub Cycle Number,SubCycleNumber,Sub cycle number,False,,,,ImagingLevel3Channels +Channel QC Faliure Type,Channel QC Faliure Type,ChannelQCFaliureType,TBD,False,True,," If Channel Passed QC is ""No - Channel Failed QC"" then ""Channel QC Faliure Type"" is required",ImagingLevel3Channels +Parameter file,Parameter file,Parameterfile,Path in Syanpse to a text file listing algorithm version numbers and relevant parameters needed to reproduce the analysis,False,,,,ImagingLevel4 +HTAN Parent Channel Metadata ID,HTAN Parent Channel Metadata ID,HTANParentChannelMetadataID,TBD,False,,,,ImagingLevel4 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ImagingLevel4 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ImagingLevel4 +Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ImagingLevel4 +Number of Features,Number of Features,NumberofFeatures, The number of features (eg channels) described,True,,,,ImagingLevel4 +Commit SHA,Commit SHA,CommitSHA,"Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]",False,,,,ImagingLevel4 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel4 +Imaging Object Class,Imaging Object Class,ImagingObjectClass,Defines the structure that the mask delineates,True,,"['plasma membrane', 'cytoplasm', 'nucleus', 'Imaging Object Class Other', 'whole cell']",,ImagingLevel4 +Number of Objects,Number of Objects,NumberofObjects, The number of objects (eg cells) described,True,,,,ImagingLevel4 +File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,ImagingLevel4 +Imaging Summary Statistic,Imaging Summary Statistic,ImagingSummaryStatistic, Function used to summarize object/feature intensity,False,,"['Median', 'Mean', 'Not Specified', '']",,ImagingLevel4 +Filename,Filename,filename,Name of a file ,True,,,,ImagingLevel4 +Imaging Object Class Description,Imaging Object Class Description,ImagingObjectClassDescription,Free text description of object class [string],False,True,," If Imaging Object Class is ""Imaging Object Class Other"" then ""Imaging Object Class Description"" is required",ImagingLevel4 +Imaging Assay Type,Imaging Assay Type,ImagingAssayType,Type of imaging assay,True,,"['CyCIF', 't-CyCIF', 'MxIF', 'MERFISH', 'IHC', 'MIBI', 'H&E', 'Not Applicable', 'GeoMX-DSP', 'IMC', 'CODEX', 'SABER', 'ExSeq', 'mIHC']",,SRRSImagingLevel2 +Image ID,Image ID,ImageID,"Unique internal image identifier. eg ""Image:0"". (To be extracted from OME-XML)",True,,,,SRRSImagingLevel2 +PhysicalSizeYUnit,PhysicalSizeYUnit,PhysicalSizeYUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),True,,"['Å', 'cm', 'nm', 'mm', 'µm']",,SRRSImagingLevel2 +PlaneCount,PlaneCount,PlaneCount,"Number of Z-planes (not to be confused with downsampled ""pyramid""). Integer >=1",True,,,,SRRSImagingLevel2 +Frame Averaging,Frame Averaging,FrameAveraging,"Number of frames averaged together (if no averaging, set to 1). Integer >= 1",False,,,,SRRSImagingLevel2 +Tseries,Tseries,Tseries,Does data file contain a time-series of images,True,,"['No', 'Yes']",,SRRSImagingLevel2 +Objective,Objective,Objective,Objective,False,,,,SRRSImagingLevel2 +File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,SRRSImagingLevel2 +Pixels BigEndian,Pixels BigEndian,PixelsBigEndian,Boolean (True/False),True,,"['False', 'True']",,SRRSImagingLevel2 +SizeC,SizeC,SizeC,Number of channels. Integer >= 1,True,,,,SRRSImagingLevel2 +PhysicalSizeX,PhysicalSizeX,PhysicalSizeX,Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.,True,,,,SRRSImagingLevel2 +SizeY,SizeY,SizeY,Size of image: Y dimension (in pixels). Integer >= 1,True,,,,SRRSImagingLevel2 +SizeT,SizeT,SizeT,Number of time points. Integer >= 1,True,,,,SRRSImagingLevel2 +Microscope,Microscope,Microscope,"Microscope type (manufacturer, model, etc) used for this experiment",True,,,,SRRSImagingLevel2 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,SRRSImagingLevel2 +Zstack,Zstack,Zstack,Does data file contain a Z-stack of images,True,,"['No', 'Yes']",,SRRSImagingLevel2 +NominalMagnification,NominalMagnification,NominalMagnification,The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units),True,,,,SRRSImagingLevel2 +Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,SRRSImagingLevel2 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,SRRSImagingLevel2 +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,SRRSImagingLevel2 +PixelType,PixelType,PixelType,"Data type for each pixel value. E.g. ""uint16""",True,,"['double', 'uint32', 'uint16', 'int16', 'float', 'int8', 'int32', 'uint8', 'bit']",,SRRSImagingLevel2 +Channel Metadata Filename,Channel Metadata Filename,ChannelMetadataFilename,Full path within Synapse project of uploaded companion CSV file containing channel-level metadata details,True,,,,SRRSImagingLevel2 +PhysicalSizeXUnit,PhysicalSizeXUnit,PhysicalSizeXUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['Å', 'cm', 'nm', 'mm', 'µm', '']",,SRRSImagingLevel2 +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,SRRSImagingLevel2 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,SRRSImagingLevel2 +DimensionOrder,DimensionOrder,DimensionOrder,The order in which the individual planes of data are interleaved.,True,,"['ZYX', 'XYCZT', 'XYTZC', 'XYZTC', 'XYZCT', 'XYCTZ']",,SRRSImagingLevel2 +SizeX,SizeX,SizeX,Size of image: X dimension (in pixels). Integer >= 1,True,,,,SRRSImagingLevel2 +SizeZ,SizeZ,SizeZ,Size of image: Z dimension (in pixels). Integer >= 1,True,,,,SRRSImagingLevel2 +Passed QC,Passed QC,PassedQC,Did all channels pass QC (if not add free text Comment),True,,"['No - Channels QC', 'Yes']",,SRRSImagingLevel2 +PhysicalSizeY,PhysicalSizeY,PhysicalSizeY,Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.,True,,,,SRRSImagingLevel2 +Pyramid,Pyramid,Pyramid,Does data file contain pyramid of images,True,,"['No', 'Yes']",,SRRSImagingLevel2 +Filename,Filename,filename,Name of a file ,True,,,,SRRSImagingLevel2 +Comment,Comment,Comment,Free text field (generally for QC comment),False,True,," If Passed QC is ""No - Channels QC"" then ""Comment"" is required",SRRSImagingLevel2 +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,RPPALevel2 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,RPPALevel2 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,RPPALevel2 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,RPPALevel2 +Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,RPPALevel2 +HTAN RPPA Antibody Table,HTAN RPPA Antibody Table,HTANRPPAAntibodyTable,A table containing antibody level metadata for RPPA,False,,,,RPPALevel2 +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,RPPALevel2 +File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",False,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf', '']",,RPPALevel2 +Assay Type,Assay Type,AssayType,"The type and level of assay this metadata applies to (e.g. RPPA, Nanostring DSP, etc.)",True,,,,RPPALevel2 +Filename,Filename,filename,Name of a file ,False,,,,RPPALevel2 +Phosphoprotein Flag,Phosphoprotein Flag,PhosphoproteinFlag,A flag the denotes if an antibody targets a phosphoprotein.,False,,"['False', 'True', '']",,RPPALevel2 +RPPA Validation Status,RPPA Validation Status,RPPAValidationStatus,Valid = RPPA and WB correlation > 0.7; Use with Caution = RPPA and WB correlation < 0.7; Under Evaluation = Antibody has given mixed results and/or evaluated by another lab; We are in the process of (re)validating; Used for QC = These antibodies are used for tissue sample quality control (QC),False,,"['Under Evaluation', 'Used for QC', 'Valid', 'Use with Caution', '']",,RPPALevel2 +GENCODE Gene Symbol Target,GENCODE Gene Symbol Target,GENCODEGeneSymbolTarget,The comma separated list of gene symbols targeted by the antibody.,False,,,,RPPALevel2 +UNIPROT Protein ID Target,UNIPROT Protein ID Target,UNIPROTProteinIDTarget,TBD,False,,,,RPPALevel2 +Catalog Number,Catalog Number,CatalogNumber,Catalog Number,False,,,,RPPALevel2 +Species,Species,Species,Host animal.,False,,"['Mouse', 'Goat', 'Rabbit', '']",,RPPALevel2 +Clone,Clone,Clone,Clone,False,,,,RPPALevel2 +HTAN RPPA Antibody Table ID,HTAN RPPA Antibody Table ID,HTANRPPAAntibodyTableID,HTAN identifier associated with RPPA antibody level metadata. Identical for every row of the table.,False,,,,RPPALevel2 +Ab Name Reported on Dataset,Ab Name Reported on Dataset,AbNameReportedonDataset,The antibody name.,False,,,,RPPALevel2 +Phospho Site,Phospho Site,PhosphoSite,The protein site for a phosphoprotein targeting antibody. Report AA and site (i.e. S442),False,,,,RPPALevel2 +Internal Ab ID,Internal Ab ID,InternalAbID,TBD,False,,,,RPPALevel2 +RPPA Dilution,RPPA Dilution,RPPADilution,The dilution ratio.,False,,,,RPPALevel2 +Clonality,Clonality,Clonality,The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Clonal', 'Non-clonal', '']",,RPPALevel2 +Vendor,Vendor,Vendor,Vendor,False,,,,RPPALevel2 +Notes,Notes,Notes,TBD,False,,,,RPPALevel2 +Phosphoprotein Flag,Phosphoprotein Flag,PhosphoproteinFlag,A flag the denotes if an antibody targets a phosphoprotein.,True,,"['False', 'True']",,HTANRPPAAntibodyTable +RPPA Validation Status,RPPA Validation Status,RPPAValidationStatus,Valid = RPPA and WB correlation > 0.7; Use with Caution = RPPA and WB correlation < 0.7; Under Evaluation = Antibody has given mixed results and/or evaluated by another lab; We are in the process of (re)validating; Used for QC = These antibodies are used for tissue sample quality control (QC),False,,"['Under Evaluation', 'Used for QC', 'Valid', 'Use with Caution', '']",,HTANRPPAAntibodyTable +GENCODE Gene Symbol Target,GENCODE Gene Symbol Target,GENCODEGeneSymbolTarget,The comma separated list of gene symbols targeted by the antibody.,True,,,,HTANRPPAAntibodyTable +UNIPROT Protein ID Target,UNIPROT Protein ID Target,UNIPROTProteinIDTarget,TBD,False,,,,HTANRPPAAntibodyTable +Catalog Number,Catalog Number,CatalogNumber,Catalog Number,False,,,,HTANRPPAAntibodyTable +Species,Species,Species,Host animal.,True,,"['Mouse', 'Goat', 'Rabbit']",,HTANRPPAAntibodyTable +Clone,Clone,Clone,Clone,False,,,,HTANRPPAAntibodyTable +HTAN RPPA Antibody Table ID,HTAN RPPA Antibody Table ID,HTANRPPAAntibodyTableID,HTAN identifier associated with RPPA antibody level metadata. Identical for every row of the table.,True,,,,HTANRPPAAntibodyTable +Ab Name Reported on Dataset,Ab Name Reported on Dataset,AbNameReportedonDataset,The antibody name.,True,,,,HTANRPPAAntibodyTable +Phospho Site,Phospho Site,PhosphoSite,The protein site for a phosphoprotein targeting antibody. Report AA and site (i.e. S442),False,,,,HTANRPPAAntibodyTable +Internal Ab ID,Internal Ab ID,InternalAbID,TBD,False,,,,HTANRPPAAntibodyTable +RPPA Dilution,RPPA Dilution,RPPADilution,The dilution ratio.,False,,,,HTANRPPAAntibodyTable +Clonality,Clonality,Clonality,The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Clonal', 'Non-clonal', '']",,HTANRPPAAntibodyTable +Vendor,Vendor,Vendor,Vendor,False,,,,HTANRPPAAntibodyTable +Notes,Notes,Notes,TBD,False,,,,HTANRPPAAntibodyTable +File Format,File Format,fileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['bedgraph', 'tiff', 'sif', 'msf', 'xml', 'Sentrix descriptor file', 'doc', 'seg', 'tif', '7z', 'maf', 'bcf', 'wiggle', 'vcf', 'mtx', 'bpm', 'dat', 'hdf5', 'chp', 'bgzip', 'locs', 'czi', 'tar', 'OME-TIFF', 'abf', 'fastq', 'bed narrowPeak', 'tagAlign', 'recal', 'scn', 'md', 'sav', 'hic', 'Python script', 'powerpoint', 'jpg', 'zip', 'tsv', 'svg', 'cloupe', 'json', 'pzfx', 'hyperlink', 'bed gappedPeak', 'gtf', 'sra', 'gct', 'ab1', 'html', 'gff3', 'sdf', 'excel', 'RData', 'mpg', 'fasta', 'mex', 'flagstat', 'sqlite', 'fig', 'dup', 'png', 'R script', 'plink', 'tranches', 'raw', 'cel', 'avi', 'csv', 'bed', 'idx', 'gzip', 'mov', 'mzML', 'idat', 'm', 'am', 'bai', 'svs', 'txt', 'DICOM', 'bam', 'rmd', 'sam', 'bed broadPeak', 'cell am', 'bigwig', 'pdf']",,HTANRPPAAntibodyTable +Filename,Filename,filename,Name of a file ,True,,,,HTANRPPAAntibodyTable diff --git a/files/Merged/mc2_rfc_test_8.30.24.csv b/files/Merged/mc2_rfc_test_8.30.24.csv deleted file mode 100644 index e166d1e..0000000 --- a/files/Merged/mc2_rfc_test_8.30.24.csv +++ /dev/null @@ -1,152 +0,0 @@ -,Attribute,Label,Description,Required,Valid Values,Component -Survival Outcome,Survival Outcome,SurvivalOutcome,Text term that describes the last known status of an individual.,False,"['Distant met recurrence/progression', 'unknown tumor status', 'Tumor free', 'Deceased', 'With tumor', 'Loco-regional recurrence/progression', 'Not Applicable', 'Not Reported', 'Not Allowed To Collect', 'Biochemical evidence of disease without structural correlate', '']",Biospecimen -Tumor Grade,Tumor Grade,TumorGrade,"Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.",False,"['G2', 'G4', 'unknown', 'G1', 'Intermediate Grade', 'G3', 'Not Applicable', 'High Grade', 'GB', 'Not Reported', 'GX', 'Low Grade', '']",Biospecimen -Biospecimen Tumor Type,Biospecimen Tumor Type,BiospecimenTumorType,"The type of tumor associated with the specimen. Multiple values permitted, comma separated.",False,"['Non-Functioning Pituitary Gland Adenoma', 'Soft Tissue Sarcoma', 'Myeloproliferative Neoplasm', 'Ewing Sarcoma', 'High Grade Ovarian Serous Adenocarcinoma', 'Histiocytic Sarcoma', 'Central Nervous System Neoplasm', 'Myeloid Leukemia', 'Uveal Neoplasm', 'Atypical Teratoid/Rhabdoid Tumor', 'T-Cell Lymphoma', 'Meningioma', 'Sinonasal Squamous Cell Carcinoma', 'Leiomyoma', 'Cerebellar Neoplasm', 'Neurofibroma', 'Cervical Small Cell Carcinoma', 'Castration-Resistant Prostate Carcinoma', 'Pan-cancer', 'Medulloblastoma', 'Rhabdomyosarcoma', 'Pituitary Gland Adenoma', 'Pancreatic Adenocarcinoma', 'Lung Small Cell Carcinoma', 'Schwannoma', 'Combined Hepatocellular Carcinoma and Cholangiocarcinoma', 'Invasive Ductal Breast Carcinoma', 'T Acute Lymphoblastic Leukemia', 'Malignant Skin Neoplasm', 'Acute Myeloid Leukemia', 'Thyroid Gland Anaplastic Carcinoma', 'Lymphoma', 'Breast Adenocarcinoma', 'Colorectal Adenocarcinoma', 'Pending Annotation', 'Leukemia', 'Rosette-Forming Glioneuronal Tumor', 'Dysembryoplastic Neuroepithelial Neoplasm', 'Multiple Myeloma', 'Breast Carcinoma', 'Malignant Ovarian Neoplasm', 'Glioblastoma', 'Skin Carcinoma', 'Skin Neoplasm', 'Pancreatic Neuroendocrine Carcinoma', 'Lung Neoplasm', 'Plasmacytoma', 'Lung Adenocarcinoma', 'Testicular Embryonal Carcinoma', 