From 2aaf215b36d15f43a452d9a8f99c284023dd4b61 Mon Sep 17 00:00:00 2001 From: elv-sb <97468221+elv-sb@users.noreply.github.com> Date: Thu, 26 Oct 2023 09:28:54 -0300 Subject: [PATCH 1/2] Update HTAN.model.csv Removed duplicate attributes in DependsOn --- HTAN.model.csv | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/HTAN.model.csv b/HTAN.model.csv index 3d32f5cc..e14a6245 100644 --- a/HTAN.model.csv +++ b/HTAN.model.csv @@ -34,7 +34,7 @@ Therapy,Clinical therapy or treatment,,"Component, HTAN Participant ID, Treatmen Diagnosis,Disease diagnosis,,"Component, HTAN Participant ID, Age at Diagnosis, Year of Diagnosis, Primary Diagnosis, Site of Resection or Biopsy, Tissue or Organ of Origin, Morphology, Tumor Grade, Progression or Recurrence, Last Known Disease Status, Days to Last Follow up, Days to Last Known Disease Status, Method of Diagnosis, Prior Malignancy, Prior Treatment, Metastasis at Diagnosis, Metastasis at Diagnosis Site, First Symptom Prior to Diagnosis, Days to Diagnosis, Percent Tumor Invasion, Residual Disease, Synchronous Malignancy, Tumor Confined to Organ of Origin, Tumor Focality, Tumor Largest Dimension Diameter, Gross Tumor Weight, Breslow Thickness, Vascular Invasion Present, Vascular Invasion Type, Anaplasia Present, Anaplasia Present Type, Laterality, Perineural Invasion Present, Lymphatic Invasion Present, Lymph Nodes Positive, Lymph Nodes Tested, Peritoneal Fluid Cytological Status, Classification of Tumor, Best Overall Response, Mitotic Count, AJCC Clinical M, AJCC Clinical N, AJCC Clinical Stage, AJCC Clinical T, AJCC Pathologic M, AJCC Pathologic N, AJCC Pathologic Stage, AJCC Pathologic T, AJCC Staging System Edition, Cog Neuroblastoma Risk Group, Cog Rhabdomyosarcoma Risk Group, Gleason Grade Group, Gleason Grade Tertiary, Gleason Patterns Percent, Greatest Tumor Dimension, IGCCCG Stage, INPC Grade, INPC Histologic Group, INRG Stage, INSS Stage, International Prognostic Index, IRS Group, IRS Stage, ISS Stage, Lymph Node Involved Site, Margin Distance, Margins Involved Site, Medulloblastoma Molecular Classification, Micropapillary Features, Mitosis Karyorrhexis Index, Non Nodal Regional Disease, Non Nodal Tumor Deposits, Ovarian Specimen Status, Ovarian Surface Involvement, Pregnant at Diagnosis, Primary Gleason Grade, Secondary Gleason Grade, Supratentorial Localization, Tumor Depth, WHO CNS Grade, WHO NTE Grade",,FALSE,Patient,,, Molecular Test,Clinical molecular test data,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index, Gene Symbol, Molecular Analysis Method, Test Result, AA Change, Antigen, Clinical Biospecimen Type, Blood Test Normal Range Upper, Blood Test Normal Range Lower, Cell Count, Chromosome, Clonality, Copy Number, Cytoband, Exon, Histone Family, Histone Variant, Intron, Laboratory Test, Loci Abnormal Count, Loci Count, Locus, Mismatch Repair Mutation, Molecular Consequence, Pathogenicity, Ploidy, Second Exon, Second Gene Symbol, Specialized Molecular Test, Test Analyte Type, Test Units, Test Value, Transcript, Variant Origin, Variant Type, Zygosity",,FALSE,Patient,,, Biospecimen,"HTAN biological entity; this can be tissue, blood, analyte and subsamples of those",,"Component, HTAN Biospecimen ID, Source HTAN Biospecimen ID, HTAN Parent ID, Timepoint Label, Collection Days from Index, Adjacent Biospecimen IDs, Biospecimen Type, Acquisition Method Type, Fixative Type, Storage Method, Processing Days from Index, Protocol Link, Site Data Source, Collection Media, Mounting Medium, Processing Location, Histology Assessment By, Histology Assessment Medium, Preinvasive Morphology, Tumor Infiltrating Lymphocytes, Degree of Dysplasia, Dysplasia Fraction, Number Proliferating Cells, Percent Eosinophil Infiltration, Percent Granulocyte Infiltration, Percent Inflam Infiltration, Percent Lymphocyte Infiltration, Percent Monocyte Infiltration, Percent Necrosis, Percent Neutrophil Infiltration, Percent Normal Cells, Percent Stromal Cells, Percent Tumor Cells, Percent Tumor Nuclei, Fiducial Marker, Slicing Method, Lysis Buffer, Method of Nucleic Acid Isolation",,FALSE,Biosample,Patient,, -SRRS Biospecimen,"SRRS-specific HTAN biological entity; this can be tissue, blood, analyte and subsamples of those, however it can be described via fewer attributes than a standard HTAN specimen",,"Component, HTAN Biospecimen ID, Source HTAN Biospecimen ID, HTAN Parent ID, Adjacent Biospecimen IDs, Biospecimen Type, Timepoint Label, Collection Days from Index, Acquisition Method Type, Ischemic Time, Ischemic Temperature, Collection Media, Topography Code, Additional Topography, Fixative Type, Storage Method, Preinvasive Morphology, Ischemic Time, Ischemic Temperature, Histologic Morphology Code, Preservation Method, Processing Days from Index, Protocol Link",,FALSE,Biosample,Patient,, +SRRS Biospecimen,"SRRS-specific HTAN biological entity; this can be tissue, blood, analyte and subsamples of those, however it can be described via fewer attributes than a standard HTAN specimen",,"Component, HTAN Biospecimen ID, Source HTAN Biospecimen ID, HTAN Parent ID, Adjacent Biospecimen IDs, Biospecimen Type, Timepoint Label, Collection Days from Index, Acquisition Method Type, Ischemic Time, Ischemic