Lift Schema Rc6 + FHIR

[bwalsh]

In order to integrate the ICEBERG schema with BMEG's schema, we need to deprecate:

case Patient
sample Specimen
aliquot Specimen.partOf
project ResearchStudy
program ResearchStudy
command Task (DiagnosticReport)
compound Compound

Definition of done:

• Schemas must validate.
• The BMEG schema should be a proper superset of ICEBERG.
• Common entities should be exactly the same.

[matthewpeterkort]

aliquot Specimen.partOf

Don't think Aliquot should be mapped to anything it FHIR, because I don't see a close analog to Aliquot in FHIR and there are 6 edges to BMEG vertices that would be broken moving it to Specimen.

Alternatively, Aliquot could be preserved in it's original form, with links to FHIR vertices File (DocumentReference), Command (Task), Sample (Specimen), and Project (ResearchStudy) and BMEG references to GeneExpression, Methylation, Transcript Expression, DrugResponse, CopyNumberAlteration, and SomaticCallset. This way, less of the schema is broken for a node type that doesn't really fit to begin with.

Also, this way, Aliquots can reference their parent FHIR Specimen Sample as a different node type without having to implement an approach where both Aliquots and Samples are both FHIR specimens, and Aliquots are linked together to Samples via Specimen.partOf Specimen.parent references.

compound Compound

By compound you're probably referring to FHIR's Substance field. This could probably get mapped to FHIR since it is less of a breaking change, there are only 3 BMEG edges that are connected to it, GenePhenotypeAssociation, ProteinCompoundAssociation, and DrugResponse.

But I think that SubstanceDefinition might be a better option than Substance because there are far more BMEG "research" like options for mapping compound fields than Substance.

See figure below:

[matthewpeterkort]

Cooked up a first draft of the schema lift here: https://github.com/bmeg/iceberg-schema-tools/tree/schema-viewer/CytoScapeSchemaViewer. Did the schema edits by hand with the help of the schema viewer. My steps / concerns / feedback can be found here: https://github.com/bmeg/iceberg-schema-tools/blob/schema-viewer/CytoScapeSchemaViewer/Bmeg_Gen3_Unified_Notes.txt

[bwalsh]

See:

• https://build.fhir.org/specimen-definitions.html#Specimen.parent
• https://build.fhir.org/specimen-definitions.html#Specimen.combined

The parent specimen could be the source from which the current specimen is derived by some processing step (e.g. an aliquot or isolate or extracted nucleic acids from clinical samples) or one of many specimens that were combined to create a pooled sample.