'Non-Hodgkin Lymphoma', 'Biliary Tract Carcinoma', 'Acute Monocytic Leukemia', 'Follicular Lymphoma', 'Precursor B-cell lymphoblastic leukemia', 'Not Applicable', 'Urothelial Carcinoma', 'Ovarian Neoplasm', 'Primary Myelofibrosis', 'Synovial Sarcoma', 'Neuroendocrine Neoplasm', 'Uterine Adenosarcoma', 'Plexiform Neurofibroma', 'Head and Neck Carcinoma', 'Cervical Neoplasm', 'Bone Neoplasm', 'Chronic Myeloid Leukemia', 'Liver and Intrahepatic Bile Duct Carcinoma', 'Intrahepatic Cholangiocarcinoma', 'Choriocarcinoma', 'Central Nervous System Cavernous Hemangioma', 'B-Cell Non-Hodgkin Lymphoma', 'Primary Central Nervous System Lymphoma', 'Prostate Carcinoma', 'Breast Neoplasm', 'Fibrosarcoma', 'Cholangiocarcinoma', 'Mesothelioma', 'Hodgkin Lymphoma', 'Renal Cell Carcinoma', 'Gastric Neoplasm', 'Triple-Negative Breast Carcinoma', 'Intestinal Neoplasm', 'Colorectal Carcinoma', 'Lung Squamous Cell Carcinoma', 'Malignant Peripheral Nerve Sheath Tumor', 'Pancreatic Carcinoma', 'Uveal Melanoma', 'Gastrointestinal Stromal Neoplasm', 'Cutaneous Melanoma', 'Head and Neck Squamous Cell Carcinoma', 'Barrett Esophagus', 'Ovarian Adenosarcoma', 'Angiosarcoma', 'Malignant Digestive System Neoplasm', 'Acinar Cell Carcinoma', 'B Acute Lymphoblastic Leukemia', 'Craniopharyngioma', 'Gallbladder Carcinoma', 'Pheochromocytoma', 'Malignant Peritoneal Neoplasm', 'Sarcoma', 'Serous Tubal Intraepithelial Carcinoma', 'Chronic Lymphocytic Leukemia', 'Cutaneous T Cell Lymphoma', 'Acute Lymphoblastic Leukemia', 'Esophageal Adenocarcinoma', 'Colorectal Neoplasm', 'Fibroepithelial Polyp', 'Glioma', 'Esophageal Squamous Cell Carcinoma', 'Carcinoma In Situ', 'Low Grade Glioma', 'Myoepithelioma', 'Malignant Glioma', 'Malignant Neoplasm', 'Esophageal Carcinoma', 'Retinoblastoma', 'Chondroblastoma', 'Plasmablastic Lymphoma', 'Hepatocellular Carcinoma', 'Cervical Carcinoma', 'Rectal Adenocarcinoma', 'Colorectal Adenoma', 'Bladder Neoplasm', 'Gastric Carcinoma', 'Pancreatic Ductal Adenocarcinoma', 'Plexiform Schwannoma', 'Luminal A Breast Carcinoma', 'Ductal Breast Carcinoma In Situ', 'Mantle Cell Lymphoma', 'Thyroid Gland Noninvasive Follicular Neoplasm with Papillary-Like Nuclear Features', 'Giant Cell Tumor', 'Basal Cell Neoplasm', 'Kaposi Sarcoma', 'Bladder Carcinoma', 'Teratoma', 'Carcinoma', 'Cellular Schwannoma', 'Ovarian Carcinoma', 'Endometrial Neoplasm', 'Prostate Adenocarcinoma', 'Astrocytoma', 'Oral Cavity Squamous Cell Carcinoma', 'Malignant Genitourinary System Neoplasm', 'Ovarian Serous Adenocarcinoma', 'Penile Carcinoma', 'Gastroesophageal Adenocarcinoma', 'Squamous Cell Carcinoma', 'Liver and Intrahepatic Bile Duct Neoplasm', 'Thyroid Gland Carcinoma', 'Lymphoid Leukemia', 'Extraventricular Neurocytoma', 'Neuroblastoma', 'Lung Non-Small Cell Carcinoma', 'Diffuse Large B-Cell Lymphoma', 'Nasopharyngeal Carcinoma', 'Myeloid Neoplasm', 'Acute Promyelocytic Leukemia', 'Clear Cell Renal Cell Carcinoma', 'Oral Cavity Neoplasm', 'Lung Carcinoma', 'Osteosarcoma', 'Colon Carcinoma', 'Malignant Brain Neoplasm', 'Adenocarcinoma', 'Brain Neoplasm', 'Prostate Neoplasm', 'Ependymoma', 'Fibrolamellar Carcinoma', 'Pilocytic Astrocytoma', 'Mycosis Fungoides', 'Colon Adenocarcinoma', 'Vascular Neoplasm', 'Basal-Like Breast Carcinoma', 'Gastroesophageal Junction Adenocarcinoma', 'Endometrial Carcinoma', 'Malignant Pancreatic Neoplasm', 'Oropharyngeal Neoplasm', 'Salivary Gland Adenoid Cystic Carcinoma', 'Melanoma', 'Head and Neck Neoplasm', 'Not-Applicable', 'Pancreatic Neoplasm', 'Marginal Zone Lymphoma', 'Gastric Adenocarcinoma', 'Neuroepithelial Neoplasm', '']",Biospecimen -Health Care Site,Health Care Site,HealthCareSite,The health care site at which the biospecimen sample was collected.,False,,Biospecimen -Biospecimen_id,Biospecimen_id,BiospecimenId,"Unique row identifier, used as a primary key for record updates",True,,Biospecimen -Component,Component,Component,"Category of metadata (e.g. Tools, Publications, etc.); provide the same one for all items/rows.",True,,Biospecimen -Biospecimen Species,Biospecimen Species,BiospecimenSpecies,The species from which the biospecimen originates,True,"['Human', 'Chicken', 'Yeast', 'Trichoplax adhaerens', 'Boar', 'Rhesus monkey', 'Rat', 'Armadillo', 'African Bush Elephant', 'unknown', 'Escherichia coli', 'Cow', 'Dog', 'Multispecies', 'Cat', 'Asian Elephant', 'Opossum', 'Horse', 'Fruit Fly', 'Rabbit', 'Guinea Pig', 'Zebrafish', 'Worm', 'Sheep', 'Mouse', 'Unspecified']",Biospecimen -Age at Sample Collection,Age at Sample Collection,AgeatSampleCollection,"Age at the time the biospecimen was collected, expressed in number of years since birth.",False,,Biospecimen -Tumor Subtype,Tumor Subtype,TumorSubtype,"The subtype related to the scientific determination and investigation, analysis and recognition of the presence and nature of disease, condition, or injury from expressed signs and symptoms of tissue growth resulting from uncontrolled cell proliferation.",False,"['LumB', 'TNBC', 'LumA', 'Not Applicable', 'HER2', '']",Biospecimen -Known Metastasis Sites,Known Metastasis Sites,KnownMetastasisSites,The text term(s) used to describe the anatomic site(s) of metastasis associated with the patient's malignant disease.,False,,Biospecimen -Timepoint,Timepoint,Timepoint,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",False,,Biospecimen -Biospecimen ID,Biospecimen ID,BiospecimenID,ID associated with a biosample,True,,Biospecimen -Individual ID,Individual ID,IndividualID,ID associated with a study participant,True,,Biospecimen -Biospecimen Type,Biospecimen Type,BiospecimenType,The type of biospecimen,True,"['Urine', 'Tissue', 'Blood', 'Analyte', 'Mouth Rinse', 'Sputum', 'Stool', 'Bone Marrow', 'Cells', 'Fluids', 'Ascites']",Biospecimen -Site of Resection or Biopsy,Site of Resection or Biopsy,SiteofResectionorBiopsy,The text term used to describe the anatomic site of the resection or biopsy of the patient's malignant disease.,False,"['Artery', 'Trachea', 'Tongue', 'Intestine', 'Lymphoid Tissue', 'Blood', 'Eye', 'Gastroesophageal Junction', 'Cervix Uteri', 'Lymphatic System', 'Endocervix', 'Thymus', 'Omentum', 'Olfactory Mucosa', 'Adrenal Gland', 'Kidney', 'Ovary', 'Vascular Endothelium', 'Placenta', 'Pending Annotation', 'Epithelium', 'Salivary Gland', 'Lung', 'Ear', 'Hippocampus', 'Pituitary Gland', 'Duodenum', 'Lymph Node', 'Pharynx', 'Foreskin', 'Adipose Tissue', 'Hematopoietic System', 'Genitourinary', 'Synovial Membrane', 'Not Applicable', 'Fallopian Tube', 'Aorta', 'Vertebra', 'Blood Vessel', 'Spinal Cord', 'Stomach', 'Cancer-Associated Fibroblast', 'Endothelium', 'Testis', 'Mammary Gland', 'Pleura', 'Gastrointestinal Tract', 'Joint', 'Periodontal Ligament', 'Vagina', 'Frontal Lobe', 'Breast', 'Bile Duct', 'Hair Follicle', 'Skin', 'Cardia', 'Ligament', 'Rectum', 'Caecum', 'Main Bronchus', 'Respiratory System', 'Embryonic Heart', 'Meninges', 'Brain', 'Alveolus', 'Intra-Abdominal Lymph Nodes', 'Uterus', 'Liver', 'Bone', 'Mesenchyme', 'Head and Neck', 'Heart Muscle', 'Embryo', 'Thyroid Gland', 'Cartilage', 'Abdominal Esophagus', 'Nervous System', 'Reproductive System', 'Intrathoracic Lymph