NCPI FHIR Implementation Guide v2
0.1.0 - ci-build

NCPI FHIR Implementation Guide v2 - Local Development build (v0.1.0) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions

: Example file metadata for a BAM-CRAM file from GREGoR - JSON Representation

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{
  "resourceType" : "Observation",
  "id" : "gregor-example-metadata",
  "meta" : {
    "profile" : [
      🔗 "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-bamcram"
    ]
  },
  "text" : {
    "status" : "generated",
    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Observation gregor-example-metadata</b></p><a name=\"gregor-example-metadata\"> </a><a name=\"hcgregor-example-metadata\"> </a><a name=\"gregor-example-metadata-en-US\"> </a><p><b>status</b>: Final</p><p><b>code</b>: <span title=\"Codes:{http://edamontology.org format_2572}\">format_2572</span></p><p><b>focus</b>: <a href=\"Patient-GSS123456.html\">Anonymous Patient (no stated gender), DoB Unknown ( https://anvil.terra.bio/#GSS123456)</a></p><p><b>specimen</b>: <a href=\"Specimen-GSS123456-01-010.html\">Specimen: identifier = GSS123456-s1; type = </a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:\">AssayStrategy</span></p><p><b>value</b>: <span title=\"Codes:\">WGS</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:\">PlatformInstrument</span></p><p><b>value</b>: <span title=\"Codes:\">IlluminaHiSeq2000</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:\">LibraryPrep</span></p><p><b>value</b>: <span title=\"Codes:\">polyA</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:\">LibrarySelection</span></p><p><b>value</b>: <span title=\"Codes:\">PolyTEnrichment</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:\">TargetRegion</span></p><p><b>value</b>: <span title=\"Codes:\">Not Applicable</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:\">Strandedness</span></p><p><b>value</b>: <span title=\"Codes:\">stranded</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:\">ReferenceGenome</span></p><p><b>value</b>: <span title=\"Codes:\">GRCh38</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:\">IsPairedEnd</span></p><p><b>value</b>: false</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:\">WorkflowTool</span></p><p><b>value</b>: <span title=\"Codes:\">bammem</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:\">WorkflowType</span></p><p><b>value</b>: <span title=\"Codes:\">alignment</span></p></blockquote></div>"
  },
  "status" : "final",
  "code" : {
    "coding" : [
      {
        "system" : "http://edamontology.org",
        "code" : "format_2572"
      }
    ]
  },
  "focus" : [
    {
      🔗 "reference" : "Patient/GSS123456"
    }
  ],
  "specimen" : {
    🔗 "reference" : "Specimen/GSS123456-01-010"
  },
  "component" : [
    {
      "code" : {
        "coding" : [
          {
            "code" : "AssayStrategy"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "code" : "WGS"
          }
        ]
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "code" : "PlatformInstrument"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "code" : "IlluminaHiSeq2000"
          }
        ]
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "code" : "LibraryPrep"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "code" : "polyA"
          }
        ]
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "code" : "LibrarySelection"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "code" : "PolyTEnrichment"
          }
        ]
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "code" : "TargetRegion"
          }
        ]
      },
      "valueCodeableConcept" : {
        "text" : "Not Applicable"
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "code" : "Strandedness"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "code" : "stranded"
          }
        ]
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "code" : "ReferenceGenome"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "code" : "GRCh38"
          }
        ]
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "code" : "IsPairedEnd"
          }
        ]
      },
      "valueBoolean" : false
    },
    {
      "code" : {
        "coding" : [
          {
            "code" : "WorkflowTool"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "code" : "bammem"
          }
        ]
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "code" : "WorkflowType"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "code" : "alignment"
          }
        ]
      }
    }
  ]
}