11 add rd cdm entirely (#13)

* edits * fix * fix * edits
BIH-CEI · Sep 28, 2024 · 16c4187 · 16c4187
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diff --git a/.github/workflows/pages.yml b/.github/workflows/pages.yml
@@ -31,15 +31,24 @@ jobs:
         mkdir -p gh-pages
         touch gh-pages/.nojekyll
         
+        function branch_exists {
+          git show-ref refs/heads/$1 > /dev/null 2>&1
+        }
+        
         function build_docs {
-          # The function will checkout a branch and build the Javadoc & documentation 
-          # into provided documentation directory.
+          # The function will checkout a branch and build the Sphinx docs 
+          # into the provided documentation directory.
           BRANCH=${1}
           DOCDIR=${2}
-        
-          git checkout ${BRANCH}
-          git fetch
-          git pull
+          
+          if branch_exists ${BRANCH}; then
+            git checkout ${BRANCH}
+            git fetch
+            git pull
+          else
+            echo "Branch ${BRANCH} does not exist. Skipping..."
+            return
+          fi
         
           ## Init the target folder.
           # We will put all site documentation there.
@@ -57,12 +66,11 @@ jobs:
           cd ..
         }
         
-        # We store the docs for `main` in `stable` dir
+        # We store the docs for `main` in `stable` dir, if it exists
         build_docs main stable
-        # We store the docs for `development` in `latest` dir
+        # We store the docs for `develop` in `latest` dir
         build_docs develop latest
 
-
     - name: Deploy documentation
       if: ${{ github.event_name == 'push' }}
       uses: JamesIves/[email protected]

diff --git a/README.md b/README.md
@@ -4,7 +4,7 @@ An ontology-based Rare Disease Common Data Model (RD CDM) to enable
 international registry use, HL7 FHIR, and GA4GH Phenopackets.
 
 <!-- Python CI and Documentation Status Badges -->
-[![Python CI](https://github.com/BIH-CEI/rd-cdm/actions/workflows/python_ci.yml/badge.svg)](https://github.com/{OWNER}/{REPO}/actions/workflows/python_ci.yml)
+[![Python CI](https://github.com/BIH-CEI/rd-cdm/actions/workflows/python_ci.yml/badge.svg)](https://github.com/BIH-CEI/rd-cdm/actions/workflows/python_ci.yml)
 [![Documentation Status](https://readthedocs.org/projects/rd-cdm/badge/?version=latest)](https://rd-cdm.readthedocs.io/en/latest/?badge=latest)
 
 <!-- JSON Creation and Validation Badges -->

diff --git a/docs/resources/resources_file.rst → docs/resources/resourscs_file.rst b/docs/resources/resources_file.rst → docs/resources/resourscs_file.rst
diff --git a/res/v2_0_0/rd_cdm_codesystems_v2_0_0.json b/res/v2_0_0/rd_cdm_codesystems_v2_0_0.json
@@ -22,6 +22,28 @@
       "url": "http://www.sequenceontology.org/",
       "synonyms": []
     },
+    {
+      "codeSystemName": "International Classification of Diseases, Ninth Revision",
+      "namespace_prefix": "ICD9",
+      "version": "unknown",
+      "url": "https://www.cdc.gov/nchs/icd/icd9.htm",
+      "synonyms": [
+        "ICD-9",
+        "ICD_9"
+      ]
+    },
+    {
+      "codeSystemName": "International Classification of Diseases, Tenth Revision, German Modification",
+      "namespace_prefix": "ICD10GM",
+      "version": "unknown",
+      "url": "https://www.bfarm.de/EN/Code-systems/Classifications/ICD/ICD-10-GM/_node.html",
+      "synonyms": [
+        "ICD10-GM",
+        "ICD-10-GM",
+        "ICD10_GM",
+        "ICD_10_GM"
+      ]
+    },
     {
       "codeSystemName": "International Classification of Diseases, Tenth Revision, Clinical Modification",
       "namespace_prefix": "ICD10CM",
@@ -75,7 +97,7 @@
       "synonyms": []
     },
     {
-      "codeSystemName": "International Classification of Functioning, Disability and Health (ICF)",
+      "codeSystemName": "International Classification of Functioning, Disability and Health",
       "namespace_prefix": "ICF",
       "version": "1.0.2",
       "url": "https://www.who.int/classifications/icf/en/",