Temperature, Collection Media, Topography Code, Additional Topography, Fixative Type, Storage Method, Preinvasive Morphology, Histologic Morphology Code, Preservation Method, Processing Days from Index, Protocol Link",,FALSE,Biosample,Patient,, Source HTAN Biospecimen ID,This is the HTAN ID that may have been assigned to the biospecimen at the site of biospecimen origin (e.g. BU).,,,,FALSE,Biosample,,, Other Assay,Metadata applying to any assay without standard descriptors. Can be used as a placeholder for minimal amount of metadata until the assay descriptors are standardized,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Assay Type",,FALSE,Assay,Biospecimen,, Assay Type,"The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)",,,,TRUE,Assay,,, @@ -44,7 +44,7 @@ scRNA-seq Level 3,Gene and Isoform expression files,,"Component, Filename, File scRNA-seq Level 4,"Data represents the relationships between cells derived from Level 3 expression data and shown as tSNE or UMAP coordinates per cell, plus all other cell-specific meta information (e.g., cell type)",,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, scRNAseq Workflow Type, scRNAseq Workflow Parameters Description, Workflow Version, Workflow Link",,FALSE,Sequencing,scRNA-seq Level 3,, Slide-seq Level 1,"Raw sequencing files for the Slide-seq assay.",,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Nucleic Acid Source, Library Construction Method, Read Indicator, Spatial Read1, Spatial Read2, End Bias, Reverse Transcription Primer, Spatial Barcode Offset, Spatial Barcode and UMI, Spike In, Sequencing Platform, Run ID, Sequencing Batch ID, Total Number Beads in Puck, Technical Replicate Group, Protocol Link, Spatial Library Construction Method, Library Preparation Days from Index, Sequencing Library Construction Days from Index, Nucleic Acid Capture Days from Index",,FALSE,Spatial Transcriptomics,Biospecimen,, Slide-seq Level 2,"Aligned sequencing files and QC for the Slide-seq assay.",,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Slide-seq Workflow Type, Workflow Version, Slide-seq Workflow Parameter Description, Workflow Link, Genomic Reference, Genomic Reference URL, Genome Annotation URL, Checksum, Spatial Barcode Tag, UMI Tag, Applied Hard Trimming",,FALSE,Spatial Transcriptomics,Slide-seq Level 1,, -Slide-seq Level 3,"Gene matrices with features and barcodes for Slide-seq as well as spatial information (bead location files).",,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Data Category, Matrix Type, Slide-seq Workflow Type, Workflow Version, Slide-seq Workflow Parameter Description, Workflow Link, Workflow Version, Beads Total, Median UMI Counts per Spot, Median Number Genes per Spatial Spot, Slide-seq Bead File Type",,FALSE,Spatial Transcriptomics,Slide-seq Level 2,, +Slide-seq Level 3,"Gene matrices with features and barcodes for Slide-seq as well as spatial information (bead location files).",,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Data Category, Matrix Type, Slide-seq Workflow Type, Workflow Version, Slide-seq Workflow Parameter Description, Workflow Link, Beads Total, Median UMI Counts per Spot, Median Number Genes per Spatial Spot, Slide-seq Bead File Type",,FALSE,Spatial Transcriptomics,Slide-seq Level 2,, Total Number Beads in Puck,Number of beads in the Slide-seq puck. Integer,,,,TRUE,Spatial Transcriptomics,,, Beads Total,Number of sequenced beads. Applies to raw counts matrix only. Integer,,,,FALSE,Spatial Transcriptomics,,, Slide-seq Workflow Type,Generic name for the workflow used to analyze the Slide-seq data set. String,,,,TRUE,Spatial Transcriptomics,,, @@ -59,13 +59,13 @@ Bulk WES Level 3,Bulk Whole Exome Sequencing called variants,,"Component, Filena scATAC-seq Level 1,"scATAC-seq files containing sequence read information, with or without alignment, as FASTQ or BAM files",,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Nucleic Acid Source, Dissociation Method, Single Nucleus Buffer, Single Cell Isolation Method, Transposition Reaction, scATACseq Library Layout, Nucleus Identifier, Nuclei Barcode Length, Nuclei Barcode Read, scATACseq Read1, scATACseq Read2, scATACseq Read3, Library Construction Method, Sequencing Platform, Threshold for Minimum Passing Reads, Total Number of Passing Nuclei, Median Fraction of Reads in Peaks, Median Fraction of Reads in Annotated cis DNA Elements, Median Passing Read Percentage, Median Percentage of Mitochondrial Reads per Nucleus,Technical Replicate Group, Total Reads, Protocol Link",,FALSE,Sequencing,Biospecimen,, scATAC-seq Level 2,"scATAC-seq files containing aligned sequence data, as a BAM file",,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Alignment Workflow Url, Alignment Workflow Type, Genomic Reference, Genomic Reference URL, Index File Name, Average Base Quality, Average Insert Size, Average Read Length, Mean Coverage, Pairs On Diff CHR, Total Reads, Proportion Reads Mapped, MapQ30, Total Uniquely Mapped, Total Unmapped reads, Proportion Reads Duplicated, Short Reads, Proportion Coverage 10x, Proportion Coverage 30X, Proportion Targets No Coverage, Proportion Base Mismatch, Median Percentage of Mitochondrial Reads per Nucleus, Contamination,Contamination