Incorporate ontologies into DICOM SNOMED to NCIt mapping

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A repository for the work of the Tools workstream for CCDH

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Incorporate ontologies into DICOM SNOMED to NCIt mapping #7

Closed gaurav closed 3 years ago

gaurav commented 4 years ago

We now have an SSSOM file containing mappings from DICOM SNOMED to NCIt using the NCI Metathesaurus as part of https://github.com/cancerDHC/operations/issues/48. In this issue, we will attempt to fill in the missing gaps by using terms from particular ontologies, in particular:

[x] The EBI Ontology Lookup Service
[x] Livestock Breed Ontology
[x] ChEBI
[ ] RadLex
[ ] AGROVOC
(Any other suggestions?)

gaurav commented 3 years ago

We now have the exact terms from:

ChEBI
Livestock Breed Ontology
The EBI Ontology Lookup Service

This puts us at 2,434 terms remaining to be matched. You can see the mappings in the SSSOM file.

My immediate next step is to see if we can group the remaining terms in some way, perhaps by looking at the hierarchical information in the NCImt. That might make it easier to figure out how to go about mapping the remaining terms.

gaurav commented 3 years ago

Added RadLex to the list as mentioned in https://github.com/cancerDHC/operations/issues/48#issuecomment-694868279.

balhoff commented 3 years ago

Since individual ontologies can be tackled as separable work items, I created #19 and will close this issue. I also created #20 for exploring use of NCImt hierarchy to aid mapping by grouping terms.