GDC -> FHIR

[bwalsh]

Use case: As a BMEG ETL author, when I have a case record from GDC, I need to know what FHIR resources will be created. As a BMEG ETL engineer, before I can write code, I need a document that outlines the mapping decisions.

e.g.

• High Level Mapping: project-> ResearchStudy sample, aliquot, portion ->Specimen disease->Condition diagnosis-> Observation, Encounter ? treatments -> MedicationAdministration files (urls TBD) -> DocumentReference -> DRS ?

• Field Level: project.project_id-> ResearchStudy.identifier

• Content Mapping: (ontology mapping) "Basal Cell Neoplasms" -> MONDO:???? "ethnicity": "not hispanic or latino", -> https://build.fhir.org/ig/HL7/US-Core/StructureDefinition-us-core-race.profile.json.html

{
  "id": "3afa1e93-1df8-4e4c-aaa4-557463f4bb77",  // FHIR: ResearchStudy.identifier
  "submitter_slide_ids": [. // FHIR: DocumentReference.identifier ? where are the urls?
    "TCGA-A7-A0DA-01Z-00-DX2",
    "TCGA-A7-A0DA-01Z-00-DX1",
    "TCGA-A7-A0DA-01A-03-TS3"
  ],
  "project": { // FHIR: ResearchStudy
    "primary_site": [   // FHIR: ResearchStudy. BodySite
      "Breast"
    ],
    "dbgap_accession_number": null,
    "project_id": "TCGA-BRCA", // FHIR: ResearchStudy.identifier
    "disease_type": [  // FHIR: ResearchStudy -> focus Condition
      "Basal Cell Neoplasms",
      "Complex Epithelial Neoplasms",
      "Adenomas and Adenocarcinomas",
      "Epithelial Neoplasms, NOS",
      "Ductal and Lobular Neoplasms",
      "Adnexal and Skin Appendage Neoplasms",
      "Fibroepithelial Neoplasms",
      "Cystic, Mucinous and Serous Neoplasms",
      "Squamous Cell Neoplasms"
    ],
    "name": "Breast Invasive Carcinoma",
    "releasable": true,
    "state": "open",
    "program": {
      "dbgap_accession_number": "phs000178",
      "program_id": "b80aa962-9650-5110-b3eb-bd087da808db",
      "name": "TCGA"
    },
    "released": true
  },
  "submitter_analyte_ids": [ //FHIR: Patient->Specimen
    "TCGA-A7-A0DA-01A-31W",
    "TCGA-A7-A0DA-01A-31D",
    "TCGA-A7-A0DA-10A-01D",
    "TCGA-A7-A0DA-01A-31R",
    "TCGA-A7-A0DA-10A-01W"
  ],
  "created_datetime": null,
  "diagnosis_ids": [  //Patient->Conditon, Diagnosis or Observation 
    "d9e34d72-793c-5407-a421-eae9280c75b1"
  ],
  "updated_datetime": "2019-08-06T14:14:07.814612-05:00",
  "case_id": "3afa1e93-1df8-4e4c-aaa4-557463f4bb77",
  "state": "released",
  "portion_ids": [ //Specimen->Specimen
    "89cd779a-c1fc-4959-9985-fbc8f6bc0f88",
    "51866cc5-8c50-41fa-a490-f23b3adb541d",
    "253d0600-ba4c-467d-bab0-2b15e38e8339",
    "190fcd17-0d7a-4d28-9958-492d56360678",
    "dba0ceee-ecdd-4b46-b79c-0bed0553933d"
  ],
  "tissue_source_site": {. // Specimen.collection
    "tissue_source_site_id": "78ed6982-33ca-5062-85f6-9fb0fca095d9",
    "code": "A7",
    "name": "Christiana Healthcare",
    "project": "Breast invasive carcinoma",
    "bcr_id": "NCH"
  },
  "submitter_portion_ids": [. //Specimen
    "TCGA-A7-A0DA-01A-11",
    "TCGA-A7-A0DA-10A-01",
    "TCGA-A7-A0DA-01A-41-A21W-30",
    "TCGA-A7-A0DA-01A-11-A13C-20",
    "TCGA-A7-A0DA-01A-31"
  ],
  "summary": {
    "file_count": 66,
    "data_categories": [
      {
        "file_count": 4,
        "data_category": "Structural Variation"
      },
      {
        "file_count": 17,
        "data_category": "Simple Nucleotide Variation"
      },
      {
        "file_count": 6,
        "data_category": "Copy Number Variation"
      },
      {
        "file_count": 4,
        "data_category": "Transcriptome Profiling"
      },
      {
        "file_count": 3,
        "data_category": "DNA Methylation"
      },
      {
        "file_count": 6,
        "data_category": "Sequencing Reads"
      },
      {
        "file_count": 15,
