add reference data

hcnv · Oct 31, 2023 · 95d789f · 95d789f
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diff --git a/data/reference/analyses.json b/data/reference/analyses.json
@@ -0,0 +1,32 @@
+[
+  {
+    "aligner": "bwa-0.7.8",
+    "analysisDate": "2021-04-23",
+    "biosampleId": "S0001",
+    "id": "INT_ID1",
+    "individualId": "NA24631",
+    "pipelineName": "GATK Pipeline 4.2.3.0",
+    "runId": "SRR10903401",
+    "variantCaller": "GATK4.0"
+  },
+  {
+    "aligner": "bwa-0.7.8",
+    "analysisDate": "2021-04-23",
+    "biosampleId": "S0002",
+    "id": "INT_ID2",
+    "individualId": "NA24694",
+    "pipelineName": "GATK Pipeline 4.2.3.0",
+    "runId": "SRR10903402",
+    "variantCaller": "GATK4.0"
+  },
+  {
+    "aligner": "bwa-0.7.8",
+    "analysisDate": "2021-04-23",
+    "biosampleId": "S0003",
+    "id": "INT_ID3",
+    "individualId": "NA24695",
+    "pipelineName": "GATK Pipeline 4.2.3.0",
+    "runId": "SRR10903403",
+    "variantCaller": "GATK4.0"
+  }
+]
diff --git a/data/reference/biosamples.json b/data/reference/biosamples.json
@@ -0,0 +1,140 @@
+[
+  {
+    "biosampleStatus": {
+      "id": "EFO:0009655",
+      "label": "abnormal sample"
+    },
+    "collectionDate": "2021-04-23",
+    "collectionMoment": "P32Y6M1D",
+    "diagnosticMarkers": [
+      {
+        "id": "NCIT:C48726",
+        "label": "T2b Stage Finding"
+      }
+    ],
+    "histologicalDiagnosis": {
+      "id": "NCIT:C39853",
+      "label": "Infiltrating Urothelial Carcinoma"
+    },
+    "id": "INT_ID1",
+    "individualId": "NA24631",
+    "pathologicalStage": {
+      "id": "NCIT:C28054",
+      "label": "Stage II"
+    },
+    "pathologicalTnmFinding": [
+      {
+        "id": "NCIT:C48726",
+        "label": "T2b Stage Finding"
+      }
+    ],
+    "sampleOriginDetail": {
+      "id": "UBERON:0001256",
+      "label": "wall of urinary bladde"
+    },
+    "sampleOriginType": {
+      "id": "EFO:000965",
+      "label": "abnormal sample"
+    },
+    "tumorGrade": {
+      "id": "NCIT:C36136",
+      "label": "Grade 2 Lesion"
+    },
+    "tumorProgression": {
+      "id": "NCIT:C84509",
+      "label": "Primary Malignant Neoplasm"
+    }
+  },
+  {
+    "biosampleStatus": {
+      "id": "EFO:0009655",
+      "label": "abnormal sample"
+    },
+    "collectionDate": "2021-04-23",
+    "collectionMoment": "P32Y6M1D",
+    "diagnosticMarkers": [
+      {
+        "id": "NCIT:C48726",
+        "label": "T2b Stage Finding"
+      }
+    ],
+    "histologicalDiagnosis": {
+      "id": "NCIT:C39853",
+      "label": "Infiltrating Urothelial Carcinoma"
+    },
+    "id": "INT_ID2",
+    "individualId": "NA24694",
+    "pathologicalStage": {
+      "id": "NCIT:C28054",
+      "label": "Stage II"
+    },
+    "pathologicalTnmFinding": [
+      {
+        "id": "NCIT:C48726",
+        "label": "T2b Stage Finding"
+      }
+    ],
+    "sampleOriginDetail": {
+      "id": "UBERON:0001256",
+      "label": "wall of urinary bladde"
+    },
+    "sampleOriginType": {
+      "id": "EFO:000965",
+      "label": "abnormal sample"
+    },
+    "tumorGrade": {
+      "id": "NCIT:C36136",
+      "label": "Grade 2 Lesion"
+    },
+    "tumorProgression": {
+      "id": "NCIT:C84509",
+      "label": "Primary Malignant Neoplasm"
+    }
+  },
+  {
+    "biosampleStatus": {
+      "id": "EFO:0009655",
+      "label": "abnormal sample"
+    },
+    "collectionDate": "2021-04-23",
+    "collectionMoment": "P32Y6M1D",
+    "diagnosticMarkers": [
+      {
+        "id": "NCIT:C48726",
+        "label": "T2b Stage Finding"
+      }
+    ],
+    "histologicalDiagnosis": {
+      "id": "NCIT:C39853",
+      "label": "Infiltrating Urothelial Carcinoma"
+    },
+    "id": "INT_ID3",
+    "individualId": "NA24695",
+    "pathologicalStage": {
+      "id": "NCIT:C28054",
+      "label": "Stage II"
+    },
+    "pathologicalTnmFinding": [
+      {
+        "id": "NCIT:C48726",
+        "label": "T2b Stage Finding"
+      }
+    ],
+    "sampleOriginDetail": {
+      "id": "UBERON:0001256",
+      "label": "wall of urinary bladde"
+    },
+    "sampleOriginType": {
+      "id": "EFO:000965",
+      "label": "abnormal sample"
+    },
+    "tumorGrade": {
+      "id": "NCIT:C36136",
+      "label": "Grade 2 Lesion"
+    },
+    "tumorProgression": {
+      "id": "NCIT:C84509",
+      "label": "Primary Malignant Neoplasm"
+    }
+  }
+]
diff --git a/data/reference/cohorts.json b/data/reference/cohorts.json
@@ -0,0 +1,21 @@
+[
+  {
+    "cohortDataTypes": [
+      {
+        "id": "EFO:0004600",
+        "label": "genomic data"
+      },
+      {
+        "id": "NCIT:C1578",
+        "label": "clinical data"
+      },
+      {
+        "id": "NCIT:C142508",
+        "label": "demographic data"
+      }
+    ],
+    "cohortName": "The Genome in a Bottle Consortium (GIAB)",
+    "cohortId": "GiaB",
+    "cohortType": "study-defined"
+  }
+]
diff --git a/data/reference/datasets.json b/data/reference/datasets.json
@@ -0,0 +1,10 @@
+[
+  {
+    "createDateTime": "2017-04-30T00:00:00+00:00",
+    "description": "The Genome in a Bottle Consortium, hosted by the National Institute of Standards and Technology (NIST) is creating reference materials and data for human genome sequencing, as well as methods for genome comparison and benchmarking. ",
+    "externalUrl": "https://www.nature.com/articles/sdata201625, https://jimb.stanford.edu/giab-resources",
+    "id": "EGAD00001008097",
+    "name": "The Genome in a Bottle Consortium (GIAB)",
+    "updateDateTime": "2017-04-30T00:00:00+00:00"
+  }
+]