HTAN-FHIR

python scripts to transform HTAN metadata to FHIR

Fetching Schema

wget https://raw.githubusercontent.com/ncihtan/schematic/main/data/schema_org_schemas/HTAN.jsonld

Fetching Data

data https://data.humantumoratlas.org/explore?selectedFilters=%5B%7B%22group%22%3A%22AtlasName%22%2C%22value%22%3A%22HTAN+OHSU%22%7D%5D and click Download Metadata

Transforming Data

$ python model.py
Assay type Bulk RNA-seq parent not an bts:Assay is bts:DataType
Assay type Bulk DNA not found in the schema
Assay type scATAC-seq parent not an bts:Assay is bts:DataType
Assay type Electron Microscopy parent not an bts:Assay is bts:DataType
Assay type RPPA parent not an bts:Assay is bts:DataType
$ g3t meta validate
{'summary': {'DocumentReference': 94880, 'Specimen': 300, 'ResearchStudy': 1, 'Task': 94880, 'ResearchSubject': 21, 'Patient': 21}}
$ g3t meta graph