        "data_category": "Biospecimen"
      },
      {
        "file_count": 10,
        "data_category": "Clinical"
      },
      {
        "file_count": 1,
        "data_category": "Proteome Profiling"
      }
    ],
    "experimental_strategies": [
      {
        "file_count": 9,
        "experimental_strategy": "RNA-Seq"
      },
      {
        "file_count": 19,
        "experimental_strategy": "WXS"
      },
      {
        "file_count": 3,
        "experimental_strategy": "miRNA-Seq"
      },
      {
        "file_count": 6,
        "experimental_strategy": "Genotyping Array"
      },
      {
        "file_count": 3,
        "experimental_strategy": "Methylation Array"
      },
      {
        "file_count": 2,
        "experimental_strategy": "Diagnostic Slide"
      },
      {
        "file_count": 1,
        "experimental_strategy": "Tissue Slide"
      },
      {
        "file_count": 1,
        "experimental_strategy": "Reverse Phase Protein Array"
      }
    ],
    "file_size": 97130551171
  },
  "slide_ids": [
    "660a62a8-5f45-45e4-a850-f67c672b54ac",
    "cc3f16de-3078-4afc-8e52-ccd9e6592b86",
    "fec083e6-27fd-41ee-b44b-7bb1f9ec2d12"
  ],
  "disease_type": "Ductal and Lobular Neoplasms",
  "analyte_ids": [
    "e5858da7-772a-4f52-a1b1-43932e48d65c",
    "e32ddaf6-666b-443e-996c-03280ca66881",
    "a1bd146e-d1db-4ed3-9aa8-934faaf05074",
    "fc66f7a2-0f47-4348-a334-0116cfb46507",
    "5ceb86fb-8f09-489c-ba5a-614dd335eaa8"
  ],
  "submitter_id": "TCGA-A7-A0DA",
  "aliquot_ids": [
    "47723567-39d1-40e9-a8ea-1bf9548db03e",
    "c8638f56-52c7-4aab-9a57-f2318f44df97",
    "878337fe-9f41-44f5-9760-3977e7d75308",
    "013b8901-2f00-46f4-b864-0a5e7d4efa6c",
    "9d04c180-7c23-490e-92cf-c018629b8b7f",
    "72c79f9e-a770-4a6c-a0a4-655ad717463c",
    "8b368315-4ed7-432f-b3e5-8bff48b32293",
    "dd1d7840-21e5-4eb8-9795-91d0659cf8d9",
    "3ad9e1b0-8de8-44b5-92e6-5d70a70070cf",
    "91c8c373-e923-4e7f-b8b3-2417e92760c7",
    "31f208e7-dfcd-431e-9a78-765befdc6ccf"
  ],
  "submitter_aliquot_ids": [
    "TCGA-A7-A0DA-01A-31W-A12T-09",
    "TCGA-A7-A0DA-01A-31D-A111-01",
    "TCGA-A7-A0DA-10A-01W-A12U-09",
    "TCGA-A7-A0DA-01A-31D-A10X-02",
    "TCGA-A7-A0DA-10A-01D-A10Z-02",
    "TCGA-A7-A0DA-10A-01D-A110-09",
    "TCGA-A7-A0DA-01A-31R-A114-13",
    "TCGA-A7-A0DA-01A-31D-A112-05",
    "TCGA-A7-A0DA-10A-01D-A113-01",
    "TCGA-A7-A0DA-01A-31R-A115-07",
    "TCGA-A7-A0DA-01A-31D-A10Y-09"
  ],
  "diagnoses": [
    {
      "synchronous_malignancy": "No",
      "ajcc_pathologic_stage": "Stage IIA",
      "days_to_diagnosis": 0,
      "created_datetime": null,
      "treatments": [
        {
          "days_to_treatment_end": null,
          "days_to_treatment_start": null,
          "treatment_id": "4be7a060-f8fa-5ff9-bda0-fa7cee7b3483",
          "submitter_id": "TCGA-A7-A0DA_treatment_1",
          "treatment_type": "Pharmaceutical Therapy, NOS",
          "regimen_or_line_of_therapy": null,
          "treatment_effect": null,
          "therapeutic_agents": null,
          "treatment_or_therapy": "yes",
          "created_datetime": "2019-04-28T13:32:45.312616-05:00",
          "initial_disease_status": null,
          "treatment_intent_type": null,
          "treatment_anatomic_site": null,
          "updated_datetime": "2019-07-31T21:18:16.285358-05:00",
          "treatment_outcome": null,
          "state": "released"
        },
        {
          "treatment_intent_type": null,
          "updated_datetime": "2019-07-31T21:18:16.285358-05:00",
          "treatment_id": "5a022fde-a913-5e23-b1bd-4e861107c38d",
          "submitter_id": "TCGA-A7-A0DA_treatment",
          "treatment_type": "Radiation Therapy, NOS",
          "state": "released",
