Updated gregor to use newer family group

NIH-NCPI · Sep 13, 2024 · 4d08aba · 4d08aba
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Showing 39 changed files with 406 additions and 1,556 deletions.
diff --git a/fsh-generated/fsh-index.json b/fsh-generated/fsh-index.json
diff --git a/fsh-generated/fsh-index.txt b/fsh-generated/fsh-index.txt
diff --git a/fsh-generated/includes/fsh-link-references.md b/fsh-generated/includes/fsh-link-references.md
@@ -5,6 +5,7 @@
 [AgeAtAssertion]: StructureDefinition-age-at-assertion.html
 [AgeAtLastVitalStatus]: StructureDefinition-research-age-at-last-vital-status.html
 [HashType]: StructureDefinition-hash-type.html
+[gregor-family-relationship-mother]: Observation-gregor-family-relationship-mother.html
 [cbtn-family-relationship-mother]: Observation-cbtn-family-relationship-mother.html
 [cbtn-family-relationship-son]: Observation-cbtn-family-relationship-son.html
 [AssayStrategyCS]: CodeSystem-assay-strategy-cs.html
@@ -35,27 +36,28 @@
 [ResearchDataDateOfBirthMethod]: CodeSystem-research-data-date-of-birth-method.html
 [EDAMOntologyTerms]: ValueSet-edam-ontology-terms.html
 [SA-000]: Specimen-SA-000.html
+[GSS123456-01-010]: Specimen-GSS123456-01-010.html
 [PT-006SP660-condition]: Observation-PT-006SP660-condition.html
-[PT-006SP660]: DocumentReference-PT-006SP660.html
-[BAM-CRAM-example]: Observation-BAM-CRAM-example.html
+[GSS123456-condition]: Observation-GSS123456-condition.html
+[GSS654321]: Patient-GSS654321.html
+[GF-6BAD9S7D]: DocumentReference-GF-6BAD9S7D.html
+[GSS123456-01-010-SG-2]: DocumentReference-GSS123456-01-010-SG-2.html
+[gregor-example-metadata]: Observation-gregor-example-metadata.html
 [FASTQ-example]: Observation-FASTQ-example.html
-[VCF-example]: Observation-VCF-example.html
-[cbtn-example-participantstudy]: ResearchSubject-cbtn-example-participantstudy.html
-[emerge-example-participantstudy]: ResearchSubject-emerge-example-participantstudy.html
-[pcgc-example-participantstudy]: ResearchSubject-pcgc-example-participantstudy.html
+[gregor-example-participantstudy]: ResearchSubject-gregor-example-participantstudy.html
+[PT-006SP660]: Patient-PT-006SP660.html
 [cbtn-study-family]: Group-cbtn-study-family.html
-[PT-KZG2CZ95]: Patient-PT-KZG2CZ95.html
-[cbtn-example-person]: Person-cbtn-example-person.html
-[6812345]: Patient-6812345.html
-[emerge-example-person]: Person-emerge-example-person.html
-[PT-005B7CZ4]: Patient-PT-005B7CZ4.html
-[pcgc-example-person]: Person-pcgc-example-person.html
+[GSS123456]: Patient-GSS123456.html
+[gregor-example-person]: Person-gregor-example-person.html
+[gregor-study-family]: Group-gregor-study-family.html
+[research-study-gregor]: ResearchStudy-research-study-gregor.html
 [NcpiFamilyRelationship]: StructureDefinition-ncpi-family-relationship.html
 [FamilyType]: StructureDefinition-family-type.html
 [NcpiFamilyTypesVS]: ValueSet-ncpi-family-types-vs.html
 [NCPISample]: StructureDefinition-ncpi-sample.html
 [NcpiGeneFusionOrExpression]: StructureDefinition-ncpi-gene-fusion-expression.html
 [kf-gsr-allowed-access]: Consent-kf-gsr-allowed-access.html
+[gregor-gru-consent]: Consent-gregor-gru-consent.html
 [HashTypeCS]: CodeSystem-example-hash-type-code-system.html
 [hmb-irb-npu-consent]: Consent-hmb-irb-npu-consent.html
 [hmb-npu-consent]: Consent-hmb-npu-consent.html
@@ -73,11 +75,6 @@
 [BodyLocationQualifierVS]: ValueSet-condition-location-vs.html
 [NcpiMAF]: StructureDefinition-ncpi-maf.html
 [MeshTerms]: ValueSet-mesh-terms.html
-[GRU]: Consent-GRU.html
-[HMB]: Consent-HMB.html
-[SD-BHJXBDQK]: ResearchStudy-SD-BHJXBDQK.html
-[SD-PREASA7S]: ResearchStudy-SD-PREASA7S.html
-[phv00407460.v2]: ResearchStudy-phv00407460.v2.html
 [NCPICollectedSample]: StructureDefinition-ncpi-collected-sample.html
 [NCPINonCollectedSample]: StructureDefinition-ncpi-non-collected-sample.html
 [NcpiCondition]: StructureDefinition-ncpi-condition.html
@@ -100,6 +97,7 @@
 [cmg-research-study-bhcmg-consent-group-irb-hmb-npu]: Group-cmg-research-study-bhcmg-consent-group-irb-hmb-npu.html
 [cmg-research-study-subject-cmg-irb-hmb-npu]: ResearchStudy-cmg-research-study-subject-cmg-irb-hmb-npu.html
 [kf-research-study-cbtn-participants]: Group-kf-research-study-cbtn-participants.html
+[gregor-research-study-participants]: Group-gregor-research-study-participants.html
 [ncpi-research-collection-pbta]: List-ncpi-research-collection-pbta.html
 [ConditionAsserter]: StructureDefinition-condition-asserter.html
 [PlatformInstrumentCS]: CodeSystem-platform-instrument-cs.html

