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Add interstitial nucleus of the vestibular nerve

Open shawntanzk opened this issue 3 years ago • 5 comments

@patrick-lloyd-ray I don't quite understand this term. Neuronames suggest it to be part of a nerve, but ABA suggests that it isn't. I think that's why this is failing - it is nucleus of brain (ABA suggests this) which has to be gray matter, but also part_of a nerve, which should be white matter. Need help here

shawntanzk avatar Aug 10 '22 10:08 shawntanzk

Here's a diff of how these changes impact the classified ontology (on -simple file):

Ontology comparison

Left

  • Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-simple.owl
  • Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2022-09-12/uberon-simple.owl
  • Loaded from: file:/work/src/ontology/../../master/src/ontology/uberon-simple.owl

Right

  • Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-simple.owl
  • Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2022-09-12/uberon-simple.owl
  • Loaded from: file:/work/src/ontology/uberon-simple.owl

Ontology imports

Ontology annotations

UBERON_8440074 http://purl.obolibrary.org/obo/UBERON_8440074

Added

github-actions[bot] avatar Aug 10 '22 12:08 github-actions[bot]

Here's a diff of your edit file (unreasoned)

Ontology comparison

Left

  • Ontology IRI: http://purl.obolibrary.org/obo/uberon/core.owl
  • Version IRI: None
  • Loaded from: file:/work/src/ontology/../../master/src/ontology/uberon-edit.obo

Right

  • Ontology IRI: http://purl.obolibrary.org/obo/uberon/core.owl
  • Version IRI: None
  • Loaded from: file:/work/src/ontology/uberon-edit.obo

Ontology imports

Ontology annotations

UBERON_8440074 http://purl.obolibrary.org/obo/UBERON_8440074

Added

github-actions[bot] avatar Aug 10 '22 12:08 github-actions[bot]

Yeah, this is a weird one.

Here's an image from ABA of the interstitial nucleus of the vestibulocochlear nerve (highlighted in purple, labeled I8) from human. The structure labeled r8 is the root of vestibulocochlear nerve. The interstitial nucleus of the vestibular nerve would be just those parts of I8 that are in the vestibular nerve portion of the vestibulocochlear nerve, which is just as you say in the definition.

Screen Shot 2022-08-10 at 12 42 44 PM

So, I think the definition is fine as you have it. I think the problem is somewhere in the axioms upstream.

The superclass UBERON:0002308 (nucleus of brain), is "A neural nucleus that is part of the brain." which is equivalent to "neural nucleus" and part_of some "brain". It also has the subclass axiom part_of some brain gray matter.

UBERON:0000125 (neural nucleus) is "A spatially aggregated collection of nerve cell bodies in the CNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections, and including nearby cells that share the same cell type, chemical phenotype, and connections." It has a subclass axiom of composed_primarily_of some gray matter, which seems fine to me.

UBERON:0003528 (brain gray matter) is defined as "A gray matter that is part of a brain [Automatically generated definition]." UBERON:0003544 (brain white matter) is defined as "The regions of the brain that are largely or entirely composed of myelinated nerve cell axons and contain few or no neural cell bodies or dendrites."

I think that the problem is here: the cells that comprise the interstitial nucleus of the vestibular nerve are some of the few with soma in white matter -- i.e., they are "gray matter" surrounded by "white matter."

The gray matter annotation on "nucleus of brain" seems to be the offending axiom here, but I don't want to recommend changing it because I suspect that it will have serious consequences for other classes. Maybe I'm misreading the problem, though, so let me know if this is consistent with what you are seeing.

patrick-lloyd-ray avatar Aug 11 '22 00:08 patrick-lloyd-ray

The gray matter annotation on "nucleus of brain" seems to be the offending axiom here, but I don't want to recommend changing it because I suspect that it will have serious consequences for other classes. Maybe I'm misreading the problem, though, so let me know if this is consistent with what you are seeing.

You are spot on on the difficulties I'm having here, and I agree with you in not wanting to change something as high up in the hierarchy as "nucleus of brain". We can fix it to UBERON:0000125 (neural nucleus) - but I think if we assume partonomy as a relationship in the hierarchy of ABA, it will still be a problem. That being said, we have talked about how using partonomy for all relationships has limitations. I think for now I will change the parent to neural nucleus. Thanks heaps! :)

shawntanzk avatar Aug 11 '22 07:08 shawntanzk

@patrick-lloyd-ray seems like it still faces the same problem - it is still unsat at the materialised stage, probably due to the white matter grey matter thing. I think this case now calls for relooking at some axioms higher up, would be interested to get @dosumis or @cmungall view on this :)

shawntanzk avatar Aug 11 '22 08:08 shawntanzk

whoops sorry this fell off my radar.

unsat debugging:

shawntan@C02DW26DML87 /Users/shawntan/documents/GitHub/uberon/src/ontology [add-interstitial-nucleus-of-the-vestibular-nerve]
% robot merge -i tmp/unreasoned.owl -i components/develops-from-chains.owl --collapse-import-closure false \
        relax   unmerge -i components/reflexivity_axioms.owl \
        unmerge -i components/develops-from-chains.owl  -output test.owl 

shawntan@C02DW26DML87 /Users/shawntan/documents/GitHub/uberon/src/ontology [add-interstitial-nucleus-of-the-vestibular-nerve]
% robot explain -i test.owl -M unsatisfiability --unsatisfiable random:10 --explanation unsat.md

Results:

src/ontology/unsat.md

interstitial nucleus of the vestibular nerve SubClassOf Nothing

shawntanzk avatar Sep 06 '22 10:09 shawntanzk

@dosumis & @cmungall - it seems to me that the following axiom is wrong as there are defs nerves in the CNS too: nerve SubClassOf part_of some peripheral nervous system As this is quite high up I'd rather have a thumbs up from you before removing it.

shawntanzk avatar Sep 06 '22 10:09 shawntanzk

@dosumis & @cmungall - it seems to me that the following axiom is wrong as there are defs nerves in the CNS too: nerve SubClassOf part_of some peripheral nervous system As this is quite high up I'd rather have a thumbs up from you before removing it.

@shawntanzk careful, you're going to strike a nerve with that one!

balhoff avatar Sep 06 '22 14:09 balhoff

Is this a nerve-root rather than part of a nerve?

see https://github.com/obophenotype/uberon/issues/286

dosumis avatar Sep 12 '22 12:09 dosumis

Thanks @dosumis - did not know that whole history. Have changed it to vestibulocochlear nerve root instead, should fix it :) Will let QC run through and hopefully all will be alright

shawntanzk avatar Sep 12 '22 12:09 shawntanzk