Error",,FALSE,Sequencing,scATAC-seq Level 1,, scATAC-seq Level 3,Processed data files containing peak information for cells,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, scATAC-seq Object ID, nCount Peaks, nFeature Peaks, Total Read-Pairs, Duplicate Read-Pairs, Chimeric Read-Pairs, Unmapped Read-Pairs, LowMapQ, Mitochondrial Read-Pairs, Passed Filters, TSS Fragments, DNase Sensitive Region Fragments, Enhancer Region Fragments, Promoter Region Fragments, On Target Fragments, Blacklist Region Fragments, Peak Region Fragments, Peak Region Cutsites, Nucleosome Signal, Nucleosome Percentile, TSS Enrichment, TSS Percentile, Pct Reads in Peaks, Blacklist Ratio, Seurat Clusters, nCount RNA, nFeature RNA, MACS2 Seqnames, MACS2 Start, MACS2 End, MACS2 Width, MACS2 Strand, MACS2 Name, MACS2 Score, MACS2 Fold Change, MACS2 Neg Log10 pvalue Summit, MACS2 Neg Log10 qvalue Summit, MACS2 Relative Summit Position",,FALSE,Sequencing,scATAC-seq Level 2,, -scmC-seq Level 1,Files contain raw scmC-seq data.,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Nucleic Acid Source, scmCseq Read1, scmCseq Read2, scmCseq Read3, Nucleic Acid Source, Single Cell Isolation Method, Single Nucleus Buffer, Single Nucleus Capture, Bisulfite Conversion, Library Layout, Nucleus Identifier, Sequencing Platform, Technical Replicate Group, Median Fraction of Reads in Peaks, Median Passing Read Percentage, Peaks Calling Software, Median Percentage of Mitochondrial Reads per Nucleus, Threshold for Minimum Passing Reads, Total Number of Passing Nuclei, Total Reads",,FALSE,Sequencing,Biospecimen,, -scmC-seq Level 2,"Files contain scmC-seq files containing aligned sequence data, as a BAM file.",,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Alignment Workflow Url, Alignment Workflow Type, Genomic Reference, Genomic Reference URL, Index File Name, Average Base Quality, Average Insert Size, Average Read Length, Contamination, Contamination Error, Mean Coverage, Pairs On Diff CHR, Total Reads, Total Uniquely Mapped, Total Unmapped reads, Proportion Reads Duplicated, Proportion Reads Mapped, Proportion Targets No Coverage, Proportion Base Mismatch, Short Reads, Proportion Reads Mapped, Proportion Targets No Coverage",,FALSE,Sequencing,scmC-seq Level 1,, +scmC-seq Level 1,Files contain raw scmC-seq data.,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Nucleic Acid Source, scmCseq Read1, scmCseq Read2, scmCseq Read3, Single Cell Isolation Method, Single Nucleus Buffer, Single Nucleus Capture, Bisulfite Conversion, Library Layout, Nucleus Identifier, Sequencing Platform, Technical Replicate Group, Median Fraction of Reads in Peaks, Median Passing Read Percentage, Peaks Calling Software, Median Percentage of Mitochondrial Reads per Nucleus, Threshold for Minimum Passing Reads, Total Number of Passing Nuclei, Total Reads",,FALSE,Sequencing,Biospecimen,, +scmC-seq Level 2,"Files contain scmC-seq files containing aligned sequence data, as a BAM file.",,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Alignment Workflow Url, Alignment Workflow Type, Genomic Reference, Genomic Reference URL, Index File Name, Average Base Quality, Average Insert Size, Average Read Length, Contamination, Contamination Error, Mean Coverage, Pairs On Diff CHR, Total Reads, Total Uniquely Mapped, Total Unmapped reads, Proportion Reads Duplicated, Proportion Reads Mapped, Proportion Targets No Coverage, Proportion Base Mismatch, Short Reads",,FALSE,Sequencing,scmC-seq Level 1,, scATAC-seq Level 4,"Data represents the relationships between cells derived from Level 3 expression data and shown as tSNE or UMAP coordinates per cell, plus all other cell-specific meta information (e.g., cell type)",,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, scATACseq Workflow Type, scATACseq Workflow Parameters Description, Workflow Version, Workflow Link",,FALSE,Sequencing,scATAC-seq Level 3,, scDNA-seq Level 1,Single-cell DNA-seq,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Sequencing Batch ID, Library Layout, Nucleic Acid Source, Library Selection Method, Read Length, Library Preparation Kit Name, Library Preparation Kit Vendor, Library Preparation Kit Version, Adapter Name, Adapter Sequence, Base Caller Name, Base Caller Version, Flow Cell Barcode, Fragment Maximum Length, Fragment Mean Length, Fragment Minimum Length, Fragment Standard Deviation Length, Lane Number, Library Strand, Multiplex Barcode, Size Selection Range, Target Depth, To Trim Adapter Sequence, Adapter Content, Basic Statistics, Encoding, Kmer Content, Overrepresented Sequences, Per Base N Content, Per Base Sequence Content, Per Base Sequence Quality, Per Sequence GC Content, Per Sequence Quality Score, Per Tile Sequence Quality, Percent GC Content, Sequence Duplication Levels, Sequence Length Distribution, Total Reads, QC Workflow Type, QC Workflow Version, QC Workflow Link",,FALSE,Sequencing,Biospecimen,, scDNA-seq Level 2,Alignment workflows downstream of scDNA-seq Level 1,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Alignment Workflow Url, Alignment Workflow Type, Genomic Reference, Genomic Reference URL, Index File Name, Average Base Quality, Average Insert Size, Average Read