          "therapeutic_agents": null,
          "treatment_or_therapy": "yes",
          "created_datetime": null
        }
      ],
      "last_known_disease_status": "not reported",
      "tissue_or_organ_of_origin": "Breast, NOS",
      "days_to_last_follow_up": 1085,
      "age_at_diagnosis": 22708,
      "primary_diagnosis": "Infiltrating duct carcinoma, NOS",
      "updated_datetime": "2019-08-08T16:21:06.649374-05:00",
      "prior_malignancy": "no",
      "year_of_diagnosis": 2009,
      "state": "released",
      "prior_treatment": "No",
      "days_to_last_known_disease_status": null,
      "ajcc_pathologic_t": "T2",
      "days_to_recurrence": null,
      "morphology": "8500/3",
      "ajcc_pathologic_n": "N0 (i-)",
      "ajcc_pathologic_m": "M0",
      "submitter_id": "TCGA-A7-A0DA_diagnosis",
      "classification_of_tumor": "not reported",
      "diagnosis_id": "d9e34d72-793c-5407-a421-eae9280c75b1",
      "icd_10_code": "C50.9",
      "site_of_resection_or_biopsy": "Breast, NOS",
      "tumor_grade": "not reported",
      "progression_or_recurrence": "not reported"
    }
  ],
  "samples": [
    {
      "sample_type_id": "01",
      "tumor_descriptor": null,
      "sample_id": "4f441e61-6bea-4a12-841d-def270804bbe",
      "sample_type": "Primary Tumor",
      "tumor_code": null,
      "created_datetime": null,
      "time_between_excision_and_freezing": null,
      "composition": null,
      "updated_datetime": "2018-11-15T21:38:54.195821-06:00",
      "days_to_collection": 177,
      "state": "released",
      "initial_weight": 350,
      "preservation_method": null,
      "portions": [
        {
          "portion_id": "190fcd17-0d7a-4d28-9958-492d56360678",
          "updated_datetime": "2018-09-06T13:49:20.245333-05:00",
          "center": {
            "code": "20",
            "center_id": "a35fab26-d715-5e48-9563-6cd6b189b989",
            "name": "MD Anderson - RPPA Core Facility (Proteomics)",
            "namespace": "mdanderson.org",
            "short_name": "MDA",
            "center_type": "CGCC"
          },
          "weight": null,
          "submitter_id": "TCGA-A7-A0DA-01A-11-A13C-20",
          "creation_datetime": 1300752000,
          "state": "released",
          "portion_number": "11",
          "is_ffpe": false,
          "created_datetime": null
        },
        {
          "portion_id": "253d0600-ba4c-467d-bab0-2b15e38e8339",
          "updated_datetime": "2021-07-13T16:15:40.505763-05:00",
          "submitter_id": "TCGA-A7-A0DA-01A-11",
          "state": "released",
          "created_datetime": "2020-08-31T15:21:12.837885-05:00"
        },
        {
          "portion_id": "51866cc5-8c50-41fa-a490-f23b3adb541d",
          "analytes": [
            {
              "amount": null,
              "aliquots": [
                {
                  "amount": null,
                  "aliquot_id": "8b368315-4ed7-432f-b3e5-8bff48b32293",
                  "source_center": "23",
                  "analyte_type": null,
                  "updated_datetime": "2018-11-27T10:30:18.223905-06:00",
                  "center": {
                    "code": "09",
                    "center_id": "956ca84c-1124-53ff-824f-fa0c84425425",
                    "name": "Washington University School of Medicine",
                    "namespace": "genome.wustl.edu",
                    "short_name": "WUSM",
                    "center_type": "GSC"
                  },
                  "submitter_id": "TCGA-A7-A0DA-01A-31W-A12T-09",
                  "concentration": 0.5,
                  "state": "released",
                  "analyte_type_id": null,
                  "created_datetime": null
                }
              ],
