Family update (#49)

* Tweaks to family role to allow members in the group to be assigned the role (one profile needed for both family and roles)

* Update GREGoR_example.fsh

* Update example to use the new family profiles

* Updated gregor to use newer family group

fsh-generated/includes/fsh-link-references.md

@@ -2,13 +2,15 @@
 [AccessPolicyDescription]: StructureDefinition-access-policy-description.html
 [AccessType]: StructureDefinition-access-type.html
 [AdaptorTrimmedCS]: CodeSystem-adaptor-trimmed-cs.html
+[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
-[cbtn-family-role-mother]: Group-cbtn-family-role-mother.html
-[cbtn-family-role-son]: Group-cbtn-family-role-son.html
 [AssayStrategyCS]: CodeSystem-assay-strategy-cs.html
+[ConditionAssertionVS]: ValueSet-condition-assertion-vs.html
+[ConditionAssertion]: CodeSystem-condition-assertion.html
 [AliquotAvailability]: StructureDefinition-aliquot-availability.html
 [NcpiBAMCRAM]: StructureDefinition-ncpi-bamcram.html
 [cmg-research-study-bhcmg]: ResearchStudy-cmg-research-study-bhcmg.html
@@ -24,53 +26,58 @@
 [CollectionTypeVS]: ValueSet-collection-type-vs.html
 [CollectionType]: CodeSystem-collection-type.html
 [AliquotConcentration]: StructureDefinition-aliquot-concentration.html
+[ConditionCodeVS]: ValueSet-condition-code-vs.html
 [Consanguinity]: StructureDefinition-consanguinity.html
 [ConsanguinityAssertionVS]: ValueSet-consanguinity-assertion-vs.html
 [kf-research-study-personnel-role-pi]: PractitionerRole-kf-research-study-personnel-role-pi.html
 [kf-research-study-personnel-role-pi-x01]: PractitionerRole-kf-research-study-personnel-role-pi-x01.html
+[ComponentElements]: CodeSystem-component-elements.html
 [ResearchDataDateOfBirthMethodVS]: ValueSet-research-data-date-of-birth-method-vs.html
 [ResearchDataDateOfBirthMethod]: CodeSystem-research-data-date-of-birth-method.html
 [EDAMOntologyTerms]: ValueSet-edam-ontology-terms.html
 [SA-000]: Specimen-SA-000.html
-[PT-006SP660]: DocumentReference-PT-006SP660.html
-[BAM-CRAM-example]: Observation-BAM-CRAM-example.html
+[GSS123456-01-010]: Specimen-GSS123456-01-010.html
+[PT-006SP660-condition]: Observation-PT-006SP660-condition.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
-[NcpiFamilyRole]: StructureDefinition-ncpi-family-role.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
 [LocationAccess]: StructureDefinition-location-access.html
 [ncpi-research-collection-kfx01]: List-ncpi-research-collection-kfx01.html
 [Label]: StructureDefinition-label-extension.html
 [BiospecimenLaterality]: StructureDefinition-biospecimen-laterality.html
+[ConditionLaterality]: StructureDefinition-condition-laterality.html
+[LateralityQualifierVS]: ValueSet-condition-laterality-vs.html
 [LibraryPrepCS]: CodeSystem-library-prep-cs.html
 [LibrarySelectionCS]: CodeSystem-library-selection-cs.html
+[NcpiSpecimenCollection]: StructureDefinition-ncpi-specimen-NcpiSpecimenCollection.html
+[SpecimenCollection]: StructureDefinition-specimen-collection.html
+[ConditionLocation]: StructureDefinition-condition-location.html
+[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
-[NcpiAnalysisFile]: StructureDefinition-ncpi-analysis-file.html
-[NcpiAssayFile]: StructureDefinition-ncpi-assay-file.html
 [NCPICollectedSample]: StructureDefinition-ncpi-collected-sample.html
 [NCPINonCollectedSample]: StructureDefinition-ncpi-non-collected-sample.html
+[NcpiCondition]: StructureDefinition-ncpi-condition.html
 [NcpiFamilyTypes]: CodeSystem-ncpi-family-types.html
 [NcpiFASTQ]: StructureDefinition-ncpi-fastq.html
 [Ncpi]: CodeSystem-ncpi.html
@@ -79,21 +86,22 @@
 [MetadataElements]: CodeSystem-metadata-elements.html
 [NcpiParticipant]: StructureDefinition-ncpi-participant.html
 [NcpiPerson]: StructureDefinition-ncpi-person.html
-[NcpiReadsFile]: StructureDefinition-ncpi-reads-file.html
 [NcpiResearchAccessPolicy]: StructureDefinition-ncpi-research-access-policy.html
 [NcpiResearchCollection]: StructureDefinition-ncpi-research-collection.html
 [NcpiResearchStudy]: StructureDefinition-ncpi-research-study.html
 [ResearchStudyGroup]: StructureDefinition-research-study-group.html
-[NcpiSequencingFile]: StructureDefinition-ncpi-sequencing-file.html
 [NcpiStudyFamily]: StructureDefinition-ncpi-study-family.html
 [NcpiStudyParticipant]: StructureDefinition-ncpi-Study-Participant.html
 [cmg-research-study-bhcmg-consent-group-hmb-npu]: Group-cmg-research-study-bhcmg-consent-group-hmb-npu.html
 [cmg-research-study-subject-cmg-hmb-npu]: ResearchStudy-cmg-research-study-subject-cmg-hmb-npu.html
 [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
+[NcpiProteomics]: StructureDefinition-ncpi-proteomics.html
 [HashExtension]: StructureDefinition-hash-extension.html
 [ReferenceGenomeCS]: CodeSystem-reference-genome-cs.html
 [kf-registered-allowed-access]: Consent-kf-registered-allowed-access.html
@@ -115,6 +123,7 @@
 [BiospecimenAvailability]: CodeSystem-biospecimen-availability.html
 [CmdAliquot]: StructureDefinition-SharedDataModelAliquot.html
 [CdmBiospecimenCollection]: StructureDefinition-SharedDataModelBiospecimenCollection.html
+[CdmCondition]: StructureDefinition-SharedDataModelCondition.html
 [CdmFamilyRelationship]: StructureDefinition-SharedDataModelFamilyRelationship.html
 [CdmFamilyRole]: StructureDefinition-SharedDataModelFamilyRole.html
 [CdmFile]: StructureDefinition-SharedDataModelFile.html
@@ -131,14 +140,15 @@
 [Description]: StructureDefinition-description.html
 [FamilyRole]: StructureDefinition-family-role.html
 [StudyFamilyFocus]: StructureDefinition-study-family-focus.html
-[StudyFamily]: StructureDefinition-study-family.html
 [StudyNameTypeVS]: ValueSet-study-name-type-vs.html
 [StudyNameType]: CodeSystem-study-name-type.html
 [StudyPersonnelRoleVS]: ValueSet-study-personnel-role-vs.html
 [StudyPersonnelRole]: CodeSystem-study-personnel-role.html
 [ncpi-research-collection-cmg]: List-ncpi-research-collection-cmg.html
 [FileFormat]: StructureDefinition-file-format.html
 [FileSize]: StructureDefinition-file-size.html
+[ConditionTypeVS]: ValueSet-condition-type-vs.html
+[ConditionType]: CodeSystem-condition-type.html
 [HashValue]: StructureDefinition-hash-value.html
 [NcpiVCF]: StructureDefinition-ncpi-vcf.html
 [ContentVersion]: StructureDefinition-content-version.html