Nodes', 'Peritoneum', 'Heart', 'Peripheral Blood Mononuclear Cell', 'Muscle', 'Prostate Gland', 'Mucosa', 'Connective and Soft Tissue', 'Larynx', 'Sclera', 'Unspecified', 'Nasal Cavity', 'Small Intestine', 'Endometrium', 'Esophagus', 'Tonsil', 'Gonad', 'Choroid', 'Sinonasal Tract', 'Lymph Nodes of Axilla or Arm', 'Pelvic Lymph Nodes', 'Oral Cavity', 'Colon', 'Lymph', 'Ascending Colon', 'Bladder', 'Spleen', 'Umbilical Cord', 'Peripheral Nerves', 'Lymph Nodes of Inguinal Region or Leg', 'Vein', 'Pancreas', 'Oral Mucosa', 'Bone Marrow', 'Cornea', 'Tendon', '']",Biospecimen -Biospecimen Composition,Biospecimen Composition,BiospecimenComposition,"The text term used to describe the type(s) of tissue contained in the biospecimen. Multiple values permitted, comma separated.",False,,Biospecimen -Preservation Method,Preservation Method,PreservationMethod,Text term that represents the method used to preserve the sample.,False,"['Cryopreservation in liquid nitrogen - live cells', 'Frozen', 'Liquid Nitrogen', 'Fresh dissociated and single cell sorted', 'unknown', 'Cryopreservation in dry ice - dead tissue', 'Fresh dissociated', 'Snap Frozen', 'Fresh', 'Cryopreserved', 'Cryopreservation in liquid nitrogen - dead tissue', 'Formalin fixed paraffin embedded - FFPE', 'Formalin fixed-buffered', 'Fresh dissociated and single cell sorted into plates', 'Negative 80 Deg C', 'Methacarn fixed paraffin embedded - MFPE', 'Not Reported', 'Formalin fixed-unbuffered', 'Fresh dissociated and single cell sorted into plates in NP40 buffer', 'OCT', '']",Biospecimen -Site of Origin,Site of Origin,SiteofOrigin,"The text term used to describe the anatomic site of origin, of the patient's malignant disease.",False,"['Artery', 'Trachea', 'Tongue', 'Intestine', 'Lymphoid Tissue', 'Blood', 'Eye', 'Gastroesophageal Junction', 'Cervix Uteri', 'Lymphatic System', 'Endocervix', 'Thymus', 'Omentum', 'Olfactory Mucosa', 'Adrenal Gland', 'Kidney', 'Ovary', 'Vascular Endothelium', 'Placenta', 'Pending Annotation', 'Epithelium', 'Salivary Gland', 'Lung', 'Ear', 'Hippocampus', 'Pituitary Gland', 'Duodenum', 'Lymph Node', 'Pharynx', 'Foreskin', 'Adipose Tissue', 'Hematopoietic System', 'Genitourinary', 'Synovial Membrane', 'Not Applicable', 'Fallopian Tube', 'Aorta', 'Vertebra', 'Blood Vessel', 'Spinal Cord', 'Stomach', 'Cancer-Associated Fibroblast', 'Endothelium', 'Testis', 'Mammary Gland', 'Pleura', 'Gastrointestinal Tract', 'Joint', 'Periodontal Ligament', 'Vagina', 'Frontal Lobe', 'Breast', 'Bile Duct', 'Hair Follicle', 'Skin', 'Cardia', 'Ligament', 'Rectum', 'Caecum', 'Main Bronchus', 'Respiratory System', 'Embryonic Heart', 'Meninges', 'Brain', 'Alveolus', 'Intra-Abdominal Lymph Nodes', 'Uterus', 'Liver', 'Bone', 'Mesenchyme', 'Head and Neck', 'Heart Muscle', 'Embryo', 'Thyroid Gland', 'Cartilage', 'Abdominal Esophagus', 'Nervous System', 'Reproductive System', 'Intrathoracic Lymph Nodes', 'Peritoneum', 'Heart', 'Peripheral Blood Mononuclear Cell', 'Muscle', 'Prostate Gland', 'Mucosa', 'Connective and Soft Tissue', 'Larynx', 'Sclera', 'Unspecified', 'Nasal Cavity', 'Small Intestine', 'Endometrium', 'Esophagus', 'Tonsil', 'Gonad', 'Choroid', 'Sinonasal Tract', 'Lymph Nodes of Axilla or Arm', 'Pelvic Lymph Nodes', 'Oral Cavity', 'Colon', 'Lymph', 'Ascending Colon', 'Bladder', 'Spleen', 'Umbilical Cord', 'Peripheral Nerves', 'Lymph Nodes of Inguinal Region or Leg', 'Vein', 'Pancreas', 'Oral Mucosa', 'Bone Marrow', 'Cornea', 'Tendon', '']",Biospecimen -Sex,Sex,Sex,Biological sex associated with the specimen donor,False,"['Other', 'M', 'unknown', 'F', '']",Biospecimen -Study Investigator,Study Investigator,StudyInvestigator,Investigator(s) associated with the project. Multiple names should be provided as a comma-separated list.,True,,Study -PersonView Key,PersonView Key,PersonViewKey,"Unique PersonView_id foreign key(s) that group the resource with other components, as part of the same person-associated studies. Please provide multiple values as a comma-separated list.",False,,Study -GrantView Key,GrantView Key,GrantViewKey,"Unique GrantView_id foreign key(s) that group the resource with other components, as part of the same grant-associated collection. Please provide multiple values as a comma-separated list.",False,,Study -ProjectView Key,ProjectView Key,ProjectViewKey,"Unique ProjectView_id foreign key(s) that group the resource with other components, as part of the same grant-associated studies. Please provide multiple values as a comma-separated list.",False,,Study -Study_id,Study_id,StudyId,A unique primary key that enables record updates using schematic.,True,,Study -Component,Component,Component,"Category of metadata (e.g. Tools, Publications, etc.); provide the same one for all items/rows.",True,,Study -Study Name,Study Name,StudyName,Name of the study,True,,Study -Study Reuse Statement,Study Reuse Statement,StudyReuseStatement,"The funder-, contributor-, patient-, etc., derived content that includes terms, conditions, or statements associated with accessing and reusing the resource(s).",False,,Study -Study Description,Study Description,StudyDescription,"Description of the study, including the types of experimental assays, model systems, types of analysis, etc.",True,,Study -Grant Theme Name,Grant Theme Name,GrantThemeName,Theme(s) associated with the grant. 1...*,True,,GrantView -Embargo End Date,Embargo End Date,EmbargoEndDate,Date at which an embargo on related resources had lifted,False,,GrantView -NIH RePORTER Link,NIH RePORTER Link,NIHRePORTERLink,Link to the search results for this grant number on the NIH Reporter website,True,,GrantView -Duration of Funding,Duration of Funding,DurationofFunding,"Duration of the funding period, in years",False,,GrantView -Grant Name,Grant Name,GrantName,Name of the grant,True,,GrantView -Grant Institution Name,Grant Institution Name,GrantInstitutionName,The full name of the institution(s) associated with the grant. (e.g. Harvard University). 1...*,True,,GrantView -Grant Number,Grant Number,GrantNumber,"Number of the grant (i.e. ""CA------"" format)",True,,GrantView -Grant Type,Grant Type,GrantType,Type of grant,True,"['R21', 'R37', 'U54', 'R01', 'U01', 'U24']",GrantView -Grant Synapse Team,Grant Synapse Team,GrantSynapseTeam,"The Synapse team associated with the grant, created by the MC2 Center",False,,GrantView -Grant Abstract,Grant Abstract,GrantAbstract,Abstract for the grant,True,,GrantView -Component,Component,Component,"Category of metadata (e.g. Tools, Publications, etc.); provide the same one for all items/rows.",True,,GrantView -Grant Institution Alias,Grant Institution Alias,GrantInstitutionAlias,The alias of the institution(s) associated with the grant (e.g. UCSD). 1...*,True,,GrantView -Grant Consortium Name,Grant Consortium Name,GrantConsortiumName,Consortium(s) associated with the grant. 1...1,True,"['CCBIR', 'CSBC', 'PS-ON', 'TEC', 'PDMC', 'Sage Bionetworks', 'ICBP', 'MetNet', 'NCI Clinical and Translational Exploratory/Developmental Studies', 'HTAN', 'NCI']",GrantView -Grant Investigator,Grant Investigator,GrantInvestigator,Investigator(s) associated witht the grant. 1...