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obophenotype / vccf-ontology

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Clarify the intent of the DPs #7

Open cmungall opened 4 months ago

cmungall commented 4 months ago

Should the DPs be consolidated in the Uberon repo?

Having said that I am likely lacking a lot of context about vccfo

E.g. I am looking at vessel

DP:

https://github.com/obophenotype/vccf-ontology/blob/main/src/patterns/dosdp-patterns/vessel.yaml

Data:

https://github.com/obophenotype/vccf-ontology/blob/main/src/patterns/data/default/vessel.tsv

This doesn't really conform to how we might do it in uberon.

E.g. if I see

def:
  text: "A vessel located in %s"

I expect a logical definition too

see principle S11 from DefinitionConstraintComponent

However, I don't think that's the purpose of this DP. I think this is more like a robot template?

E.g.

defined_class label human_label parent location xrefs synonym synonym_xrefs taxon
2 VCCF:1000000 left atrium left atrium (Human) UBERON:0002079 heart chamber https://en.wikipedia.org/wiki/Heart Left atrium FMA::7097 http://purl.obolibrary.org/obo/NCBITaxon_9606

The Uberon DP would be a laterality one here.

cmungall commented 4 months ago

So we also have this

https://github.com/obophenotype/vccf-ontology/blob/main/src/templates/vessel_organ_crosswalk.tsv

I don't really get why we're dividing the axioms between two TSVs

anitacaron commented 4 months ago

The DOSDP is still in draft mode, and we need to discuss that in the meeting. The second template is different because it comes from a different source.