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obophenotype / uberon

An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology
http://obophenotype.github.io/uberon/
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basioccipital bone relationship to occipital bone #1196

Closed wdahdul closed 8 years ago

wdahdul commented 8 years ago

Please remove the part_of relation between basioccipital bone UBERON:0001692 and occipital bone Uberon:0001676. In protege it appears to come from this general class axiom: 'basioccipital bone' and ('part of' some Mammalia) SubClassOf 'part of' some 'occipital bone'

cmungall commented 8 years ago

The axiom is annotated with ISBN10:0073040584 (Kardong, which I don't have handy right now)

Is this wrong? Do you have an example where the mammalian basioccipital is not part of the occipital?

Skull needs a lot of work

balhoff commented 8 years ago

I found the problem in the Phenoscape KB that led to this issue. Basioccipital bone phenotypes were being provided by the KB as justification for inference of presence of occipital bone in some taxa. It is not a result of that class axiom for mammalian basioccipital. It is a result of bad interaction of the MP hierarchy and the Uberon hierarchy in the EQ mappings. In MP, abnormal basioccipital bone morphology is a subclass of abnormal occipital bone morphology. The EQ semantics of these map to Uberon anatomy terms, but I guess MP is not automatically classified.

I wonder if we should strip the class hierarchy from model organism phenotype ontologies before bringing them into the KB.

balhoff commented 8 years ago

Or possibly all the anatomy terms referenced in MP need to be scoped to the right taxon so that fish phenotypes cannot be classified under MP terms.

balhoff commented 8 years ago

I think we can close this issue unless @wdahdul thinks this is actually incorrect for mammals. The issues in Phenoscape are more related to proper scoping of entities referenced in MP when used in a broader taxonomic context.

wdahdul commented 8 years ago

Yes, I agree with closing this item. Wasila

On Feb 23, 2016, at 11:04 AM, Jim Balhoff notifications@github.com wrote:

I think we can close this issue unless @wdahdul thinks this is actually incorrect for mammals. The issues in Phenoscape are more related to proper scoping of entities referenced in MP when used in a broader taxonomic context.

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