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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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UBERON:0001367 'external anal sphincter' isn't a subclass of 'anal sphincter' #2344

Closed paolaroncaglia closed 2 years ago

paolaroncaglia commented 2 years ago

Quick placeholder ticket to look into what needs fixing here - what axioms may need revising/adding

Uberon term UBERON:0001367 'external anal sphincter'

Suggested revision and reasons Should be a subclass of 'anal sphincter'

Note for self - noticed while addressing an HCA ticket

paolaroncaglia commented 2 years ago

Currently, UBERON:0001367 'external anal sphincter' is not a(n inferred) subclass of 'anal sphincter', like 'internal anal sphincter' is, because it isn't a subclass of 'sphincter muscle'. I'll assert the missing superclass.

cmungall commented 2 years ago

can you instead assert the part-of that will give us the inference

should mirror internal

image

or even better investigate what is missing:

id: UBERON:0001367
name: external anal sphincter
is_a: UBERON:0004832 {source="MA"} ! anal region skeletal muscle
relationship: part_of UBERON:0006867 {source="FMA"} ! anal part of perineum
relationship: surrounds UBERON:0001245 ! anus

shouldn't this be sufficient?

we really need abductive reasoning:

ask the reasoner: why isn't EAS is_a AS? Suggest to me repair axioms

cmungall commented 2 years ago

doh, I see what is missing

'external anal sphincter' should be asserted as a subclass of sphincter muscle

however I see literature saying the EAS is not a true sphincter, which is presumably why we don't say this

paolaroncaglia commented 2 years ago

@cmungall

doh, I see what is missing 'external anal sphincter' should be asserted as a subclass of sphincter muscle

Yep, that's what I said I'd do ;-)

however I see literature saying the EAS is not a true sphincter, which is presumably why we don't say this

Ah ok, could you please provide dbxrefs while you have them handy? So I can add an rdfs:comment to EAS to that extent, and I won't add the asserted sphincter muscle parent. Thanks.

uberon commented 2 years ago

tbh it may be simpler and less 'surprising' to be more, errm, relaxed with the definition our sphincter term, we can just add a note to EAS that it's sometimes considered to be not 'true'

it's a bit odd at the moment as IAS is a single-child of AS and those are always bad.. design practice

On Tue, Mar 29, 2022 at 1:39 PM paolaroncaglia @.***> wrote:

@cmungall https://github.com/cmungall

doh, I see what is missing 'external anal sphincter' should be asserted as a subclass of sphincter muscle

Yep, that's what I said I'd do ;-)

however I see literature saying the EAS is not a true sphincter, which is presumably why we don't say this

Ah ok, could you please provide dbxrefs while you have them handy? So I can add an rdfs:comment to EAS to that extent, and I won't add the asserted sphincter muscle parent. Thanks.

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paolaroncaglia commented 2 years ago

To do for UBERON:0001367 'external anal sphincter':

RDruzinsky commented 2 years ago

This is an interesting question. Except for location, I am not sure that there should be a class 'anal sphincter' with subclasses 'external anal sphincter' and 'internal anal sphincter' because they develop from completely separate anlage.

Thoughts?

Robert E. Druzinsky, Ph.D. Clinical Associate Professor Dept. of Oral Biology College of Dentistry University of Illinois at Chicago 801 S. Paulina Chicago, IL 60612 @.***

Office: 312-996-0406 Lab: 312-996-0629 Website: www.peerj.com/RobertDruzinsky

On Thu, Mar 10, 2022 at 8:20 AM paolaroncaglia @.***> wrote:

Quick placeholder ticket to look into what needs fixing here - what axioms may need revising/adding

Uberon term UBERON:0001367 'external anal sphincter'

Suggested revision and reasons Should be a subclass of 'anal sphincter'

Note for self - noticed while addressing an HCA ticket https://github.com/HumanCellAtlas/ontology/issues/103

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cmungall commented 2 years ago

Well there may be other reasons to group beyond lineage

but point taken we want to avoid deceptive or useless grouping classes where the commonality is primarily lexical

FWIW some other ontologies group the same way

image

Historically uberon has generally been liberal in including groupings, but also liberal in applying annotations to them that flag them as groupings. We don't need to retain that policy though