{
  "resourceType": "StructureDefinition",
  "url": "https://simplifier.net/genomicsfhirprofiles/genomics-specimen-1",
  "name": "Genomics-Specimen-1",
  "title": "Genomics-Specimen-1",
  "status": "draft",
  "experimental": false,
  "purpose": "Specimen for genomics",
  "kind": "resource",
  "abstract": false,
  "type": "Specimen",
  "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Specimen",
  "derivation": "constraint",
  "snapshot": {},
  "differential": {
    "element": [
      {
        "id": "Specimen.id",
        "path": "Specimen.id",
        "short": "Logical id for the specimen resource",
        "definition": "The logical id for the specimen resource, as used in the URL for the resource. Once assigned, this value never changes."
      },
      {
        "id": "Specimen.meta.id",
        "path": "Specimen.meta.id",
        "min": 1
      },
      {
        "id": "Specimen.text",
        "path": "Specimen.text",
        "short": "Text summary of the resource, for human consumption"
      },
      {
        "id": "Specimen.extension",
        "path": "Specimen.extension",
        "slicing": {
          "discriminator": [
            {
              "type": "value",
              "path": "url"
            }
          ],
          "rules": "open"
        }
      },
      {
        "id": "Specimen.extension:tumorID",
        "path": "Specimen.extension",
        "sliceName": "tumorID",
        "short": "Identifies Tumor ID",
        "definition": "Identifies Tumor ID",
        "min": 0,
        "max": "1",
        "type": [
          {
            "code": "Extension",
            "profile": "https://simplifier.net/genomicsfhirprofiles/genomics-extension-tumourid-1"
          }
        ]
      },
      {
        "id": "Specimen.identifier",
        "path": "Specimen.identifier",
        "short": "Sample Identifier",
        "definition": "Sample Identifier",
        "comment": "Repeating element / used for sample ID from NGIS, and Accession ID from Labs",
        "min": 1
      },
      {
        "id": "Specimen.identifier.value",
        "path": "Specimen.identifier.value",
        "short": "Unique sample identifier",
        "definition": "Unique sample identifier",
        "min": 1
      },
      {
        "id": "Specimen.type",
        "path": "Specimen.type",
        "comment": "Maps from Questionnaire"
      },
      {
        "id": "Specimen.type.coding.system",
        "path": "Specimen.type.coding.system",
        "short": "Identity of the coding system",
        "min": 1
      },
      {
        "id": "Specimen.type.coding.code",
        "path": "Specimen.type.coding.code",
        "min": 1
      },
      {
        "id": "Specimen.type.coding.display",
        "extension": [
          {
            "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable",
            "valueBoolean": true
          }
        ],
        "path": "Specimen.type.coding.display",
        "short": "Text description of code"
      },
      {
        "id": "Specimen.subject",
        "path": "Specimen.subject",
        "short": "Where the specimen came from.",
        "definition": "Where the specimen came from. Reference Link to Patient Resource in API call.",
        "type": [
          {
            "code": "Reference",
            "targetProfile": "http://hl7.org/fhir/StructureDefinition/Patient",
            "aggregation": [
              "contained"
            ]
          }
        ]
      },
      {
        "id": "Specimen.collection.collected[x]:collectedDateTime",
        "path": "Specimen.collection.collectedDateTime",
        "sliceName": "collectedDateTime",
        "type": [
          {
            "code": "dateTime"
          }
        ]
      },
      {
        "id": "Specimen.collection.method.coding",
        "path": "Specimen.collection.method.coding",
        "short": "DNA extraction Protocol CodesetValue",
        "min": 1,
        "max": "1"
      },
      {
        "id": "Specimen.collection.method.coding.system",
        "path": "Specimen.collection.method.coding.system",
        "comment": "URI for terminology system definition\r\nDNA extraction ProtocolURI for terminology system definition",
        "min": 1
      },
      {
        "id": "Specimen.collection.method.coding.code",
        "path": "Specimen.collection.method.coding.code",
        "short": "DNA extraction Protocol code",
        "definition": "DNA extraction Protocol code",
        "comment": "Populated by GLH\r\nDNA Extraction protocol value\r\nNote that FHIR strings may not exceed 1MB in size",
        "min": 1
      },
      {
        "id": "Specimen.collection.method.coding.display",
        "extension": [
          {
            "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable",
            "valueBoolean": true
          }
        ],
        "path": "Specimen.collection.method.coding.display",
        "short": "Text representation of code value",
        "comment": "Is there a text description of selection in database?\r\nNote that FHIR strings may not exceed 1MB in size"
      },
      {
        "id": "Specimen.collection.bodySite",
        "path": "Specimen.collection.bodySite",
        "comment": "How does this relate to Bodysite information collected by NGIS?"
      },
      {
        "id": "Specimen.collection.bodySite.coding.system",
        "path": "Specimen.collection.bodySite.coding.system",
        "min": 1
      },
      {
        "id": "Specimen.collection.bodySite.coding.code",
        "path": "Specimen.collection.bodySite.coding.code",
        "short": "Prolonged Sample Storage Protocol code",
        "min": 1
      }
    ]
  }
}