FHIRizer: Transforming and Harmonizing GDC, Cellosaurus, and ICGC into FHIR format

https://github.com/bmeg/fhirizer​

Transforming and Harmonizing Data: FHIRizing GDC, Cellosaurus, and ICGC

1. Schema mapping translation:

        - High level: Case -> Patient

         data structure entity mapping

        - Field level: Case submitter_id -> Patient.identifier

          data structure entity field mapping

        - Content: AJCC(v8) TNM stage snomed ids

     standardizing information for interoperability

Transforming and Harmonizing Data: FHIRizing GDC, Cellosaurus, and ICGC

2. Schema transformation: maintaining data quality and consistency

   - Utilizing Pydantic models to enforce schema validation and  data integrity.

   - Ensuring that all mapped fields adhere to the required standards and formats.

Transforming and Harmonizing Data: FHIRizing GDC, Cellosaurus, and ICGC

3. Data generation and validation:

- FHIR-compliant resources from transformed data

- gen3 tracker: g3t meta validate

Transforming and Harmonizing Data: FHIRizing GDC, Cellosaurus, and ICGC

3. Data generation and validation:

- FHIR-compliant resources from transformed data

- gen3 tracker: g3t meta validate

1. Schema mapping translation:

        - High level: Case -> Patient

         data structure entity mapping

        - Field level: Case submitter_id -> Patient.identifier

           translation

        - Content: AJCC(v8) TNM stage snomed ids

     standardizing information for interoperability

2. Schema transformation: maintaining data quality and consistency

   - Utilizing Pydantic models to enforce schema validation and  data integrity.

   - Ensuring that all mapped fields adhere to the required standards and formats.

 CDA integration

use-case driven agile development

Demo