Length, Mean Coverage, Pairs On Diff CHR, Total Reads, Proportion Reads Mapped, MapQ30, Total Uniquely Mapped, Total Unmapped reads,Proportion Reads Duplicated, Short Reads, Proportion Coverage 10x, Proportion Coverage 30X, Proportion Targets No Coverage, Proportion Base Mismatch, Proportion Mitochondrial Reads, Contamination, Contamination Error",,FALSE,Sequencing,scDNA-seq Level 1,, Bulk Methylation-seq Level 1,"Raw data for bulk methylation sequencing, such as FASTQs and unaligned BAMs",,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Nucleic Acid Source, Bisulfite Conversion, Sequencing Platform, Replicate Type, Bulk Methylation Assay Type, Total DNA Input",,FALSE,Sequencing,Biospecimen,, -Bulk Methylation-seq Level 2,"Aligned primary data for bulk methylation sequencing, such as gene expression matrix files, VCFs, etc.",,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Alignment Workflow Url, Trimmer, Bulk Methylation Genomic Reference, Genomic Reference URL, Index File Name, Alignment Workflow Type, Duplicate Removal Software, Mean Coverage, Library Layout, Average Base Quality, Average Insert Size, Average Read Length, Contamination, Contamination Error, Pairs On Diff CHR, Total Reads, Total Uniquely Mapped, Total Unmapped reads, Proportion Reads Duplicated, Proportion Reads Mapped, Proportion Targets No Coverage, Proportion Base Mismatch, Short Reads, Proportion of Minimum CpG Coverage 10X, Proportion Coverage 30X, Proportion Reads Duplicated, Proportion Targets No Coverage",,FALSE,Sequencing,"Bulk Methylation-seq Level 1, Biospecimen",, +Bulk Methylation-seq Level 2,"Aligned primary data for bulk methylation sequencing, such as gene expression matrix files, VCFs, etc.",,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Alignment Workflow Url, Trimmer, Bulk Methylation Genomic Reference, Genomic Reference URL, Index File Name, Alignment Workflow Type, Duplicate Removal Software, Mean Coverage, Library Layout, Average Base Quality, Average Insert Size, Average Read Length, Contamination, Contamination Error, Pairs On Diff CHR, Total Reads, Total Uniquely Mapped, Total Unmapped reads, Proportion Reads Duplicated, Proportion Reads Mapped, Proportion Targets No Coverage, Proportion Base Mismatch, Short Reads, Proportion of Minimum CpG Coverage 10X, Proportion Coverage 30X",,FALSE,Sequencing,"Bulk Methylation-seq Level 1, Biospecimen",, Bulk Methylation-seq Level 3,"Sample level summary data for bulk methylation sequencing, such as t-SNE plot coordinates, etc.",,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID,DMC Calling Tool, DMC Calling Workflow URL, DMR Calling Tool, DMR Calling Workflow URL, pUC19 methylation ratio, Lambda methylation ratio, DMC data file format, DMR data file Format",,FALSE,Sequencing,"Bulk Methylation-seq Level 2, Biospecimen",, Imaging Level 1,Raw imaging data,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Imaging Assay Type, Protocol Link, Software and Version, Commit SHA, Pre-processing Completed, Pre-processing Required, Comment",,FALSE,Assay,Biospecimen,, Imaging Level 2,Raw and pre-processed image data,,"Component, Filename, File Format, HTAN Participant ID, HTAN Parent Biospecimen ID, HTAN Data File ID, Channel Metadata Filename, Imaging Assay Type, Protocol Link, Software and Version, Microscope, Objective, NominalMagnification, LensNA, WorkingDistance,WorkingDistanceUnit, Immersion, Pyramid, Zstack, Tseries, Passed QC, Comment, FOV number, FOVX, FOVXUnit, FOVY, FOVYUnit, Frame Averaging, Image ID, DimensionOrder, PhysicalSizeX, PhysicalSizeXUnit, PhysicalSizeY, PhysicalSizeYUnit, PhysicalSizeZ, PhysicalSizeZUnit, Pixels BigEndian, PlaneCount, SizeC, SizeT, SizeX, SizeY, SizeZ, PixelType, MERFISH Positions File, MERFISH Codebook File",,FALSE,Assay,Imaging Level 1,, @@ -163,7 +163,7 @@ RPPA Level 2,Array based protemics. Each dilution curve of spot intensities is f HTAN RPPA Antibody Table,A table containing antibody level metadata for RPPA,,"HTAN RPPA Antibody Table ID, Filename, File Format, Ab Name Reported on Dataset, GENCODE Gene Symbol Target, UNIPROT Protein ID Target, Phosphoprotein Flag, Vendor, Catalog Number, Internal Ab ID, Species, RPPA Dilution, Phospho Site, RPPA Validation Status, Clone, Clonality, Antibody Notes",,TRUE,RPPA Level 2,RPPA Level 2,, RPPA Level 3,Level 3 Reverse Phase Protein Array (RPPA) data contains intra-batch normalized intensities.,,"Component, Filename, File Format, HTAN Participant ID, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, HTAN Data File ID, Assay Type, Software and Version, Normalization Method",,FALSE,Assay,Biospecimen,, RPPA Level 4,Level 4 Reverse Phase Protein Array (RPPA) data contains intra-batch corrected intensities.,,"Component, Filename, File Format, HTAN Participant ID, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, HTAN Data File ID, Assay Type, Batch Correction Method",,FALSE,Assay,RPPA Level 2,, -Mass Spectrometry Level 1,"Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 1",,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, MS Batch ID, MS-based Assay Type, Analyte Type, MS-based Targeted, MS Instrument Vendor and Model, MS Source, Polarity, Mass Range Low Value, Mass Range