*,True,,GrantView -Grant Start Date,Grant Start Date,GrantStartDate,The start date of the grant YYYY-MM-DD format,True,,GrantView -Grant Synapse Project,Grant Synapse Project,GrantSynapseProject,"The Synapse project associated with the grant, created by the MC2 Center",False,,GrantView -GrantView_id,GrantView_id,GrantViewId,A unique primary key that enables record updates using schematic.,True,,GrantView -File Description,File Description,FileDescription,Description of the file.,False,,FileView -File Species,File Species,FileSpecies,"The species the data was collected on. Multiple values permitted, comma separated.",True,,FileView -Biospecimen Key,Biospecimen Key,BiospecimenKey,Unique Biospecimen_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list.,False,,FileView -FileView_id,FileView_id,FileViewId,A unique primary key that enables record updates using schematic.,True,,FileView -DatasetView Key,DatasetView Key,DatasetViewKey,Unique DatasetView_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list.,False,,FileView -Data Use Codes,Data Use Codes,DataUseCodes,"DUO code - A data item that is used to indicate consent permissions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used.",False,,FileView -File Assay,File Assay,FileAssay,The assay the file is representative of.,True,"['Deep Mutational Scanning', 'Multiplexed Immunofluorescence', 'Micropipette Aspiration', 'Electron Diffraction', 'QFISH', 'Multi-Angle Light Scattering', 'Gene Silencing', 'Whole Exome Sequencing', 'Vibrational Spectroscopy', 'Bioluminescence Imaging', 'Confocal Reflectance Quantitative Phase Microscopy', 'Global Chromatin Profiling', 'Comparative Genomic Hybridization', 'Hydrophilic Interaction Chromatography', 'Intravital Microscopy', 'siRNA', 'SDS-PAGE', 'In Situ Hybridization', 'Allograft', 'PlateSeq', 'Surveyor Nuclease Assay', 'Computed Tomography', 'Not Applicable', 'ImmunoFISH', 'Gas Chromatography Mass Spectrometry', 'Wound-Healing Assay', 'Magnetic Tweezers', 'Antitumor Drug Screening Assay', 'Virus Plaque Assay', 'TUNEL assay', 'Barcode-Seq', 'Optogenetic Assay', 'Forster Resonance Energy Transfer', 'Cell Adhesion Assay', 'Enzyme Activity Assay', 'Cytometric Bead Array Assay', 'Optical Stretcher', 'Plasmid Construction', 'Dynamic Contrast-Enhanced Magnetic Resonance Imaging', 'DNA Gene-Expression Microarray', 'High Throughput Screening', 'Synthesis', 'Tiling Array', 'Modeling', 'Bioelectrochemical Analysis', 'Mint-ChIP', 'Magnetic Twisting Cytometry', 'Phylogenetic Analysis', 'DBiT-Seq', 'Scanning Angle Interference Microscopy', 'Reverse-Phase High-Performance liquid Chromatography', '3C', 'Fluorescent Cell Barcoding', 'Fluorescence Activated Cell Sorting', 'Luciferase Reporter Assay', 'Field-Emission Scanning Electron Microscopy', 'Single-Molecule Localization Microscopy', 'Circular Dichroism Spectroscopy', 'DNase-Seq', 'Gene Set Enrichment Analysis', 'TIRF Microscopy', 'Patient Derived Xenograft', 'Mammosphere Formation Assay', 'Fluorescence Imaging', 'Immunohistochemistry Staining Method', 'Computational Modeling', 'Target Engagement Assay', 'MeRIP-Seq', 'Reduced Representation Bisulfite Sequencing', 'NanoString Digital Spatial Profiling', 'Transwell Assay', 'Reverse Phase Protein Array', 'ATAC-Seq', 'Whole Genome Sequencing', 'Suspended Microchannel Resonator', 'Cell Cycle Assay', 'Small-Angle X-ray Scattering', 'cDNA Array', 'RAS Protein Family Activation Assay', 'Tissue Microarray', 'Differential Scanning Fluorimetry', 'Computational Tool', 'Autoradiography', 'Surface Plasmon Resonance', 'Global Run-On Sequencing', 'Southern Blotting', 'Gene Ontology Enrichment Analysis', 'Unspecified', 'Von Kossa Staining', 'Electron Paramagnetic Resonance Spectroscopy', 'Mass Cytometry', 'Nm-seq', 'Proteomics Assay', 'Nuclear Magnetic Resonance', 'Atomic Force Microscopy', 'Hi-C', 'Cell Viability Assay', 'Scratch Assay', 'Fluorescence Lifetime Imaging Microscopy', 'Fourier-Transform Infrared Spectroscopy', 'Single-Molecule Tracking', '16S Ribosomal Gene Sequencing Assay', '5C', 'Photolithography', 'Bio-Layer Interferometry', 'MEMA Cell Growth Assay', 'Luminescent Cell Viability Assay', 'Colorimetric Cell Viability Assay', 'Clonality Analysis', 'Nanopore Sequencing', 'RNA Sequencing', 'Western Blotting', 'Survival Analysis', 'Shotgun Mass Spectrometry', 'Paraquat Survival Assay', 'Tandem Mass Tagging', 'Optical Tweezers', 'Microscopy', 'Deep Learning', 'Picrosirius Staining', 'Phagocytosis Assay', 'Nanopatterning', 'Transmission Electron Microscopy', 'Clinical Study', 'mRNA Sequencing', 'Thin-Layer Chromatography', 'Lattice Light Sheet Microscopy', 'Visium Spatial Gene Expression', 'Co-culture Assay', 'Imaging Mass Cytometry', 'eCLIP-Seq', 'Inductively-Coupled Plasma Mass Spectrometry', 'MicroRNA Expression Array', 'Nested PCR', 'Differential Interference Contrast Microscopy', 'Metabolite Profiling Assay', 'scSLAM-seq', 'DRIP-seq', 'Traction Force Microscopy', 'Quantitative Multiplex Immunofluorescence', 'Atomic Absorption Spectrophotometry', 'Stimulated Raman Scattering', 'qPCR', 'X-Ray Micro-Computed Tomography', 'Angiogenesis Assay', 'Optical Mapping', 'PET-CT', 'Artificial Intelligence', 'ChIP-qPCR assay', 'Bicinchoninic Acid Assay', 'MULTI-Seq', 'Immobilized Metal Affinity Chromatography', 'Microfluidics', 'Dye Endocytosis Assay', 'L1000 mRNA Profiling Assay', 'Fourier Transform Ion Cyclotron Resonance Mass Spectrometry', 'MicroRNA Sequencing', 'Tandem Mass Spectrometry', 'Immunofluorescent Staining Method', 'Image Cytometry', 'ChIP-Seq', 'Cell-spreading Assay', 'Scanning Electron Microscopy', '10x Multiome', 'Soft Agar Assay', 'Second-Harmonic Imaging Microscopy', 'Dideoxy Chain Termination DNA Sequencing', 'CRISPR', 'X-Ray Diffraction', 'Tissue Engineering', 'Next Generation Sequencing', 'Multiplexed Ion Beam Imaging', 'Fluorescence Correlation Spectroscopy', 'Hydrogels', 'Statistical Modeling', 'DNA Sequencing', 'Methylation-Specific PCR', 'High-Content Screen', 'Single Nucleus RNA-Sequencing', 'Methyl Binding Domain Sequencing', 'HL-Chip', 'ChIA-PET', 'Optical Coherence Tomography', 'Epidemiological Method', 'Nano-hmC-Seal', 'Ribosomal P Protein Antibody Measurement', 'UV Photocrosslinking', 'Targeted Transcriptome Sequencing', 'In Vivo Bioluminescence', 'Isothermal Titration Calorimetry', 'Immunoprecipitation', 'Gelatin Zymography', 'Synthetic Genetic Array', '3C-qPCR', 'Binding Assay', 'Fluorescent In Situ Sequencing', 'Chimeric Antigen Receptor T-Cell Therapy', 'Murine Model', 'Immunoassay', 'Flow Cytometry', 'ATP Bioluminescence Assay', 'Drop-Seq', 'Magnetic Resonance Imaging', 'Permeability Assay', 'Stochastic Optical Reconstruction Microscopy', 'Thermal Shift Assay', 'Affinity Purification Mass Spectrometry', 'Dynamic Light Scattering', 'Single Cell Gel Electrophoresis', 'Knife-Edge Scanning Microscopy', 'RIP-Seq', 'RT-PCR', 'Pending Annotation', 'Magnetically Activated Cell Sorting', 'Raman Spectroscopy', 'CUT&RUN', 'Dynamic Susceptibility Contrast-Enhanced Magnetic Resonance Imaging', 'Data Integration', '3D Cell Culture', 'Cerenkov Luminescence Imaging', 'Cell Proliferation Assay', 'Targeted Error