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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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Ensure WBbt is coherent when combined with Uberon #1405

Closed cmungall closed 6 years ago

cmungall commented 6 years ago

Moved from https://github.com/geneontology/simple-annoton-editor/issues/32

DNC and VNC are unsat:

image

this is probably because of an inappropriate taxon equivalence for somatic nervous system @raymond91125

raymond91125 commented 6 years ago

I need to add the definition in. Somatic nervous system in the nematode actually means 'Part of the nervous system that is NOT pharyngeal'.

cmungall commented 6 years ago

ok, good. It's definitely different from vertebrate SNS

balhoff commented 6 years ago

Not sure why we aren't seeing the same unsatisfiable classes. I am loading these:

balhoff commented 6 years ago

head muscle:

head_muscle

balhoff commented 6 years ago

Z4.appaaaa nucleus (and also Z4.appaaap nucleus):

z4

cmungall commented 6 years ago

I LOVE THAT WORM HAS A ZAPPA NUCLEUS

The spermathecum thing came up before: #367

we weakened the restriction that they were only in females, as they are found in worm hermaphrodites. We swapped for a never-in male reproductive system. This is still too strong I think? It should never be never-in male (as herms have both M and F reproductive systems).

I love using a reasoner with worms we find such interesting stuff! cc @vanaukenk @raymond91125

On this topic, I think we should follow @dosumis suggestion from way back and have more specific terms for insect and worm spermathecum, in uberon it's currently a loose grouping.

I note that the GO definition is fly-centric

def: "The process in which the anatomical structures of a spermathecum, a sperm storage organ, are generated and organized. Paired spermathecae lie at the anterior end of the insect uterus on the dorsal side. Each spermatheca consists of an oval shaped capsule, connected to the uterus by a spermathecal stalk." [PMID:12679097]
comment: See also the fly_anatomy.ontology term 'spermathecum ; FBbt:00004921'.

the core of the def is generic (if this is the def then I think the name 'sperm storage organ' is better). But the gloss of the def is fly centric. We need to be clearer with our defs.

Note it's been used for worm and flies: http://amigo.geneontology.org/amigo/term/GO:0035211