Taxon constraints on UBERON_0000023 "wing" #721

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fbastian opened this Issue Jun 23, 2015 · 1 comment

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Currently, we only have:

id: UBERON_0000023
name: wing
relationship: only_in_taxon NCBITaxon:33213
relationship: never_in_taxon NCBITaxon:9606

For Bgee, I would suggest the following, as it's not possible to use several only_in_taxon:

relationship: never_in_taxon NCBITaxon:9443 ! Primates
relationship: never_in_taxon NCBITaxon:314147 ! Glyres
relationship: never_in_taxon NCBITaxon:91561 ! Cetartiodactyla 
relationship: never_in_taxon NCBITaxon:9263 ! Metatheria  
relationship: never_in_taxon NCBITaxon:9254 ! Prototheria  
relationship: never_in_taxon NCBITaxon:8457 ! Sauropsida  
relationship: never_in_taxon NCBITaxon:8292 ! Amphibia (if you don't consider flying frogs as having wings)  
relationship: never_in_taxon NCBITaxon:6231 ! Nematoda  
relationship: never_in_taxon NCBITaxon:118072 ! Coelacanthimorpha  
relationship: never_in_taxon NCBITaxon:7878 ! Dipnoi  
relationship: never_in_taxon NCBITaxon:186634 ! Otomorpha (because sister taxon 'Euteleosteomorpha' contains 'flying fish'; do we consider that flying fish have wings?)  

cmungall added a commit that referenced this issue Jul 1, 2015

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cmungall Jul 1, 2015

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Yeh, it's kind of arbitrary with all these gliding creatures. We use PATO to define wing, see: http://purl.obolibrary.org/obo/UBERON_0000023

appendage and (has quality some aliform )

which is defined as... "Shape quality inhering in a bearer by virtue of the bearer's being shaped like a wing"

circular!

There is an argument for obsoleting wing. I'm not sure it does anyone any good. It might still be useful to have a kb somewhere that says that this PATO quality inheres in this entity in taxa A, B, ... but that is phenoscape's job, and we traditionally have these axioms outside the ontology.

I think we would still want to precoordinate fin vs limb of course... the differentiae here is classically autopod presence?

Closing this issue which is about TCs. For discussion on the general pattern see #727

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cmungall commented Jul 1, 2015

Yeh, it's kind of arbitrary with all these gliding creatures. We use PATO to define wing, see: http://purl.obolibrary.org/obo/UBERON_0000023

appendage and (has quality some aliform )

which is defined as... "Shape quality inhering in a bearer by virtue of the bearer's being shaped like a wing"

circular!

There is an argument for obsoleting wing. I'm not sure it does anyone any good. It might still be useful to have a kb somewhere that says that this PATO quality inheres in this entity in taxa A, B, ... but that is phenoscape's job, and we traditionally have these axioms outside the ontology.

I think we would still want to precoordinate fin vs limb of course... the differentiae here is classically autopod presence?

Closing this issue which is about TCs. For discussion on the general pattern see #727

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