Correction Sequencing', 'Fluorescence Recovery After Photo-Bleaching', 'TCR Sequencing', 'Immunocytochemistry', 'Cross-Linking Immunoprecipitation High-throughput Sequencing', 'Chemotaxis Assay', 'Microcontact Printing', 'Quantitative Point Accumulation for Imaging in Nanoscale Topography', 'RNAi Screen', 'UPLC-MSMS', 'scCGI-seq', 'Spectroscopy', 'Electrospray Ionization Time-of-Flight Mass Spectrometry', 'Diffusion Weighted Imaging', 'Immunotherapy', '3D Bioprinting', 'In Vitro Selection', 'Time-Correlated Single Photon Counting', 'Dark Field Microscopy', 'Direct Long-Read RNA Sequencing', 'Hematoxylin and Eosin Staining Method', 'Cell Fractionation', 'FAIRE-Seq', 'Tuba-Seq', 'Brightfield Microscopy', 'In Vitro Cell Killing Assay', 'Brillouin Microscopy', 'smFISH', 'Imaging', 'Chemiluminescent Assay', 'Fluorescent Antibody Procedure', 'Liquid Chromatography Mass Spectrometry', 'Organoid', 'Electron Microscopy', 'TRAP Staining', 'Monolayer Stress Microscopy', 'Xenograft', 'Questionnaire', 'Cryo-Electron Tomography', ""3' RNA-seq"", 'Targeted Therapy Agent', 'HiChIP', 'Micropipette Adhesion Assay', 'TAB-Seq', 'CITE-seq', 'Ultrasound Imaging', 'Photoacoustic Imaging', 'Label-free Protein Quantification by LC/MS', 'Precision Run-On Sequencing', 'Metastatic Colonization Assay', 'Cell Culture', 'Desorption Electrospray Ionization', 'Atomic Absorption Spectroscopy', 'Size Exclusion Chromatography', 'Total Internal Reflection Fluorescence Microscopy', 'Migration Assay', 'Co-Immunoprecipitation', 'FISH', 'Karyotyping', 'Collision-Induced Dissociation', 'Viral Transduction', 'Multiplexed Error-Robust Fluorescence In Situ Hybridization', 'Cyclic Immunofluorescence', 'Micro-computed Tomography', 'Single Cell ATAC-Seq', 'Invasion Assay', 'RIP', 'Positron Emission Tomography', 'Dual-Luciferase Reporter Assay', 'Low-Vacuum Scanning Electron Microscopy', 'Multi-Isotope Mass Spectrometry', 'Transcription profiling by NanoString', 'Stimulated Emission Depletion Microscopy', 'Co-Immunoprecipitation Mass Spectrometry', 'DNA Methylation Array', 'Targeted Genome Sequencing', 'Mass Spectrometry', 'Point Accumulation for Imaging in Nanoscale Topography', 'Reporter Gene Assay', 'Multiscale Light Sheet Microscopy', 'Partial Wave Spectroscopy', 'HPLC-MSMS', 'Molecular Simulations', 'Cytokine Expression Profile', 'Rheometry', 'Cell-free Circulating Tumor DNA Assay', 'Multiphoton Microscopy', 'scNT-Seq', 'Genotyping', 'Trichrome Staining Method', 'Dynamic Force Spectroscopy', 'Human Induced Pluripotent Stem Cell-derived Cardiomyocytes Culture', 'CASFISH', 'Structural Variant Analysis', 'CLIP-qPCR', 'Cryo-Electron Microscopy', 'Bisulfite Sequencing', 'Single-Cell BCR Sequencing', '4C', 'Cross-Linking Mass Spectrometry', 'Multiparametric Magnetic Resonance Imaging', 'Multiplexed Immunohistochemistry', 'Interference Reflection Microscopy', 'Widefield Fluorescence Microscopy', 'MeDIP', 'Single-Cell TCR Sequencing', 'In Vitro Model', 'Amplicon Sequencing', 'Single-Cell Barcode Chip', 'Whole Genome Bisulfite Sequencing', 'CellTiter-Glo Luminescent Cell Viability Assay', 'Liquid Chromatography/Tandem Mass Spectrometry', 'Nanowire', 'RT-qPCR', 'Proximity Ligation Assay', 'CUT&Tag-Sequencing', 'Enzyme-Linked Immunospot Assay', 'MNase-Seq', 'Endotoxin Assay', 'PCR', 'Sirius Red Staining', 'Time Lapse Microscopy', 'Alcian Blue Staining Method', 'Ribo-Seq', 'Graphite Furnace Atomic Absorption Spectrometry', 'Electrophoretic Mobility Shift Assay', 'seqFISH', 'Optical Emission Spectroscopy', 'In-Cell Western Assay', 'Droplet Digital PCR', 'Pull-Down Assay', 'In Vitro Translation', 'Focused Ion Beam Scanning Electron Microscopy', 'Single Molecule Forster Resonance Energy Transfer', 'Single Cell RNA-Sequencing', 'Efferocytosis Assay', 'Synaptophysin Staining Method', 'Apoptosis Assay', 'snRNA-seq', 'shRNA', 'Confocal Microscopy', 'X-Ray Crystallography', 'Energy-Dispersive X-Ray Spectroscopy', 'Mathematical Modeling', 'Single Cell Cytokine Detection Chip Assay', 'Single Cell DNA Sequencing', 'Macrophage Polarization Assay', 'smRNA-seq', '10-cell RNA Sequencing', 'Fluorescence Microscopy', 'ELISA', 'MALDI-TOF Mass Spectrometry', 'ChIP-PCR', 'Super-Resolution Microscopy', 'Single Nucleotide Polymorphism Array', 'Cytochemical Stain', 'Cytotoxicity Assay']",FileView -File Design,File Design,FileDesign,The overall design of the dataset or file.,False,,FileView -File Alias,File Alias,FileAlias,"Alias of the file. Must be unique. Can be the GEO identifier such as GSE12345, or a DOI. No Greek Letters.",True,,FileView -File Tumor Type,File Tumor Type,FileTumorType,"The tumor type(s), if applicable, of the data collected. Multiple values permitted, comma separated.",False,,FileView -File Level,File Level,FileLevel,The processing level the file can be mapped to.,True,"['Level 3', 'Level 1', 'Auxilliary', 'Not Applicable', 'Level 4', 'Level 2']",FileView -Filename,Filename,Filename,Name of a file,True,,FileView -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,FileView -Component,Component,Component,"Category of metadata (e.g. Tools, Publications, etc.); provide the same one for all items/rows.",True,,FileView -Study Key,Study Key,StudyKey,"The unique Study_id foreign keys associated with the resource, found in the grant Study information. Used to group the resource with other components. Please provide multiple values as a comma-separated list.",False,,FileView -File Tissue,File Tissue,FileTissue,"Tissue type(s) associated with the file. Multiple values permitted, comma separated.",False,,FileView -File Url,File Url,FileUrl,The url of where the file is stored.,True,,FileView -Biospecimen Key,Biospecimen Key,BiospecimenKey,Unique Biospecimen_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list.,False,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles -Slide ID,Slide ID,SlideID,"For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide.",True,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles -Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles -VisiumRNALevel3 Key,VisiumRNALevel3 Key,VisiumRNALevel3Key,Unique VisiumRNALevel3_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,False,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles -Visium File Type,Visium File Type,VisiumFileType,The file type generated for the visium experiment.,True,"['json scale factors', 'probe dataset csv', 'features', 'high res image', 'fiducial image jpg', 'reference png', 'detected jpg', 'low res image', 'filtered mex', 'detected image png', 'reference jpg', 'barcodes', 'qc result html', 'tissue_positions', 'fiducial image png', 'unfiltered mex']",10xVisiumSpatialTranscriptomics-AuxiliaryFiles -VisiumRNALevel2 Key,VisiumRNALevel2 Key,VisiumRNALevel2Key,Unique VisiumRNALevel2_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,False,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles -VisiumAux_id,VisiumAux_id,VisiumAuxId,"Unique row identifier, used as a primary key for record updates",True,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles -Capture Area,Capture Area,CaptureArea,"Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.",False,"['D', 