High Value, Data Collection Mode, MS Scan Mode, MS Labeling, Protocol Link, LC Instrument Vendor and Model, LC Column Vendor and Model, LC Resin, LC Length Value, LC Temp Value, LC ID Value, LC Flow Rate, LC Gradient, LC Mobile Phase A, LC Mobile Phase B, Software and Version, Protocol Link, MS Instrument Metadata File",,FALSE,Assay,Biospecimen,, +Mass Spectrometry Level 1,"Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 1",,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, MS Batch ID, MS-based Assay Type, Analyte Type, MS-based Targeted, MS Instrument Vendor and Model, MS Source, Polarity, Mass Range Low Value, Mass Range High Value, Data Collection Mode, MS Scan Mode, MS Labeling, Protocol Link, LC Instrument Vendor and Model, LC Column Vendor and Model, LC Resin, LC Length Value, LC Temp Value, LC ID Value, LC Flow Rate, LC Gradient, LC Mobile Phase A, LC Mobile Phase B, Software and Version, MS Instrument Metadata File",,FALSE,Assay,Biospecimen,, Mass Spectrometry Level 2,"Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 2",,"Component, Filename, File Format, HTAN Data File ID, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, MS Assay Category, Software and Version, Mass Spectrometry Auxiliary File",,FALSE,Assay,Mass Spectrometry Level 1,, Mass Spectrometry Level 3,"Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 3",,"Component, Filename, File Format, HTAN Data File ID, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, MS Assay Category, Software and Version, Mass Spectrometry Auxiliary File",,FALSE,Assay,Mass Spectrometry Level 2,, Mass Spectrometry Level 4,"Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 4",,"Component, Filename, File Format, HTAN Data File ID, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, MS Assay Category, Software and Version, Mass Spectrometry Auxiliary File",,FALSE,Assay,Mass Spectrometry Level 3,, @@ -591,7 +591,7 @@ Recist Targeted Regions Number,"Numeric value that represents the number of base Recist Targeted Regions Sum,"Numeric value that represents the sum of baseline target lesions, as described by the Response Evaluation Criteria in Solid Tumours (RECIST) criteria.",,,,FALSE,Follow Up,,, Scan Tracer Used,The text term used to describe the type of tracer used during the imaging or scan of the patient.,"Acetate, Axumin, Choline, PSMA, Sodium Fluoride",,,FALSE,Follow Up,,, Progression or Recurrence,Yes/No/unknown indicator to identify whether a patient has had a new tumor event after initial treatment.,"Yes - Progression or Recurrence, No, unknown, Not Reported",,,TRUE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3121376&version=1.0, -Yes - Progression or Recurrence,The patient has had a new tumor event after initial treatment,,"Progression or Recurrence Type, Days to Progression, Days to Progression Free, Days to Recurrence, Days to Recurrence, Progression or Recurrence Anatomic Site",,FALSE,Diagnosis,,, +Yes - Progression or Recurrence,The patient has had a new tumor event after initial treatment,,"Progression or Recurrence Type, Days to Progression, Days to Progression Free, Days to Recurrence, Progression or Recurrence Anatomic Site",,FALSE,Diagnosis,,, Progression or Recurrence Anatomic Site,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,"Abdomen NOS,Abdominal esophagus,Accessory sinus NOS,Acoustic nerve,Adrenal gland NOS,Ampulla of Vater,Anal canal,Anterior 2/3 of tongue NOS,Anterior floor of mouth,Anterior mediastinum,Anterior surface of epiglottis,Anterior wall of bladder,Anterior wall of nasopharynx,Anus NOS,Aortic body and other paraganglia,Appendix,Ascending colon,Autonomic nervous system NOS,Axillary tail of breast,Base of tongue NOS,Bladder neck,Bladder NOS,Blood,Body of pancreas,Body of penis,Body of stomach,Bone marrow,Bone of limb NOS,Bone NOS,Bones of skull and face and associated joints,Border of tongue,Brain stem,Brain NOS,Branchial cleft,Breast NOS,Broad ligament,Cardia NOS,Carotid body,Cauda equina,Cecum,Central portion of breast,Cerebellum NOS,Cerebral meninges,Cerebrum,Cervical esophagus,Cervix uteri,Choroid,Ciliary body,Cloacogenic zone,Colon NOS,Commissure of lip,Conjunctiva,Connective subcutaneous and other soft tissues of abdomen,Connective subcutaneous and other soft tissues of head face and neck,Connective subcutaneous and other soft tissues of lower limb and hip,Connective subcutaneous and other soft tissues of pelvis,Connective subcutaneous and other soft tissues of thorax,Connective subcutaneous and other soft tissues of trunk NOS,Connective subcutaneous and other soft tissues of upper limb and shoulder,Connective subcutaneous and other soft tissues NOS,Cornea NOS,Corpus uteri,Cortex of adrenal gland,Cranial nerve NOS,Craniopharyngeal duct,Descended testis,Descending colon,Dome of bladder,Dorsal surface of tongue NOS,Duodenum,Endocervix,Endocrine gland NOS,Endometrium,Epididymis,Esophagus NOS,Ethmoid sinus,Exocervix,External ear,External lip NOS,External lower lip,External upper lip,Extrahepatic bile duct,Eye NOS,Eyelid,Fallopian tube,Female genital tract NOS,Floor of mouth NOS,Frontal lobe,Frontal sinus,Fundus of stomach,Fundus uteri,Gallbladder,Gastric antrum,Gastrointestinal tract NOS,Glans