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>

fsh-generated/resources/CodeSystem-adaptor-trimmed-cs.json

@@ -15,7 +15,11 @@
     {
       "code": "no",
       "display": "No"
+    },
+    {
+      "code": "unknown",
+      "display": "Unknown"
     }
   ],
-  "count": 2
+  "count": 3
 }

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
 }

fsh-generated/resources/CodeSystem-library-prep-cs.json

@@ -11,7 +11,11 @@
     {
       "code": "polyA",
       "display": "polyA"
+    },
+    {
+      "code": "unknown",
+      "display": "Unknown"
     }
   ],
-  "count": 1
+  "count": 2
 }

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
 }

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
 }

fsh-generated/resources/CodeSystem-reference-genome-cs.json

@@ -14,8 +14,20 @@
     },
     {
       "code": "GRCh38",
-      "display": "GRCh38"
+      "display": "CRCh38"
+    },
+    {
+      "code": "GRCh38p13",
+      "display": "GRCh38.p13"
+    },
+    {
+      "code": "GRCh38p14",
+      "display": "GRCh38.p14"
+    },
+    {
+      "code": "unknown",
+      "display": "Unknown"
     }
   ],
-  "count": 2
+  "count": 5
 }

fsh-generated/resources/CodeSystem-strandedness-cs.json

@@ -15,7 +15,11 @@
     {
       "code": "unstranded",
       "display": "Unstranded"
+    },
+    {
+      "code": "unknown",
+      "display": "Unknown"
     }
   ],
-  "count": 2
+  "count": 3
 }

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
 }

fsh-generated/resources/CodeSystem-workflow-type-cs.json

@@ -15,7 +15,11 @@
     {
       "code": "somatic",
       "display": "Somatic"
+    },
+    {
+      "code": "unknown",
+      "display": "Unknown"
     }
   ],
-  "count": 2
+  "count": 3
 }