Integrate BioPortal into SNOMED-in-DICOM mappings

cancerDHC / umls-rrf-scala

A very basic library for parsing files in the UMLS RRF format

MIT License

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Integrate BioPortal into SNOMED-in-DICOM mappings #22

Open gaurav opened 3 years ago

gaurav commented 3 years ago

There are two ways in which we'd like to do this:

[x] Use BioPortal to do term searches, as it appears to have some terms that the Ontology Lookup Service doesn't have (https://github.com/gaurav/umls-rrf-scala/issues/14)
- [ ] Access BioPortal's lexical and ID-based mappings from SNOMED to other ontologies and see if we can use that to fill in gaps (https://github.com/gaurav/umls-rrf-scala/issues/15).

gaurav commented 3 years ago

I've added support for searching BioPortal, which includes terms from RadLex as well. You can see the results in our shared Google Drive (search for "BioPortal" for BioPortal matches and "radlex.org" for RadLex terms). Many of the BioPortal matches came from the Ontology of Consumer Health Vocabulary (OCHV) and the Systematized Nomenclature of Medicine, International Version (SNMI) and the Interlinking Ontology for Biological Concepts (IOBC). We now have 1,710 terms remaining to map.

gaurav commented 3 years ago

It does look like the BioPortal search API only gives us "prefLabel" and "synonym" matches, so we will need to use the mapping API to find that mapping information.