Updates to clean up IG in preperation for next week's meeting

NIH-NCPI · Sep 17, 2024 · c9b63c7 · c9b63c7
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diff --git a/fsh-generated/resources/CodeSystem-component-elements.json b/fsh-generated/resources/CodeSystem-component-elements.json
@@ -0,0 +1,29 @@
+{
+  "resourceType": "CodeSystem",
+  "status": "draft",
+  "content": "complete",
+  "name": "ComponentElements",
+  "id": "component-elements",
+  "title": "Elements of Component",
+  "description": "Slicing for elements of component",
+  "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/component-elements",
+  "concept": [
+    {
+      "code": "ageAtOnset",
+      "display": "Age at Onset"
+    },
+    {
+      "code": "ageAtResolution",
+      "display": "Age at Resolution"
+    },
+    {
+      "code": "otherModifiers",
+      "display": "Other Modifiers"
+    },
+    {
+      "code": "stage",
+      "display": "Stage"
+    }
+  ],
+  "count": 4
+}
diff --git a/fsh-generated/resources/CodeSystem-condition-assertion.json b/fsh-generated/resources/CodeSystem-condition-assertion.json
@@ -0,0 +1,27 @@
+{
+  "resourceType": "CodeSystem",
+  "status": "draft",
+  "content": "complete",
+  "name": "ConditionAssertion",
+  "id": "condition-assertion",
+  "title": "Assertion of Condition Codes",
+  "description": "Code System for assertion of condition presence",
+  "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/condition-assertion",
+  "concept": [
+    {
+      "code": "Present",
+      "display": "Present"
+    },
+    {
+      "code": "Absent",
+      "display": "Absent"
+    },
+    {
+      "code": "Unknown",
+      "display": "Unknown"
+    }
+  ],
+  "experimental": false,
+  "caseSensitive": true,
+  "count": 3
+}
diff --git a/fsh-generated/resources/CodeSystem-condition-type.json b/fsh-generated/resources/CodeSystem-condition-type.json
@@ -0,0 +1,39 @@
+{
+  "resourceType": "CodeSystem",
+  "status": "draft",
+  "content": "complete",
+  "name": "ConditionType",
+  "id": "condition-type",
+  "title": "Type of Condition",
+  "description": "Code System for type of condition",
+  "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/condition-type",
+  "concept": [
+    {
+      "code": "Phenotypic-Feature",
+      "display": "Phenotypic Feature"
+    },
+    {
+      "code": "Disease",
+      "display": "Disease"
+    },
+    {
+      "code": "Comorbidity",
+      "display": "Comorbidity"
+    },
+    {
+      "code": "Histology",
+      "display": "Histology"
+    },
+    {
+      "code": "Clinical-Finding",
+      "display": "Clinical Finding"
+    },
+    {
+      "code": "EHR-Condition-Code",
+      "display": "EHR Condition Code"
+    }
+  ],
+  "experimental": false,
+  "caseSensitive": true,
+  "count": 6
+}
diff --git a/fsh-generated/resources/Consent-gregor-gru-consent.json b/fsh-generated/resources/Consent-gregor-gru-consent.json
@@ -0,0 +1,64 @@
+{
+  "resourceType": "Consent",
+  "id": "gregor-gru-consent",
+  "meta": {
+    "profile": [
+      "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-research-access-policy"
+    ]
+  },
+  "category": [
+    {
+      "coding": [
+        {
+          "code": "research",
+          "system": "http://terminology.hl7.org/CodeSystem/consentcategorycodes",
+          "display": "Research Information Access"
+        }
+      ]
+    }
+  ],
+  "provision": {
+    "purpose": [
+      {
+        "code": "GRU",
+        "system": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-access-code",
+        "display": "General Research Use"
+      }
+    ],
+    "type": "permit"
+  },
+  "extension": [
+    {
+      "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/access-policy-description",
+      "valueMarkdown": "Use of the data is limited only by the terms of the model Data Use Certification."