              "submitter_id": "TCGA-A7-A0DA-01A-31W",
              "concentration": null,
              "analyte_type_id": "W",
              "created_datetime": null,
              "analyte_id": "a1bd146e-d1db-4ed3-9aa8-934faaf05074",
              "well_number": null,
              "analyte_type": "Repli-G (Qiagen) DNA",
              "updated_datetime": "2018-09-06T13:49:20.245333-05:00",
              "spectrophotometer_method": null,
              "state": "released",
              "a260_a280_ratio": null
            },
            {
              "amount": null,
              "aliquots": [
                {
                  "amount": null,
                  "aliquot_id": "013b8901-2f00-46f4-b864-0a5e7d4efa6c",
                  "source_center": "23",
                  "analyte_type": null,
                  "updated_datetime": "2018-11-27T10:30:18.223905-06:00",
                  "center": {
                    "code": "02",
                    "center_id": "c8611490-4cbd-5651-8de2-64484a515eec",
                    "name": "Harvard Medical School",
                    "namespace": "hms.harvard.edu",
                    "short_name": "HMS",
                    "center_type": "CGCC"
                  },
                  "submitter_id": "TCGA-A7-A0DA-01A-31D-A10X-02",
                  "concentration": 0.15,
                  "state": "released",
                  "analyte_type_id": null,
                  "created_datetime": null
                },
                {
                  "amount": null,
                  "aliquot_id": "878337fe-9f41-44f5-9760-3977e7d75308",
                  "source_center": "23",
                  "analyte_type": null,
                  "updated_datetime": "2018-11-27T10:30:18.223905-06:00",
                  "center": {
                    "code": "09",
                    "center_id": "956ca84c-1124-53ff-824f-fa0c84425425",
                    "name": "Washington University School of Medicine",
                    "namespace": "genome.wustl.edu",
                    "short_name": "WUSM",
                    "center_type": "GSC"
                  },
                  "submitter_id": "TCGA-A7-A0DA-01A-31D-A10Y-09",
                  "concentration": 0.08,
                  "state": "released",
                  "analyte_type_id": null,
                  "created_datetime": null
                },
                {
                  "amount": null,
                  "aliquot_id": "91c8c373-e923-4e7f-b8b3-2417e92760c7",
                  "source_center": "23",
                  "analyte_type": null,
                  "updated_datetime": "2018-11-27T10:30:18.223905-06:00",
                  "center": {
                    "code": "01",
                    "center_id": "5069ce55-a23f-57c4-a28c-70a3c3cb0e4c",
                    "name": "Broad Institute of MIT and Harvard",
                    "namespace": "broad.mit.edu",
                    "short_name": "BI",
                    "center_type": "CGCC"
                  },
                  "submitter_id": "TCGA-A7-A0DA-01A-31D-A111-01",
                  "concentration": 0.15,
                  "state": "released",
                  "analyte_type_id": null,
                  "created_datetime": null
                },
                {
                  "amount": null,
                  "aliquot_id": "dd1d7840-21e5-4eb8-9795-91d0659cf8d9",
                  "source_center": "23",
                  "analyte_type": null,
                  "updated_datetime": "2018-11-27T10:30:18.223905-06:00",
                  "center": {
                    "code": "05",
                    "center_id": "7ef3885b-37ce-5e16-8ba3-9d75b6690008",
                    "name": "Johns Hopkins / University of Southern California",