diff --git a/res/v2_0_0/rd_cdm_data_elements_v2_0_0.json b/res/v2_0_0/rd_cdm_data_elements_v2_0_0.json
@@ -12,10 +12,10 @@
         "n/a"
       ],
       "valueSet": null,
-      "fhirExpression_v4.0.1": "Patient.identifier.value",
-      "recommendedVS_fhir": null,
-      "phenopacketSchemaElement_v2.0": "Individual.id",
-      "recommendedVS_phenopacket": null,
+      "fhirExpression_v4_0_1": "Patient.identifier.value",
+      "recommendedDataSpec_fhir": "n/a",
+      "phenopacketSchemaElement_v2_0": "Individual.id",
+      "recommendedDataSpec_phenopackets": "string",
       "description": "The (local) patient-related identification code."
     },
     {
@@ -26,14 +26,13 @@
       "elementCodeSystem": "SNOMED",
       "dataType": "Date",
       "dataSpecification": [
-        "YYYY-MM-DD",
-        "ISO 8601"
+        "YYYY-MM-DD"
       ],
       "valueSet": null,
-      "fhirExpression_v4.0.1": "Encounter.period.start",
-      "recommendedVS_fhir": null,
-      "phenopacketSchemaElement_v2.0": "Individual.time_at_last_encounter",
-      "recommendedVS_phenopacket": null,
+      "fhirExpression_v4_0_1": "Encounter.period.start",
+      "recommendedDataSpec_fhir": "n/a",
+      "phenopacketSchemaElement_v2_0": "Individual.time_at_last_encounter",
+      "recommendedDataSpec_phenopackets": "TimeElement",
       "description": "The date of admission or data capture of the individual."
     },
     {
@@ -49,10 +48,10 @@
         "YYYY-MM-DD"
       ],
       "valueSet": null,
-      "fhirExpression_v4.0.1": "Patient.birthDate",
-      "recommendedVS_fhir": null,
-      "phenopacketSchemaElement_v2.0": "Individual.date_of_birth",
-      "recommendedVS_phenopacket": null,
+      "fhirExpression_v4_0_1": "Patient.birthDate",
+      "recommendedDataSpec_fhir": "n/a",
+      "phenopacketSchemaElement_v2_0": "Individual.date_of_birth",
+      "recommendedDataSpec_phenopackets": "TimeElement",
       "description": "The individual's date of birth."
     },
     {
@@ -65,20 +64,235 @@
       "dataSpecification": [
         "VSe / VSc"
       ],
-      "valueSet": {
-        "valueSetName": "Sex at Birth Value Set v2.0.0",
-        "valueSetOrigin": "RD CDM v2.0.0",
-        "valueSetLink": "https://github.com/BIH-CEI/rd-cdm",
-        "display": "Sex at Birth",
-        "valueSetCode": "281053000",
-        "valueSetCodeSystem": "SNOMED",
-        "valueSetChoices": []
-      },
-      "fhirExpression_v4.0.1": "Patient.extension:individual-recordedSexOrGender",
-      "recommendedVS_fhir": "Recorded Sex Or Gender Type",
-      "phenopacketSchemaElement_v2.0": "Individual.sex",
-      "recommendedVS_phenopacket": "Sex",
+      "valueSet": "Sex at Birth Value Set v2.0.0",
+      "fhirExpression_v4_0_1": "Patient.extension:individual-recordedSexOrGender",
+      "recommendedDataSpec_fhir": "Recorded Sex Or Gender Type",
+      "phenopacketSchemaElement_v2_0": "Individual.sex",
+      "recommendedDataSpec_phenopackets": "Sex",
       "description": "The individual's sex that was assigned at birth."
+    },
+    {
+      "ordinal": "2.3",
+      "section": "2. Personal Information",
+      "elementName": "Karyotypic Sex",
+      "elementCode": "1296886006",
+      "elementCodeSystem": "SNOMED",
+      "dataType": "Code",
+      "dataSpecification": [
+        "VSc"
+      ],
+      "valueSet": "Karyotypic Sex Value Set v2.0.0",
+      "fhirExpression_v4_0_1": "Observation.value",
+      "recommendedDataSpec_fhir": "n/a",
+      "phenopacketSchemaElement_v2_0": "Individual.karyotypic_sex",
+      "recommendedDataSpec_phenopackets": "Karyotypic Sex",
+      "description": "The chromosomal sex of an individual."
+    },
+    {
+      "ordinal": "2.4",
+      "section": "2. Personal Information",
+      "elementName": "Gender Identity",
+      "elementCode": "263495000",
+      "elementCodeSystem": "SNOMED",
