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biopragmatics / obo-db-ingest

🗄️ Conversion of biomedical nomenclatures like HGNC to OBO
https://biopragmatics.github.io/obo-db-ingest/
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HGNC gene family IDs fail to resolve #2

Closed cmungall closed 2 years ago

cmungall commented 2 years ago 
[Term]
id: hgnc:5956
name: IHH
def: "Indian hedgehog signaling molecule" [pubmed:7590746, pubmed:14770182]
xref: ccds:CCDS33380
xref: ena:L38517
xref: ensembl:ENSG00000163501
xref: merops:C46.003
xref: ncbigene:3549
xref: omim:600726
xref: orphanet:122605
xref: refseq:NM_002181
xref: ucsc:uc002vjo.3
xref: vega:OTTHUMG00000154631
is_a: hgnc.genefamily:1373 ! Hedgehog signaling molecule family
is_a: hgnc.genefamily:1691 ! MicroRNA protein coding host genes
relationship: ro:0002205 uniprot:Q14623
relationship: ro:HOM0000017 rgd:620021
relationship: ro:HOM0000017 mgi:96533
relationship: ro:0002162 ncbitaxon:9606
property_value: locus_group "protein-coding gene" xsd:string
property_value: locus_type "gene with protein product" xsd:string
property_value: location "2q35" xsd:string
synonym: "BDA1" EXACT alias_symbol []
synonym: "HHG2" EXACT alias_symbol []
synonym: "Indian hedgehog (Drosophila) homolog" EXACT previous_name []

https://bioregistry.io/hgnc.genefamily:1373 --> https://registry.identifiers.org/deprecation/resources/MIR:00100671/1373

with a 404 "go home" message :-(

image

cmungall commented 2 years ago

also: should link be is_a? If so it would be good to have the gene families in the .obo, or an easy way to obtain the .obo so we can make something that links up

note that is_a/subClassOf is a very powerful commitments. it means here that you would be committing to the hgnc gene family IDs being classifies under SO:gene which may not be HGNC's intent. It also effectively prohibits a class "gene family" unless one is happy with individual genes classified there (unless gene family is a metaclass)

cthoyt commented 2 years ago

I agree, for ontology stuff this is very heavy. What relation might be better?

Will fix that identifiers.org issue ASAP

cthoyt commented 2 years ago

member of from RO seems appropriate

cthoyt commented 2 years ago

hgnc.genefamily has been deprecated in favor of hgnc.genegroup, so I updated PyOBO to reflect this. I also changed the relationship to be RO member of in 57c99e0. There are new exports in this repo (including one with the hgnc gene group hierarchy)