                    "namespace": "jhu-usc.edu",
                    "short_name": "JHU_USC",
                    "center_type": "CGCC"
                  },
                  "submitter_id": "TCGA-A7-A0DA-01A-31D-A112-05",
                  "concentration": 0.15,
                  "state": "released",
                  "analyte_type_id": null,
                  "created_datetime": null
                }
              ],
              "submitter_id": "TCGA-A7-A0DA-01A-31D",
              "concentration": 0.15,
              "analyte_type_id": "D",
              "created_datetime": null,
              "analyte_id": "e5858da7-772a-4f52-a1b1-43932e48d65c",
              "well_number": null,
              "analyte_type": "DNA",
              "updated_datetime": "2018-09-06T13:49:20.245333-05:00",
              "spectrophotometer_method": "UV Spec",
              "state": "released",
              "a260_a280_ratio": 1.97
            },
            {
              "amount": null,
              "aliquots": [
                {
                  "amount": null,
                  "aliquot_id": "9d04c180-7c23-490e-92cf-c018629b8b7f",
                  "source_center": "23",
                  "analyte_type": null,
                  "updated_datetime": "2018-11-27T10:30:18.223905-06:00",
                  "center": {
                    "code": "07",
                    "center_id": "ee7a85b3-8177-5d60-a10c-51180eb9009c",
                    "name": "University of North Carolina",
                    "namespace": "unc.edu",
                    "short_name": "UNC",
                    "center_type": "CGCC"
                  },
                  "submitter_id": "TCGA-A7-A0DA-01A-31R-A115-07",
                  "concentration": 0.15,
                  "state": "released",
                  "analyte_type_id": null,
                  "created_datetime": null
                },
                {
                  "amount": null,
                  "aliquot_id": "c8638f56-52c7-4aab-9a57-f2318f44df97",
                  "source_center": "23",
                  "analyte_type": null,
                  "updated_datetime": "2018-11-27T10:30:18.223905-06:00",
                  "center": {
                    "code": "13",
                    "center_id": "6eba705a-0f00-5aa2-b1d0-04dbf62100cc",
                    "name": "Canada's Michael Smith Genome Sciences Centre",
                    "namespace": "bcgsc.ca",
                    "short_name": "BCGSC",
                    "center_type": "CGCC"
                  },
                  "submitter_id": "TCGA-A7-A0DA-01A-31R-A114-13",
                  "concentration": 0.15,
                  "state": "released",
                  "analyte_type_id": null,
                  "created_datetime": null
                }
              ],
              "submitter_id": "TCGA-A7-A0DA-01A-31R",
              "concentration": 0.15,
              "analyte_type_id": "R",
              "created_datetime": null,
              "analyte_id": "fc66f7a2-0f47-4348-a334-0116cfb46507",
              "well_number": null,
              "analyte_type": "RNA",
              "updated_datetime": "2018-09-06T13:49:20.245333-05:00",
              "spectrophotometer_method": "UV Spec",
              "state": "released",
              "a260_a280_ratio": 1.98
            }
          ],
          "slides": [
            {
              "percent_stromal_cells": 47,
              "submitter_id": "TCGA-A7-A0DA-01A-03-TS3",
              "section_location": "TOP",
              "percent_tumor_cells": 30,
              "number_proliferating_cells": null,
              "slide_id": "fec083e6-27fd-41ee-b44b-7bb1f9ec2d12",
              "percent_eosinophil_infiltration": null,