+      "dataType": "Code",
+      "dataSpecification": [
+        "VSe / VSc"
+      ],
+      "valueSet": "Gender Identity Value Set v2.0.0",
+      "fhirExpression_v4_0_1": "Patient.extension:individual-genderIdentity",
+      "recommendedDataSpec_fhir": "Gender Identity",
+      "phenopacketSchemaElement_v2_0": "Individual.gender",
+      "recommendedDataSpec_phenopackets": "OntologyClass",
+      "description": "The self-assigned gender of the individual."
+    },
+    {
+      "ordinal": "2.5",
+      "section": "2. Personal Information",
+      "elementName": "Country of Birth",
+      "elementCode": "370159000",
+      "elementCodeSystem": "SNOMED",
+      "dataType": "Code",
+      "dataSpecification": [
+        "VS"
+      ],
+      "valueSet": null,
+      "fhirExpression_v4_0_1": "Patient.extension:patient-birthPlace",
+      "recommendedDataSpec_fhir": "DataType: Address",
+      "phenopacketSchemaElement_v2_0": "n/a",
+      "recommendedDataSpec_phenopackets": "n/a",
+      "description": "The individual's country of birth."
+    },
+    {
+      "ordinal": "3.1",
+      "section": "3. Patient Status",
+      "elementName": "Vital Status",
+      "elementCode": "278844005",
+      "elementCodeSystem": "SNOMED",
+      "dataType": "Code",
+      "dataSpecification": [
+        "VSe / VSc"
+      ],
+      "valueSet": "Vital Status Value Set v2.0.0",
+      "fhirExpression_v4_0_1": "Patient.deceased.deceasedBoolean|Observation.value",
+      "recommendedDataSpec_fhir": "Boolean|Code",
+      "phenopacketSchemaElement_v2_0": "Individual.VitalStatus.status",
+      "recommendedDataSpec_phenopackets": "Value Set: Status",
+      "description": "The individual\u2019s general clinical status or vital status."
+    },
+    {
+      "ordinal": "3.2",
+      "section": "3. Patient Status",
+      "elementName": "Time of Death",
+      "elementCode": "398299004",
+      "elementCodeSystem": "SNOMED",
+      "dataType": "Date",
+      "dataSpecification": [
+        "YYYY",
+        "YYYY-MM",
+        "YYYY-MM-DD"
+      ],
+      "valueSet": null,
+      "fhirExpression_v4_0_1": "Patient.deceasedDateTime",
+      "recommendedDataSpec_fhir": "DateTime",
+      "phenopacketSchemaElement_v2_0": "Individual.VitalStatus.time_of_death",
+      "recommendedDataSpec_phenopackets": "TimeElement",
+      "description": "If deceased, the individual\u2019s date of death."
+    },
+    {
+      "ordinal": "3.3",
+      "section": "3. Patient Status",
+      "elementName": "Cause of Death",
+      "elementCode": "184305005",
+      "elementCodeSystem": "SNOMED",
+      "dataType": "Code",
+      "dataSpecification": [
+        "ICD-10CM"
+      ],
+      "valueSet": null,
+      "fhirExpression_v4_0_1": "Observation.value.coding.code",
+      "recommendedDataSpec_fhir": "Code|CodeableConcept",
+      "phenopacketSchemaElement_v2_0": "Individual.VitalStatus.cause_of_death",
+      "recommendedDataSpec_phenopackets": "OntologyClass",
+      "description": "If deceased, the individual\u2019s primary cause of death."
+    },
+    {
+      "ordinal": "3.4",
+      "section": "3. Patient Status",
+      "elementName": "Age Category",
+      "elementCode": "105727008",
+      "elementCodeSystem": "SNOMED",
+      "dataType": "Code",
+      "dataSpecification": [
+        "VSe"
+      ],
+      "valueSet": "Age Category Value Set v2.0.0",
+      "fhirExpression_v4_0_1": "Observation.value.coding.code",
+      "recommendedDataSpec_fhir": "CodableConcept",
+      "phenopacketSchemaElement_v2_0": "Individual.time_at_last_encounter.ontology_class",
+      "recommendedDataSpec_phenopackets": "TimeElement",
+      "description": "The individual's age category at the time of data capture."
+    },
+    {
+      "ordinal": "3.5",
+      "section": "3. Patient Status",
+      "elementName": "Length of Gestation at Birth [weeks+days]",