penis,Glottis,Greater curvature of stomach NOS,Gum NOS,Hard palate,Head of pancreas,Head face or neck NOS,Heart,Hematopoietic system NOS,Hepatic flexure of colon,Hypopharyngeal aspect of aryepiglottic fold,Hypopharynx NOS,Ileum,Ill-defined sites within respiratory system,Intestinal tract NOS,Intra-abdominal lymph nodes,Intrahepatic bile duct,Intrathoracic lymph nodes,Islets of Langerhans,Isthmus uteri,Jejunum,Kidney NOS,Labium majus,Labium minus,Lacrimal gland,Laryngeal cartilage,Larynx NOS,Lateral floor of mouth,Lateral wall of bladder,Lateral wall of nasopharynx,Lateral wall of oropharynx,Lesser curvature of stomach NOS,Lingual tonsil,Lip NOS,Liver,Long bones of lower limb and associated joints,Long bones of upper limb scapula and associated joints,Lower gum,Lower limb NOS,Lower lobe lung,Lower third of esophagus,Lower-inner quadrant of breast,Lower-outer quadrant of breast,Lung NOS,Lymph node NOS,Lymph nodes of axilla or arm,Lymph nodes of head face and neck,Lymph nodes of inguinal region or leg,Lymph nodes of multiple regions,Main bronchus,Major salivary gland NOS,Male genital organs NOS,Mandible,Maxillary sinus,Meckel diverticulum,Mediastinum NOS,Medulla of adrenal gland,Meninges NOS,Middle ear,Middle lobe lung,Middle third of esophagus,Mouth NOS,Mucosa of lip NOS,Mucosa of lower lip,Mucosa of upper lip,Myometrium,Nasal cavity,Nasopharynx NOS,Nervous system NOS,Nipple,Occipital lobe,Olfactory nerve,Optic nerve,Orbit NOS,Oropharynx NOS,Other ill-defined sites,Other specified parts of female genital organs,Other specified parts of male genital organs,Other specified parts of pancreas,Ovary,Overlapping lesion of accessory sinuses,Overlapping lesion of bladder,Overlapping lesion of bones joints and articular cartilage,Overlapping lesion of bones joints and articular cartilage of limbs,Overlapping lesion of brain,Overlapping lesion of brain and central nervous system,Overlapping lesion of breast,Overlapping lesion of cervix uteri,Overlapping lesion of colon,Overlapping lesion of connective subcutaneous and other soft tissues,Overlapping lesion of corpus uteri,Overlapping lesion of digestive system,Overlapping lesion of endocrine glands and related structures,Overlapping lesion of esophagus,Overlapping lesion of eye and adnexa,Overlapping lesion of female genital organs,Overlapping lesion of floor of mouth,Overlapping lesion of heart mediastinum and pleura,Overlapping lesion of hypopharynx,Overlapping lesion of ill-defined sites,Overlapping lesion of larynx,Overlapping lesion of lip,Overlapping lesion of lip oral cavity and pharynx,Overlapping lesion of lung,Overlapping lesion of major salivary glands,Overlapping lesion of male genital organs,Overlapping lesion of nasopharynx,Overlapping lesion of other and unspecified parts of mouth,Overlapping lesion of palate,Overlapping lesion of pancreas,Overlapping lesion of penis,Overlapping lesion of peripheral nerves and autonomic nervous system,Overlapping lesion of rectum anus and anal canal,Overlapping lesion of respiratory system and intrathoracic organs,Overlapping lesion of retroperitoneum and peritoneum,Overlapping lesion of skin,Overlapping lesion of small intestine,Overlapping lesion of stomach,Overlapping lesion of tongue,Overlapping lesion of tonsil,Overlapping lesion of urinary organs,Overlapping lesion of vulva,Overlapping lesions of oropharynx,Palate NOS,Pancreas NOS,Pancreatic duct,Parametrium,Parathyroid gland,Paraurethral gland,Parietal lobe,Parotid gland,Pelvic bones sacrum coccyx and associated joints,Pelvic lymph nodes,Pelvis NOS,Penis NOS,Peripheral nerves and autonomic nervous system of abdomen,Peripheral nerves and autonomic nervous system of head face and neck,Peripheral nerves and autonomic nervous system of lower limb and hip,Peripheral nerves and autonomic nervous system of pelvis,Peripheral nerves and autonomic nervous system of thorax,Peripheral nerves and autonomic nervous system of trunk NOS,Peripheral nerves and autonomic nervous system of upper limb and shoulder,Peritoneum NOS,Pharynx NOS,Pineal gland,Pituitary gland,Placenta,Pleura NOS,Postcricoid region,Posterior mediastinum,Posterior wall of bladder,Posterior wall of hypopharynx,Posterior wall of nasopharynx,Posterior wall of oropharynx,Prepuce,Prostate gland,Pylorus,Pyriform sinus,Rectosigmoid junction,Rectum NOS,Renal pelvis,Reticuloendothelial system NOS,Retina,Retromolar area,Retroperitoneum,Rib sternum clavicle and associated joints,Round ligament,Scrotum NOS,Short bones of lower limb and associated joints,Short bones of upper limb and associated joints,Sigmoid colon,Skin of lip NOS,Skin of lower limb and hip,Skin of other and unspecified parts of face,Skin of scalp and neck,Skin of trunk,Skin of upper limb and shoulder,Skin NOS,Small intestine NOS,Soft palate NOS,Specified parts of peritoneum,Spermatic cord,Sphenoid sinus,Spinal cord,Spinal meninges,Spleen,Splenic flexure of colon,Stomach NOS,Subglottis,Sublingual gland,Submandibular gland,Superior wall of nasopharynx,Supraglottis,Tail of pancreas,Temporal lobe,Testis NOS,Thoracic esophagus,Thorax NOS,Thymus,Thyroid gland,Tongue NOS,Tonsil NOS,Tonsillar fossa,Tonsillar pillar,Trachea,Transverse colon,Trigone of bladder,Undescended