Update ICEES API to Return Ontology Identifiers

ResearchSoftwareInstitute / greendatatranslator

Green Team Data Translator Software Engineering and Development

BSD 3-Clause "New" or "Revised" License

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Update ICEES API to Return Ontology Identifiers #157

Open stevencox opened 5 years ago

stevencox commented 5 years ago

Being a Translator service, ICEES responses should be annotated with semantic data.

Identifiers:

Where items like diseases and chemicals (including drugs) are concerned, ICEES should return identifiers from ontologies like MONDO, PUBCHEM, CHEBI, or phenotypes from HPO, etc.

Types:

Each node ICEES returns should also specify a type from the biolink-model.

karafecho commented 5 years ago

I've pulled MONDO and HPO IDs from Bionames and mapped them to feature variables. Vini Alves and Joyce Borba (Alex's lab) are working with me to map IDs from SMILES, CASRN, RxNorm, SNOMED, and NCIthesaurus. ETA is Monday, 11/12/18. If there are other ontologies or IDs of interest, just let me know.

karafecho commented 5 years ago

This task is complete (for the time being). Identifiers can be found in this spreadsheet. @xu-hao will be updating the ICEES API to return identifiers. This may require a second mapping from the identifiers in the spreadsheet to appropriate ICEES concepts.