              "created_datetime": null,
              "percent_inflam_infiltration": null,
              "percent_neutrophil_infiltration": 0,
              "percent_lymphocyte_infiltration": 2,
              "percent_granulocyte_infiltration": null,
              "updated_datetime": "2018-09-06T13:49:20.245333-05:00",
              "percent_necrosis": 3,
              "percent_normal_cells": 20,
              "percent_monocyte_infiltration": 0,
              "state": "released",
              "percent_tumor_nuclei": 75
            }
          ],
          "updated_datetime": "2018-09-06T13:49:20.245333-05:00",
          "weight": 30,
          "submitter_id": "TCGA-A7-A0DA-01A-31",
          "creation_datetime": 1292284800,
          "state": "released",
          "portion_number": "31",
          "is_ffpe": false,
          "created_datetime": null
        },
        {
          "portion_id": "89cd779a-c1fc-4959-9985-fbc8f6bc0f88",
          "updated_datetime": "2018-09-06T13:49:20.245333-05:00",
          "center": {
            "code": "30",
            "center_id": "9a5b07b4-68f3-5d62-8fb6-b96903561b43",
            "name": "Washington University School of Medicine Proteomics",
            "namespace": "genome.wustl.edu",
            "short_name": "WUSM",
            "center_type": "CGCC"
          },
          "weight": null,
          "submitter_id": "TCGA-A7-A0DA-01A-41-A21W-30",
          "creation_datetime": 1333411200,
          "state": "released",
          "portion_number": "41",
          "is_ffpe": false,
          "created_datetime": null
        }
      ],
      "intermediate_dimension": null,
      "time_between_clamping_and_freezing": null,
      "freezing_method": null,
      "pathology_report_uuid": "69AC5937-3FFD-40FB-9922-79DB3CED7510",
      "submitter_id": "TCGA-A7-A0DA-01A",
      "tumor_code_id": null,
      "shortest_dimension": null,
      "oct_embedded": "false",
      "days_to_sample_procurement": null,
      "longest_dimension": null,
      "current_weight": null,
      "is_ffpe": false,
      "tissue_type": "Not Reported"
    },
    {
      "sample_type_id": "01",
      "sample_id": "6d250ffa-8365-4c5a-90ee-fa7f447a6071",
      "submitter_id": "TCGA-A7-A0DA-01Z",
      "sample_type": "Primary Tumor",
      "created_datetime": "2018-05-17T12:10:31.746556-05:00",
      "oct_embedded": "No",
      "updated_datetime": "2018-11-15T21:10:03.529893-06:00",
      "days_to_sample_procurement": 0,
      "state": "released",
      "is_ffpe": true,
      "tissue_type": "Not Reported",
      "preservation_method": "FFPE",
      "portions": [
        {
          "portion_id": "6d9dc38a-af71-5a43-a57d-5221a18f488e",
          "slides": [
            {
              "updated_datetime": "2018-08-23T19:24:29.874737-05:00",
              "submitter_id": "TCGA-A7-A0DA-01Z-00-DX1",
              "section_location": "Not Reported",
              "state": "released",
              "slide_id": "660a62a8-5f45-45e4-a850-f67c672b54ac",
              "created_datetime": "2018-05-17T13:32:38.220752-05:00"
            }
          ]
        },
        {
          "portion_id": "0e3cfb35-43e2-543e-b24c-7f5f62c2f937",
          "slides": [
            {
              "updated_datetime": "2018-08-23T19:24:29.874737-05:00",
              "submitter_id": "TCGA-A7-A0DA-01Z-00-DX2",
              "section_location": "Not Reported",
              "state": "released",
              "slide_id": "cc3f16de-3078-4afc-8e52-ccd9e6592b86",
              "created_datetime": "2018-05-17T13:34:27.834235-05:00"
            }
          ]
        }
      ]
    },
    {
      "sample_type_id": "10",
      "tumor_descriptor": null,
      "sample_id": "bb28c682-0071-4642-bab6-768b0fc322c6",