'A', 'D1', 'B1', 'A1', 'C1', 'C', 'B', '']",10xVisiumSpatialTranscriptomics-AuxiliaryFiles -VisiumRNALevel4 Key,VisiumRNALevel4 Key,VisiumRNALevel4Key,Unique VisiumRNALevel4_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,False,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles -Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. URL,False,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles -Component,Component,Component,"Category of metadata (e.g. Tools, Publications, etc.); provide the same one for all items/rows.",True,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles -VisiumRNALevel1 Key,VisiumRNALevel1 Key,VisiumRNALevel1Key,Unique VisiumRNALevel1_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,False,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles -Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),False,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles -Filename,Filename,Filename,Name of a file,True,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles -Permeabilization Time,Permeabilization Time,PermeabilizationTime,Fixed and stained tissue sections are permeabilized for different times. Each Capture Area captures polyadenylated mRNA from the attached tissue section. Measure is provided in minutes.,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Spatial Read1,Spatial Read1,SpatialRead1,Read 1 content description,True,"['Spatial Barcode and UMI', 'cDNA']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Slide Version,Slide Version,SlideVersion,Version of imaging slide used. Slide version is critical for the analysis of the sequencing data as different slides have different capture area layouts.,True,"['V3', 'V1', 'V4', 'V2']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Spatial Read2,Spatial Read2,SpatialRead2,Read 2 content description,True,"['Spatial Barcode and UMI', 'cDNA']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Component,Component,Component,"Category of metadata (e.g. Tools, Publications, etc.); provide the same one for all items/rows.",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Spatial Library Construction Method,Spatial Library Construction Method,SpatialLibraryConstructionMethod,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],True,"['Smart-seq2', '10xV1.1', 'Drop-seq', 'inDropsV3', 'TruDrop', 'inDropsV2', '10xV1.0', '10xV3', 'Nextera XT', 'Smart-SeqV4', '10xV2', '10xV3.1']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Biospecimen Key,Biospecimen Key,BiospecimenKey,Unique Biospecimen_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list.,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -File Alias,File Alias,FileAlias,"Alias of the file. Must be unique. Can be the GEO identifier such as GSE12345, or a DOI. No Greek Letters.",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable',False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Sequencing Library Construction Days from Index,Sequencing Library Construction Days from Index,SequencingLibraryConstructionDaysfromIndex,Number of days between sample for assay was received in lab and day of sequencing library construction [number]. If not applicable please enter 'Not Applicable',True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,"['R2', 'R1', 'R1&R2', 'I1', 'Other']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -VisiumRNALevel1_id,VisiumRNALevel1_id,VisiumRNALevel1Id,"Unique row identifier, used as a primary key for record updates",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Slide ID,Slide ID,SlideID,"For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide.",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -DV200,DV200,DV200,Represents the percentage of RNA fragments that are >200 nucleotides in size. Number,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -End Bias,End Bias,EndBias,"The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript",True,"['3 Prime', 'Full Length Transcript', '5 Prime']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -RIN,RIN,RIN,A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products. Number,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Filename,Filename,Filename,Name of a file,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Reverse Transcription Primer,Reverse Transcription Primer,ReverseTranscriptionPrimer,"An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA",True,"['Oligo-dT', 'Random', 'Feature barcoding', 'Poly-dT']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,"['Illumina NextSeq', 'Illumina Genome Analyzer II', 'Illumina HiSeq X Ten', 'PacBio RS', 'GridION', 'Revio', 'Other', 'Illumina Next Seq 500', 'Illumina Genome Analyzer IIx', 'Illumina Next Seq 550', 'unknown', 'NovaSeq 6000', 'Illumina HiSeq 4000', 'Ion Torrent Proton', 'AB SOLiD 2', 'Complete Genomics', 'NovaSeqS4', 'Ion Torrent S5', 'Illumina HiSeq 2000', 'Illumina NextSeq 1000', 'Illumina HiSeq 2500', 'Illumina Next Seq 2500', 'Ultima Genomics UG100', 'Illumina MiSeq', 'PacBio Sequel2', 'Not Reported', 'Illumina NovaSeq 6000', 'AB SOLiD 3', 'Oxford Nanopore minION', 'Illumina HiSeq X Five', '454 GS FLX Titanium', 'Ion Torrent PGM', 'Illumina NextSeq 2000', 'AB SOLiD 4', 'PromethION']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Capture Area,Capture Area,CaptureArea,"Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.",False,"['D', 'A', 'D1', 'B1', 'A1', 'C1', 'C', 'B', '']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Image Re-orientation,Image Re-orientation,ImageRe-orientation,"To ensure good fiducial alignment and tissue spots detection, it is important to correct for this shift in orientation.",False,"['False', 'True', '']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Whitelist Spatial Barcode File Link,Whitelist Spatial Barcode File Link,WhitelistSpatialBarcodeFileLink,Link to file listing all possible spatial barcodes. URL,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence; ftp or reference URL will be accepted.,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -Component,Component,Component,"Category of metadata (e.g. Tools, Publications, etc.); provide the same one for all items/rows.",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -Spatial Barcode Tag,Spatial Barcode Tag,SpatialBarcodeTag,"SAM tag for spot barcode field; please provide a valid tag-type pair, consisting of a tag (e.g. CB or CR) and type (e.g. Z) separated by a colon.",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -Biospecimen Key,Biospecimen Key,BiospecimenKey,Unique Biospecimen_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list.,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -File Alias,File Alias,FileAlias,"Alias of the file. Must be unique. Can be the GEO identifier such as GSE12345, or a DOI. No Greek Letters.",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -Checksum,Checksum,Checksum,TBD,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -VisiumRNALevel1 Key,VisiumRNALevel1 Key,VisiumRNALevel1Key,Unique VisiumRNALevel1_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -VisiumRNALevel2_id,VisiumRNALevel2_id,VisiumRNALevel2Id,"Unique