+      "elementCode": "412726003",
+      "elementCodeSystem": "SNOMED",
+      "dataType": "String",
+      "dataSpecification": [
+        "XX+X"
+      ],
+      "valueSet": null,
+      "fhirExpression_v4_0_1": "Observation.component:weeks.valueQuantity|Observation.component:days.valueQuantity",
+      "recommendedDataSpec_fhir": "Quantity",
+      "phenopacketSchemaElement_v2_0": "n/a",
+      "recommendedDataSpec_phenopackets": "n/a",
+      "description": "The duration of the pregnancy in weeks and days, formatted as XX+X (weeks+days)."
+    },
+    {
+      "ordinal": "3.6",
+      "section": "3. Patient Status",
+      "elementName": "Undiagnosed RD Case",
+      "elementCode": "723663001",
+      "elementCodeSystem": "SNOMED",
+      "dataType": "Code",
+      "dataSpecification": [
+        "VSe"
+      ],
+      "valueSet": "Undiagnosed RD Case Value Set v2.0.0",
+      "fhirExpression_v4_0_1": "(Condition.code)",
+      "recommendedDataSpec_fhir": "Code(e.g. ORDO:616874 - Rare disorder without a determined diagnosis after full investigation)",
+      "phenopacketSchemaElement_v2_0": "(Disease.term)",
+      "recommendedDataSpec_phenopackets": "(OntologyClass (e.g. ORDO:616874 - Rare disorder without a determined diagnosis after full investigation))",
+      "description": "Identifies cases where an RD diagnosis has not been established."
+    },
+    {
+      "ordinal": "4.1",
+      "section": "4. Care Pathway",
+      "elementName": "Encounter Start",
+      "elementCode": "encounter.period.start",
+      "elementCodeSystem": "HL7FHIR",
+      "dataType": "Date",
+      "dataSpecification": [
+        "YYYY-MM-DD"
+      ],
+      "valueSet": null,
+      "fhirExpression_v4_0_1": "Encounter.period.start",
+      "recommendedDataSpec_fhir": "DateTime",
+      "phenopacketSchemaElement_v2_0": "n/a",
+      "recommendedDataSpec_phenopackets": "n/a",
+      "description": "The beginning of an encounter of the individual."
+    },
+    {
+      "ordinal": "4.2",
+      "section": "4. Care Pathway",
+      "elementName": "Encounter End",
+      "elementCode": "encounter.period.end",
+      "elementCodeSystem": "HL7FHIR",
+      "dataType": "Date",
+      "dataSpecification": [
+        "YYYY-MM-DD"
+      ],
+      "valueSet": null,
+      "fhirExpression_v4_0_1": "Encounter.period.end",
+      "recommendedDataSpec_fhir": "DateTime",
+      "phenopacketSchemaElement_v2_0": "n/a",
+      "recommendedDataSpec_phenopackets": "n/a",
+      "description": "The end of an encounter of the individual."
+    },
+    {
+      "ordinal": "4.3",
+      "section": "4. Care Pathway",
+      "elementName": "Encounter Status",
+      "elementCode": "305058001",
+      "elementCodeSystem": "SNOMED",
+      "dataType": "Code",
+      "dataSpecification": [
+        "VSe / VSc"
+      ],
+      "valueSet": "Encounter Status Value Set v2.0.0",
+      "fhirExpression_v4_0_1": "Encounter.status",
+      "recommendedDataSpec_fhir": "ValueSet: EncounterStatus",
+      "phenopacketSchemaElement_v2_0": "n/a",
+      "recommendedDataSpec_phenopackets": "n/a",
+      "description": "The status of an encounter of the individual at the time of data capture."
+    },
+    {
+      "ordinal": "4.4",
+      "section": "4. Care Pathway",
+      "elementName": "Encounter Class",
+      "elementCode": "encounter.class",
+      "elementCodeSystem": "HL7FHIR",
+      "dataType": "Code",
+      "dataSpecification": [
+        "VSe / VSc"
+      ],
+      "valueSet": "Encounter Class Value Set v2.0.0",
+      "fhirExpression_v4_0_1": "Encounter.class",
+      "recommendedDataSpec_fhir": "ValueSet: EncounterClass",
+      "phenopacketSchemaElement_v2_0": "n/a",
+      "recommendedDataSpec_phenopackets": "n/a",
+      "description": "The class of an encounter of the individual at the time of data capture."
     }
   ]
 }