testis,unknown primary site,Upper gum,Upper limb NOS,Upper lobe lung,Upper respiratory tract NOS,Upper third of esophagus,Upper-inner quadrant of breast,Upper-outer quadrant of breast,Urachus,Ureter,Ureteric orifice,Urethra,Urinary system NOS,Uterine adnexa,Uterus NOS,Uvula,Vagina NOS,Vallecula,Ventral surface of tongue NOS,Ventricle NOS,Vertebral column,Vestibule of mouth,Vulva NOS,Waldeyer ring,Biliary tract NOS,Cheek mucosa,Clitoris,Overlapping lesion of biliary tract,unknown,Not Reported",,,FALSE,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6161026&version=1.0, Treatment Anatomic Site,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,"Abdomen NOS,Abdominal esophagus,Accessory sinus NOS,Acoustic nerve,Adrenal gland NOS,Ampulla of Vater,Anal canal,Anterior 2/3 of tongue NOS,Anterior floor of mouth,Anterior mediastinum,Anterior surface of epiglottis,Anterior wall of bladder,Anterior wall of nasopharynx,Anus NOS,Aortic body and other paraganglia,Appendix,Ascending colon,Autonomic nervous system NOS,Axillary tail of breast,Base of tongue NOS,Bladder neck,Bladder NOS,Blood,Body of pancreas,Body of penis,Body of stomach,Bone marrow,Bone of limb NOS,Bone NOS,Bones of skull and face and associated joints,Border of tongue,Brain stem,Brain NOS,Branchial cleft,Breast NOS,Broad ligament,Cardia NOS,Carotid body,Cauda equina,Cecum,Central portion of breast,Cerebellum NOS,Cerebral meninges,Cerebrum,Cervical esophagus,Cervix uteri,Choroid,Ciliary body,Cloacogenic zone,Colon NOS,Commissure of lip,Conjunctiva,Connective subcutaneous and other soft tissues of abdomen,Connective subcutaneous and other soft tissues of head face and neck,Connective subcutaneous and other soft tissues of lower limb and hip,Connective subcutaneous and other soft tissues of pelvis,Connective subcutaneous and other soft tissues of thorax,Connective subcutaneous and other soft tissues of trunk NOS,Connective subcutaneous and other soft tissues of upper limb and shoulder,Connective subcutaneous and other soft tissues NOS,Cornea NOS,Corpus uteri,Cortex of adrenal gland,Cranial nerve NOS,Craniopharyngeal duct,Descended testis,Descending colon,Dome of bladder,Dorsal surface of tongue NOS,Duodenum,Endocervix,Endocrine gland NOS,Endometrium,Epididymis,Esophagus NOS,Ethmoid sinus,Exocervix,External ear,External lip NOS,External lower lip,External upper lip,Extrahepatic bile duct,Eye NOS,Eyelid,Fallopian tube,Female genital tract NOS,Floor of mouth NOS,Frontal lobe,Frontal sinus,Fundus of stomach,Fundus uteri,Gallbladder,Gastric antrum,Gastrointestinal tract NOS,Glans penis,Glottis,Greater curvature of stomach NOS,Gum NOS,Hard palate,Head of pancreas,Head face or neck NOS,Heart,Hematopoietic system NOS,Hepatic flexure of colon,Hypopharyngeal aspect of aryepiglottic fold,Hypopharynx NOS,Ileum,Ill-defined sites within respiratory system,Intestinal tract NOS,Intra-abdominal lymph nodes,Intrahepatic bile duct,Intrathoracic lymph nodes,Islets of Langerhans,Isthmus uteri,Jejunum,Kidney NOS,Labium majus,Labium minus,Lacrimal gland,Laryngeal cartilage,Larynx NOS,Lateral floor of mouth,Lateral wall of bladder,Lateral wall of nasopharynx,Lateral wall of oropharynx,Lesser curvature of stomach NOS,Lingual tonsil,Lip NOS,Liver,Long bones of lower limb and associated joints,Long bones of upper limb scapula and associated joints,Lower gum,Lower limb NOS,Lower lobe lung,Lower third of esophagus,Lower-inner quadrant of breast,Lower-outer quadrant of breast,Lung NOS,Lymph node NOS,Lymph nodes of axilla or arm,Lymph nodes of head face and neck,Lymph nodes of inguinal region or leg,Lymph nodes of multiple regions,Main bronchus,Major salivary gland NOS,Male genital organs NOS,Mandible,Maxillary sinus,Meckel diverticulum,Mediastinum NOS,Medulla of adrenal gland,Meninges NOS,Middle ear,Middle lobe lung,Middle third of esophagus,Mouth NOS,Mucosa of lip NOS,Mucosa of lower lip,Mucosa of upper lip,Myometrium,Nasal cavity,Nasopharynx NOS,Nervous system NOS,Nipple,Occipital lobe,Olfactory nerve,Optic nerve,Orbit NOS,Oropharynx NOS,Other ill-defined sites,Other specified parts of female genital organs,Other specified parts of male genital organs,Other specified parts of pancreas,Ovary,Overlapping lesion of accessory sinuses,Overlapping lesion of bladder,Overlapping lesion of bones joints and articular cartilage,Overlapping lesion of bones joints and articular cartilage of limbs,Overlapping lesion of brain,Overlapping lesion of brain and central nervous system,Overlapping lesion of breast,Overlapping lesion of cervix uteri,Overlapping lesion of colon,Overlapping lesion of connective subcutaneous and other soft tissues,Overlapping lesion of corpus uteri,Overlapping lesion of digestive system,Overlapping lesion of endocrine glands and related structures,Overlapping lesion of esophagus,Overlapping lesion of eye and adnexa,Overlapping lesion of female genital organs,Overlapping lesion of floor of mouth,Overlapping lesion of heart mediastinum and pleura,Overlapping lesion of hypopharynx,Overlapping lesion of ill-defined sites,Overlapping lesion of larynx,Overlapping lesion of lip,Overlapping lesion of lip oral cavity and pharynx,Overlapping lesion of lung,Overlapping lesion of major salivary