      "sample_type": "Blood Derived Normal",
      "tumor_code": null,
      "created_datetime": null,
      "time_between_excision_and_freezing": null,
      "composition": null,
      "updated_datetime": "2018-11-15T21:38:54.195821-06:00",
      "days_to_collection": 177,
      "state": "released",
      "initial_weight": null,
      "preservation_method": null,
      "portions": [
        {
          "portion_id": "dba0ceee-ecdd-4b46-b79c-0bed0553933d",
          "analytes": [
            {
              "amount": null,
              "aliquots": [
                {
                  "amount": null,
                  "aliquot_id": "31f208e7-dfcd-431e-9a78-765befdc6ccf",
                  "source_center": "23",
                  "analyte_type": null,
                  "updated_datetime": "2018-11-27T11:57:18.467265-06:00",
                  "center": {
                    "code": "02",
                    "center_id": "c8611490-4cbd-5651-8de2-64484a515eec",
                    "name": "Harvard Medical School",
                    "namespace": "hms.harvard.edu",
                    "short_name": "HMS",
                    "center_type": "CGCC"
                  },
                  "submitter_id": "TCGA-A7-A0DA-10A-01D-A10Z-02",
                  "concentration": 0.15,
                  "state": "released",
                  "analyte_type_id": null,
                  "created_datetime": null
                },
                {
                  "amount": null,
                  "aliquot_id": "47723567-39d1-40e9-a8ea-1bf9548db03e",
                  "source_center": "23",
                  "analyte_type": null,
                  "updated_datetime": "2018-11-27T11:57:18.467265-06:00",
                  "center": {
                    "code": "09",
                    "center_id": "956ca84c-1124-53ff-824f-fa0c84425425",
                    "name": "Washington University School of Medicine",
                    "namespace": "genome.wustl.edu",
                    "short_name": "WUSM",
                    "center_type": "GSC"
                  },
                  "submitter_id": "TCGA-A7-A0DA-10A-01D-A110-09",
                  "concentration": 0.08,
                  "state": "released",
                  "analyte_type_id": null,
                  "created_datetime": null
                },
                {
                  "amount": null,
                  "aliquot_id": "72c79f9e-a770-4a6c-a0a4-655ad717463c",
                  "source_center": "23",
                  "analyte_type": null,
                  "updated_datetime": "2018-11-27T11:57:18.467265-06:00",
                  "center": {
                    "code": "01",
                    "center_id": "5069ce55-a23f-57c4-a28c-70a3c3cb0e4c",
                    "name": "Broad Institute of MIT and Harvard",
                    "namespace": "broad.mit.edu",
                    "short_name": "BI",
                    "center_type": "CGCC"
                  },
                  "submitter_id": "TCGA-A7-A0DA-10A-01D-A113-01",
                  "concentration": 0.15,
                  "state": "released",
                  "analyte_type_id": null,
                  "created_datetime": null
                }
              ],
              "submitter_id": "TCGA-A7-A0DA-10A-01D",
              "concentration": 0.15,
              "analyte_type_id": "D",
              "created_datetime": null,
              "analyte_id": "5ceb86fb-8f09-489c-ba5a-614dd335eaa8",
              "well_number": null,
              "analyte_type": "DNA",
              "updated_datetime": "2018-09-06T13:49:20.245333-05:00",
              "spectrophotometer_method": "UV Spec",
              "state": "released",