row identifier, used as a primary key for record updates",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -UMI Tag,UMI Tag,UMITag,"SAM tag for the UMI field; please provide a valid tag-type pair, consisting of a tag (e.g. UB or UR) and type (e.g. Z) separated by a colon.",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -Applied Hard Trimming,Applied Hard Trimming,AppliedHardTrimming,Was Hard Trimming applied,True,"['False', 'True']",10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. URL,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -Filename,Filename,Filename,Name of a file,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -Genome Annotation URL,Genome Annotation URL,GenomeAnnotationURL,Link to the human genome annotation (GTF) file; ftp or reference URL will be accepted.,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -Capture Area,Capture Area,CaptureArea,"Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.",False,"['D', 'A', 'D1', 'B1', 'A1', 'C1', 'C', 'B', '']",10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -Mean Reads per Spatial Spot,Mean Reads per Spatial Spot,MeanReadsperSpatialSpot,"The number of reads, both under and outside of tissue, divided by the number of barcodes associated with a spot under tissue.",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -VisiumRNALevel3_id,VisiumRNALevel3_id,VisiumRNALevel3Id,"Unique row identifier, used as a primary key for record updates",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -Sequencing Saturation,Sequencing Saturation,SequencingSaturation,"The fraction of reads originating from an already-observed UMI. This is a function of library complexity and sequencing depth. More specifically, this is the fraction of confidently mapped, valid spot-barcode, valid UMI reads that had a non-unique (spot-barcode, UMI, gene).",False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -Spots under tissue,Spots under tissue,Spotsundertissue,The number of barcodes associated with a spot under tissue.,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -Visium File Type,Visium File Type,VisiumFileType,The file type generated for the visium experiment.,True,"['json scale factors', 'probe dataset csv', 'features', 'high res image', 'fiducial image jpg', 'reference png', 'detected jpg', 'low res image', 'filtered mex', 'detected image png', 'reference jpg', 'barcodes', 'qc result html', 'tissue_positions', 'fiducial image png', 'unfiltered mex']",10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -Component,Component,Component,"Category of metadata (e.g. Tools, Publications, etc.); provide the same one for all items/rows.",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -Biospecimen Key,Biospecimen Key,BiospecimenKey,Unique Biospecimen_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list.,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -VisiumAux Key,VisiumAux Key,VisiumAuxKey,Unique VisiumAux_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -File Alias,File Alias,FileAlias,"Alias of the file. Must be unique. Can be the GEO identifier such as GSE12345, or a DOI. No Greek Letters.",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -Median UMI Counts per Spot,Median UMI Counts per Spot,MedianUMICountsperSpot,The median number of UMI counts per tissue covered spot.,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. URL,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -Proportion Reads Mapped to Transcriptome,Proportion Reads Mapped to Transcriptome,ProportionReadsMappedtoTranscriptome,Fraction of reads that mapped to a unique gene in the transcriptome. The read must be consistent with annotated splice junctions. These reads are considered for UMI counting.,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -Filename,Filename,Filename,Name of a file,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -Median Number Genes per Spatial Spot,Median Number Genes per Spatial Spot,MedianNumberGenesperSpatialSpot,The median number of genes detected per spot under tissue-associated barcode. Detection is defined as the presence of at least 1 UMI count.,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -VisiumRNALevel2 Key,VisiumRNALevel2 Key,VisiumRNALevel2Key,Unique VisiumRNALevel2_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -Capture Area,Capture Area,CaptureArea,"Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.",False,"['D', 'A', 'D1', 'B1', 'A1', 'C1', 'C', 'B', '']",10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -Biospecimen Key,Biospecimen Key,BiospecimenKey,Unique Biospecimen_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list.,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 -Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 -VisiumRNALevel3 Key,VisiumRNALevel3 Key,VisiumRNALevel3Key,Unique VisiumRNALevel3_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 -Visium Workflow Type,Visium Workflow Type,VisiumWorkflowType,Generic name for the workflow used to analyze the visium data set.,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 -Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. URL,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 -Component,Component,Component,"Category of metadata (e.g. Tools, Publications, etc.); provide the same one for all items/rows.",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 -VisiumRNALevel4_id,VisiumRNALevel4_id,VisiumRNALevel4Id,"Unique row identifier, used as a primary key for record updates",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 -Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 -Visium Workflow Parameters Description,Visium Workflow Parameters Description,VisiumWorkflowParametersDescription,Parameters used to run the workflow.,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 -Filename,Filename,Filename,Name of a file,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 diff --git a/files/config.yml b/files/config.yml index 55e5574..bd856fb 100644 --- a/files/config.yml +++ b/files/config.yml @@ -1 +1 @@ -schema_url: https://github.com/mc2-center/data-models/raw/rfc-test-branch/mc2.model.jsonld +schema_url: HTAN diff --git a/js/PrepareRender.js b/js/PrepareRender.js index 261055e..2e8d244 100644 --- a/js/PrepareRender.js +++ b/js/PrepareRender.js @@ -12,16 +12,16 @@ $.get('files/config.yml').done(function (data) { }) //////////////////for using static files - // if (schema == "HTAN") { - // var tangled_tree_data = parseJSON('files/JSON/HTAN_tangled_tree.json'); - // } + if (schema == "HTAN") { + var tangled_tree_data = parseJSON('files/JSON/HTAN_tangled_tree.json'); + } - // tangled_tree_data.then(tangled_tree_dta => { - // //get tangle tree layout - // var chart_dta = chart(tangled_tree_dta); + tangled_tree_data.then(tangled_tree_dta => { + //get tangle tree layout + var chart_dta = chart(tangled_tree_dta); - // //draw collapsible tree - // createCollapsibleTree(chart_dta, schema); - // }) + //draw collapsible tree + createCollapsibleTree(chart_dta, schema); + }) }) \ No newline at end of file