glands,Overlapping lesion of male genital organs,Overlapping lesion of nasopharynx,Overlapping lesion of other and unspecified parts of mouth,Overlapping lesion of palate,Overlapping lesion of pancreas,Overlapping lesion of penis,Overlapping lesion of peripheral nerves and autonomic nervous system,Overlapping lesion of rectum anus and anal canal,Overlapping lesion of respiratory system and intrathoracic organs,Overlapping lesion of retroperitoneum and peritoneum,Overlapping lesion of skin,Overlapping lesion of small intestine,Overlapping lesion of stomach,Overlapping lesion of tongue,Overlapping lesion of tonsil,Overlapping lesion of urinary organs,Overlapping lesion of vulva,Overlapping lesions of oropharynx,Palate NOS,Pancreas NOS,Pancreatic duct,Parametrium,Parathyroid gland,Paraurethral gland,Parietal lobe,Parotid gland,Pelvic bones sacrum coccyx and associated joints,Pelvic lymph nodes,Pelvis NOS,Penis NOS,Peripheral nerves and autonomic nervous system of abdomen,Peripheral nerves and autonomic nervous system of head face and neck,Peripheral nerves and autonomic nervous system of lower limb and hip,Peripheral nerves and autonomic nervous system of pelvis,Peripheral nerves and autonomic nervous system of thorax,Peripheral nerves and autonomic nervous system of trunk NOS,Peripheral nerves and autonomic nervous system of upper limb and shoulder,Peritoneum NOS,Pharynx NOS,Pineal gland,Pituitary gland,Placenta,Pleura NOS,Postcricoid region,Posterior mediastinum,Posterior wall of bladder,Posterior wall of hypopharynx,Posterior wall of nasopharynx,Posterior wall of oropharynx,Prepuce,Prostate gland,Pylorus,Pyriform sinus,Rectosigmoid junction,Rectum NOS,Renal pelvis,Reticuloendothelial system NOS,Retina,Retromolar area,Retroperitoneum,Rib sternum clavicle and associated joints,Round ligament,Scrotum NOS,Short bones of lower limb and associated joints,Short bones of upper limb and associated joints,Sigmoid colon,Skin of lip NOS,Skin of lower limb and hip,Skin of other and unspecified parts of face,Skin of scalp and neck,Skin of trunk,Skin of upper limb and shoulder,Skin NOS,Small intestine NOS,Soft palate NOS,Specified parts of peritoneum,Spermatic cord,Sphenoid sinus,Spinal cord,Spinal meninges,Spleen,Splenic flexure of colon,Stomach NOS,Subglottis,Sublingual gland,Submandibular gland,Superior wall of nasopharynx,Supraglottis,Tail of pancreas,Temporal lobe,Testis NOS,Thoracic esophagus,Thorax NOS,Thymus,Thyroid gland,Tongue NOS,Tonsil NOS,Tonsillar fossa,Tonsillar pillar,Trachea,Transverse colon,Trigone of bladder,Undescended testis,unknown primary site,Upper gum,Upper limb NOS,Upper lobe lung,Upper respiratory tract NOS,Upper third of esophagus,Upper-inner quadrant of breast,Upper-outer quadrant of breast,Urachus,Ureter,Ureteric orifice,Urethra,Urinary system NOS,Uterine adnexa,Uterus NOS,Uvula,Vagina NOS,Vallecula,Ventral surface of tongue NOS,Ventricle NOS,Vertebral column,Vestibule of mouth,Vulva NOS,Waldeyer ring,Biliary tract NOS,Cheek mucosa,Clitoris,Overlapping lesion of biliary tract,unknown,Not Reported",,,FALSE,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6161026&version=1.0, NCI Atlas Cancer Site,"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","Bladder, Brain And Other Nervous System, Female Breast, In situ Female Breast, Cervix Uteri, Less Than Age, Malignant Childhood Neoplasm, Colon And Rectum, Esophagus, Kidney And Renal Pelvis, Leukemia, Liver And Bile Duct, Lung And Bronchus, Cutaneous Melanoma, Non-Hodgkin's Lymphoma, Oral Cavity And Pharynx, Ovary, Pancreas, Prostate Gland, Stomach, Thyroid Gland, Uterus",,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=7639473&version=1.0, From a2cc1d33f0fb4ba60bfa109b74dcba2e7cb0fae3 Mon Sep 17 00:00:00 2001 From: elv-sb Date: Thu, 26 Oct 2023 12:40:34 +0000 Subject: [PATCH 2/2] GitHub Action: convert *.model.csv to *.model.jsonld --- HTAN.model.jsonld | 30 ------------------------------ 1 file changed, 30 deletions(-) diff --git a/HTAN.model.jsonld b/HTAN.model.jsonld index 7d89472d..05931814 100644 --- a/HTAN.model.jsonld +++ b/HTAN.model.jsonld @@ -4853,12 +4853,6 @@ { "@id": "bts:PreinvasiveMorphology" }, - { - "@id": "bts:IschemicTime" - }, - { - "@id": "bts:IschemicTemperature" - }, { "@id": "bts:HistologicMorphologyCode" }, @@ -5469,9 +5463,6 @@ { "@id": "bts:WorkflowLink" }, - { - "@id": "bts:WorkflowVersion" - }, { "@id": "bts:BeadsTotal" }, @@ -6714,9 +6705,6 @@ { "@id": "bts:ScmCseqRead3" }, - { - "@id": "bts:NucleicAcidSource" - }, { "@id": "bts:SingleCellIsolationMethod" }, @@ -6860,12 +6848,6 @@ }, { "@id": "bts:ShortReads" - }, - { - "@id": "bts:ProportionReadsMapped" - }, - { - "@id": "bts:ProportionTargetsNoCoverage" } ], "sms:validationRules": [] @@ -7364,12 +7346,6 @@ }, { "@id": "bts:ProportionCoverage30X" - }, - { - "@id": "bts:ProportionReadsDuplicated" - }, - { - "@id": "bts:ProportionTargetsNoCoverage" } ], "sms:validationRules": [] @@ -10727,9 +10703,6 @@ { "@id": "bts:SoftwareandVersion" }, - { - "@id": "bts:ProtocolLink" - }, { "@id": "bts:MSInstrumentMetadataFile" } @@ -26947,9 +26920,6 @@ { "@id": "bts:DaystoRecurrence" }, - { - "@id": "bts:DaystoRecurrence" - }, { "@id": "bts:ProgressionorRecurrenceAnatomicSite" }