              "a260_a280_ratio": 1.97
            },
            {
              "amount": null,
              "aliquots": [
                {
                  "amount": null,
                  "aliquot_id": "3ad9e1b0-8de8-44b5-92e6-5d70a70070cf",
                  "source_center": "23",
                  "analyte_type": null,
                  "updated_datetime": "2018-11-27T11:57:18.467265-06:00",
                  "center": {
                    "code": "09",
                    "center_id": "956ca84c-1124-53ff-824f-fa0c84425425",
                    "name": "Washington University School of Medicine",
                    "namespace": "genome.wustl.edu",
                    "short_name": "WUSM",
                    "center_type": "GSC"
                  },
                  "submitter_id": "TCGA-A7-A0DA-10A-01W-A12U-09",
                  "concentration": 0.5,
                  "state": "released",
                  "analyte_type_id": null,
                  "created_datetime": null
                }
              ],
              "submitter_id": "TCGA-A7-A0DA-10A-01W",
              "concentration": null,
              "analyte_type_id": "W",
              "created_datetime": null,
              "analyte_id": "e32ddaf6-666b-443e-996c-03280ca66881",
              "well_number": null,
              "analyte_type": "Repli-G (Qiagen) DNA",
              "updated_datetime": "2018-09-06T13:49:20.245333-05:00",
              "spectrophotometer_method": null,
              "state": "released",
              "a260_a280_ratio": null
            }
          ],
          "updated_datetime": "2018-09-06T13:49:20.245333-05:00",
          "weight": null,
          "submitter_id": "TCGA-A7-A0DA-10A-01",
          "creation_datetime": 1273795200,
          "state": "released",
          "portion_number": "01",
          "is_ffpe": false,
          "created_datetime": null
        }
      ],
      "intermediate_dimension": null,
      "time_between_clamping_and_freezing": null,
      "freezing_method": null,
      "pathology_report_uuid": null,
      "submitter_id": "TCGA-A7-A0DA-10A",
      "tumor_code_id": null,
      "shortest_dimension": null,
      "oct_embedded": "false",
      "days_to_sample_procurement": null,
      "longest_dimension": null,
      "current_weight": null,
      "is_ffpe": false,
      "tissue_type": "Not Reported"
    }
  ],
  "sample_ids": [
    "bb28c682-0071-4642-bab6-768b0fc322c6",
    "6d250ffa-8365-4c5a-90ee-fa7f447a6071",
    "4f441e61-6bea-4a12-841d-def270804bbe"
  ],
  "demographic": {  // Patient(us-core extensions) +  Observation maybe
    "race": "white",
    "gender": "female",
    "ethnicity": "not hispanic or latino",
    "vital_status": "Alive",
    "age_at_index": 62,
    "submitter_id": "TCGA-A7-A0DA_demographic",
    "days_to_birth": -22708,
    "created_datetime": null,
    "year_of_birth": 1947,
    "demographic_id": "fb49b217-29cd-5368-8589-b46f2b3fe2ef",
    "updated_datetime": "2019-07-31T21:18:16.285358-05:00",
    "state": "released",
    "year_of_death": null
  },
  "submitter_sample_ids": [
    "TCGA-A7-A0DA-10A",
    "TCGA-A7-A0DA-01A",
    "TCGA-A7-A0DA-01Z"
  ],
  "exposures": [. //Observation -> Patient
    {
      "cigarettes_per_day": null,
      "alcohol_history": "Not Reported",
      "updated_datetime": "2019-07-31T21:18:16.285358-05:00",
      "exposure_id": "a7d2ea16-132a-51ad-be10-bfee634165ee",
      "submitter_id": "TCGA-A7-A0DA_exposure",
      "years_smoked": null,
      "state": "released",
      "created_datetime": null,
      "alcohol_intensity": null
    }
  ],
  "primary_site": "Breast",
  "submitter_diagnosis_ids": [
    "TCGA-A7-A0DA_diagnosis"
  ]
}

[teslajoy]

handled via https://github.com/bmeg/fhirizer