+    },
+    {
+      "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/access-type",
+      "valueCodeableConcept": {
+        "coding": [
+          {
+            "code": "controlled",
+            "system": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-access-type"
+          }
+        ]
+      }
+    }
+  ],
+  "status": "draft",
+  "scope": {
+    "coding": [
+      {
+        "code": "research",
+        "system": "http://terminology.hl7.org/CodeSystem/consentscope"
+      }
+    ]
+  },
+  "policyRule": {
+    "coding": [
+      {
+        "code": "cric",
+        "system": "http://terminology.hl7.org/CodeSystem/consentpolicycodes"
+      }
+    ]
+  }
+}
diff --git a/fsh-generated/resources/DocumentReference-GF-6BAD9S7D.json b/fsh-generated/resources/DocumentReference-GF-6BAD9S7D.json
@@ -0,0 +1,81 @@
+{
+  "resourceType": "DocumentReference",
+  "id": "GF-6BAD9S7D",
+  "meta": {
+    "profile": [
+      "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-file"
+    ]
+  },
+  "identifier": [
+    {
+      "value": "GF-6BAD9S7D"
+    }
+  ],
+  "extension": [
+    {
+      "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/content-version",
+      "valueString": "V1"
+    },
+    {
+      "valueCodeableConcept": {
+        "coding": [
+          {
+            "code": "format_3016",
+            "system": "http://edamontology.org",
+            "display": "VCF"
+          }
+        ]
+      },
+      "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/file-format"
+    },
+    {
+      "valueQuantity": {
+        "value": 1044770380,
+        "unit": "bytes"
+      },
+      "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/file-size"
+    },
+    {
+      "extension": [
+        {
+          "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/hash-value",
+          "valueString": "8f107912d862cf91fbfb77bf9c1bab36-4"
+        },
+        {
+          "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/hash-type",
+          "valueCode": "etag"
+        }
+      ],
+      "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/hash-extension"
+    }
+  ],
+  "content": [
+    {
+      "attachment": {
+        "url": "s3://kf-strides-study-us-east-1-prd-sd-54g4wg4r/harmonized-data/family-variants/155bb529-2e7b-474f-ba24-cd0656d5f3d0.CGP.filtered.deNovo.vep.vcf.gz"
+      },
+      "extension": [
+        {
+          "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/location-access",
+          "valueReference": {
+            "reference": "Consent/kf-gru-dac-consent"
+          }
+        }
+      ]
+    }
+  ],
+  "subject": {
+    "reference": "Patient/PT-006SP660"
+  },
+  "description": "Annotated Variant Call",
+  "type": {
+    "coding": [
+      {
+        "code": "operation_3227",
+        "system": "http://edamontology.org",
+        "display": "Variant calling"
+      }
+    ]
+  },
+  "status": "current"
+}
diff --git a/fsh-generated/resources/DocumentReference-GSS123456-01-010-SG-2.json b/fsh-generated/resources/DocumentReference-GSS123456-01-010-SG-2.json
@@ -0,0 +1,81 @@
+{
+  "resourceType": "DocumentReference",
+  "id": "GSS123456-01-010-SG-2",
+  "meta": {
+    "profile": [
+      "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-file"
+    ]
+  },
+  "identifier": [
+    {
+      "value": "GSS123456-01-010-SG-2"
+    }
+  ],
+  "extension": [
+    {
+      "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/content-version",
+      "valueString": "V1"
+    },
+    {
+      "valueCodeableConcept": {
+        "coding": [
+          {
+            "code": "format_2572",
+            "system": "http://edamontology.org",
+            "display": "BAM"
+          }
+        ]
+      },
+      "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/file-format"
+    },
+    {
+      "valueQuantity": {
+        "value": 1044770380,
+        "unit": "bytes"
+      },
+      "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/file-size"
+    },
+    {
+      "extension": [
+        {
+          "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/hash-value",
+          "valueString": "9c2460c4647fdc57261f040042863fa0"
+        },
+        {
+          "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/hash-type",
+          "valueCode": "md5"
+        }
+      ],
+      "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/hash-extension"
+    }
+  ],
+  "content": [
+    {
+      "attachment": {
+        "url": "gs://fc-secure-a1f0e28d-c9d9-43bb-b4ba-5e0h81784fb1/GSS123456/SR_GS/GSS123456.bam"
+      },
+      "extension": [
+        {
+          "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/location-access",
+          "valueReference": {
+            "reference": "Consent/kf-gru-dac-consent"
+          }
+        }
+      ]
+    }
+  ],
+  "subject": {
+    "reference": "Patient/GSS123456"
+  },
+  "description": "Aligned DNA short read",
+  "type": {
+    "coding": [
+      {
+        "code": "operation_3198",
+        "system": "http://edamontology.org",
+        "display": "Read mapping"
+      }
+    ]
+  },
+  "status": "current"
+}
diff --git a/fsh-generated/resources/Group-gregor-research-study-participants.json b/fsh-generated/resources/Group-gregor-research-study-participants.json
@@ -0,0 +1,19 @@
+{
+  "resourceType": "Group",
+  "id": "gregor-research-study-participants",
+  "meta": {
+    "profile": [
+      "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-group"
+    ]
+  },
+  "identifier": [
+    {
+      "system": "https://anvil.terra.bio/",
+      "value": "GREGoR Participants"
+    }
+  ],
+  "type": "person",
+  "actual": true,
+  "name": "Participants from the GREGoR research study GSS U08 GRU",
+  "quantity": 555
+}