Closed sierra-moxon closed 3 years ago
We should use the T codes
e.g T039 not phsf
Bioportal uses STY, we could ask for this in bioregistry.io http://bioregistry.io/registry/sty -- can you make a ticket? https://github.com/bioregistry/bioregistry/issues
we can make URLs
http://purl.bioontology.org/ontology/STY/T039
but given there is a hierarchy I don't see the value of curating broad/narrows that can be inferred?
mappings for codes like phsf -> T codes here: https://metamap.nlm.nih.gov/Docs/SemanticTypes_2018AB.txt
Request to add STY: https://github.com/bioregistry/bioregistry/issues/83
We should just go ahead and add STY in the biolink yaml header for now
I've added STY to the Bioregistry and made a new deployment. Here's the new entry: https://bioregistry.io/registry/sty. Please let me know if there's anything else I can add
Thanks @cthoyt!
OK, my PR fixes things such that we use STY for semantic types. I also got rid of UMLSST as it was redundant
We still have this:
UMLSSG: 'https://metamap.nlm.nih.gov/Docs/SemGroups_2018.txt/group#'
but this 404s
how about https://lhncbc.nlm.nih.gov/semanticnetwork/SemanticNetworkArchive.html
which points to https://lhncbc.nlm.nih.gov/semanticnetwork/download/sg_archive/SemGroups-v04.txt
Throughout the model, we have mappings like: "UMLSST:phsf" that use broad UMLS categories(?) as a sort of identifier. I'd like to propose removing them as they don't resolve.
Are they critical for the node normalizer, or other downstream components that would be harmed if we removed them? @cbizon @RichardBruskiewich @mbrush