diff --git a/fsh-generated/includes/menu.xml b/fsh-generated/includes/menu.xml
@@ -101,25 +101,10 @@
     </a>
     <ul class="dropdown-menu">
       <li>
-        <a href="example_research_study.html">Research Study</a>
+        <a href="example_cbtn.html">CBTN Example</a>
       </li>
       <li>
-        <a href="example_participant.html">Participant-level Data</a>
-      </li>
-      <li>
-        <a href="example_phenotype_condition.html">Phenotype/Condition</a>
-      </li>
-      <li>
-        <a href="example_family.html">Family</a>
-      </li>
-      <li>
-        <a href="example_specimen.html">Specimen</a>
-      </li>
-      <li>
-        <a href="example_assays.html">Assays</a>
-      </li>
-      <li>
-        <a href="example_files.html">File Data</a>
+        <a href="example_gregor.html">GREGoR Example</a>
       </li>
     </ul>
   </li>

diff --git a/fsh-generated/resources/CodeSystem-adaptor-trimmed-cs.json b/fsh-generated/resources/CodeSystem-adaptor-trimmed-cs.json
@@ -15,7 +15,11 @@
     {
       "code": "no",
       "display": "No"
+    },
+    {
+      "code": "unknown",
+      "display": "Unknown"
     }
   ],
-  "count": 2
+  "count": 3
 }
diff --git a/fsh-generated/resources/CodeSystem-assay-strategy-cs.json b/fsh-generated/resources/CodeSystem-assay-strategy-cs.json
@@ -11,7 +11,11 @@
     {
       "code": "WGS",
       "display": "Whole Genome Sequencing"
+    },
+    {
+      "code": "unknown",
+      "display": "Unknown"
     }
   ],
-  "count": 1
+  "count": 2
 }
diff --git a/fsh-generated/resources/CodeSystem-library-prep-cs.json b/fsh-generated/resources/CodeSystem-library-prep-cs.json
@@ -11,7 +11,11 @@
     {
       "code": "polyA",
       "display": "polyA"
+    },
+    {
+      "code": "unknown",
+      "display": "Unknown"
     }
   ],
-  "count": 1
+  "count": 2
 }
diff --git a/fsh-generated/resources/CodeSystem-library-selection-cs.json b/fsh-generated/resources/CodeSystem-library-selection-cs.json
@@ -11,7 +11,11 @@
     {
       "code": "PolyTEnrichment",
       "display": "Poly-T Enrichment"
+    },
+    {
+      "code": "unknown",
+      "display": "Unknown"
     }
   ],
-  "count": 1
+  "count": 2
 }
diff --git a/fsh-generated/resources/CodeSystem-platform-instrument-cs.json b/fsh-generated/resources/CodeSystem-platform-instrument-cs.json
@@ -11,7 +11,11 @@
     {
       "code": "IlluminaHiSeq2000",
       "display": "Illumina HiSeq2000"
+    },
+    {
+      "code": "unknown",
+      "display": "Unknown"
     }
   ],
-  "count": 1
+  "count": 2
 }
diff --git a/fsh-generated/resources/CodeSystem-reference-genome-cs.json b/fsh-generated/resources/CodeSystem-reference-genome-cs.json
@@ -23,7 +23,11 @@
     {
       "code": "GRCh38p14",
       "display": "GRCh38.p14"
+    },
+    {
+      "code": "unknown",
+      "display": "Unknown"
     }
   ],
-  "count": 4
+  "count": 5
 }
diff --git a/fsh-generated/resources/CodeSystem-strandedness-cs.json b/fsh-generated/resources/CodeSystem-strandedness-cs.json
@@ -15,7 +15,11 @@
     {
       "code": "unstranded",
       "display": "Unstranded"
+    },
+    {
+      "code": "unknown",
+      "display": "Unknown"
     }
   ],
-  "count": 2
+  "count": 3
 }
diff --git a/fsh-generated/resources/CodeSystem-workflow-tool-cs.json b/fsh-generated/resources/CodeSystem-workflow-tool-cs.json
@@ -15,7 +15,11 @@
     {
       "code": "GATKHaplotypeCaller",
       "display": "GATK-Haplotype Caller"
+    },
+    {
+      "code": "unknown",
+      "display": "Unknown"
     }
   ],
-  "count": 2
+  "count": 3
 }
diff --git a/fsh-generated/resources/CodeSystem-workflow-type-cs.json b/fsh-generated/resources/CodeSystem-workflow-type-cs.json
@@ -15,7 +15,11 @@
     {
       "code": "somatic",
       "display": "Somatic"
+    },
+    {
+      "code": "unknown",
+      "display": "Unknown"
     }
   ],
-  "count": 2
+  "count": 3
 }
diff --git a/fsh-generated/resources/Consent-GRU.json b/fsh-generated/resources/Consent-GRU.json
diff --git a/fsh-generated/resources/Consent-HMB.json b/fsh-generated/resources/Consent-HMB.json