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Manually classify ocular adnexa #1189

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cmungall opened this Issue Dec 22, 2015 · 13 comments

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cmungall commented Dec 22, 2015

We currently have axioms of the form:

(part_of some 'orbital region') DisjointUnion (part_of some 'ocular adnexa'), (part_of some 'eyeball')

See: https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern

ie the orbital region consists solely of parts of the ocular adnexa and parts of the eyeball, and these do not comingle

We can write this in a more compact (non-official) syntax like: orbital_region = ocular_adnexa + eyeball

Unfortunately Elk is not complete w.r.t these axioms, so we should manually classify, e.g. based on prolog reasoning

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We expect to end up with:

  • conjunctiva
  • extraocular muscles
  • nasolacrimal system
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cmungall commented Dec 22, 2015

We expect to end up with:

  • conjunctiva
  • extraocular muscles
  • nasolacrimal system
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Currently conjunctiva is not classifying as adnexa as it's asserted part-of the eyeball

MA has 'conjunctiva part_of anterior segment of eye'

It looks like we interpreted that as being part-of the anterior segment of the eyeBALL, and followed MA's lead. MA is technically correct that the conjunctiva is in the anterior segment of the EYE (ie eyeball plus directly associated apparatus), but AFAICT the 'anterior segment' qualifier is typically applied just to the globe and not the associated apparatus. cc @tfhayamizu

We will change uberon so conjunctiva is no longer eyeball, which will yield the correct classification

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cmungall commented Dec 22, 2015

Currently conjunctiva is not classifying as adnexa as it's asserted part-of the eyeball

MA has 'conjunctiva part_of anterior segment of eye'

It looks like we interpreted that as being part-of the anterior segment of the eyeBALL, and followed MA's lead. MA is technically correct that the conjunctiva is in the anterior segment of the EYE (ie eyeball plus directly associated apparatus), but AFAICT the 'anterior segment' qualifier is typically applied just to the globe and not the associated apparatus. cc @tfhayamizu

We will change uberon so conjunctiva is no longer eyeball, which will yield the correct classification

cmungall added a commit that referenced this issue Dec 22, 2015

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agree that conjunctiva is not part of the anterior segment (of the eyeball)

also agree that anterior segment is only the globe, w parts such as ciliary body, cornea, pupil, lens, iris, and aqueous humor

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mellybelly commented Dec 22, 2015

agree that conjunctiva is not part of the anterior segment (of the eyeball)

also agree that anterior segment is only the globe, w parts such as ciliary body, cornea, pupil, lens, iris, and aqueous humor

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the ciliary ganglia are not in @pnrobinson's list nor are they listed as adnexa in HPO. However, according to my rules they are classified as such (they are in the orbital region). Discuss

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cmungall commented Dec 22, 2015

the ciliary ganglia are not in @pnrobinson's list nor are they listed as adnexa in HPO. However, according to my rules they are classified as such (they are in the orbital region). Discuss

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My procedure automatically includes extraocular muscles as expected. Also include the common tendinous ring (currently classified as in the ocular region)?

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cmungall commented Dec 22, 2015

My procedure automatically includes extraocular muscles as expected. Also include the common tendinous ring (currently classified as in the ocular region)?

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RE ciliary ganglia, innervating the ciliary body and in close proximity, I'd probably want to see them included in adnexia, especially if you were going to include the rectus muscles.

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mellybelly commented Dec 22, 2015

RE ciliary ganglia, innervating the ciliary body and in close proximity, I'd probably want to see them included in adnexia, especially if you were going to include the rectus muscles.

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Accessory CG too?

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cmungall commented Dec 22, 2015

Accessory CG too?

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RDruzinsky Dec 22, 2015

Harderian apparatus UBERON_0015153 should be included in the adnexa, too. Right?

RDruzinsky commented Dec 22, 2015

Harderian apparatus UBERON_0015153 should be included in the adnexa, too. Right?

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RE Accessory CG - yes include. lovely paper here: https://journals.viamedica.pl/folia_morphologica/article/viewFile/16223/12861
see figure 6 for Accessory CG. Lots of diversity in CGs !!

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mellybelly commented Dec 22, 2015

RE Accessory CG - yes include. lovely paper here: https://journals.viamedica.pl/folia_morphologica/article/viewFile/16223/12861
see figure 6 for Accessory CG. Lots of diversity in CGs !!

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@RDruzinsky c2a8e5c#diff-c138f865f3844d4ca864af8f4e32dae7R117678 includes all ocular glands into the adnexa, including the harderian

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cmungall commented Dec 22, 2015

@RDruzinsky c2a8e5c#diff-c138f865f3844d4ca864af8f4e32dae7R117678 includes all ocular glands into the adnexa, including the harderian

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what about

UBERON:0013398 ! choroidal gland

I think this should be adnexal, but currently part-of the eyeball

@wdahdul do you know anything about these?

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cmungall commented Dec 22, 2015

what about

UBERON:0013398 ! choroidal gland

I think this should be adnexal, but currently part-of the eyeball

@wdahdul do you know anything about these?

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RDruzinsky Dec 23, 2015

I believe that the choroidal gland is not really a gland. Rather, it is a
network of vessels associated with the optic nerve. I think that it should
remain a part_of the eye, rather than an adnexal part_of the orbit.

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
druzinsk@uic.edu

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

On Tue, Dec 22, 2015 at 5:27 PM, Chris Mungall notifications@github.com
wrote:

what about

UBERON:0013398 http://purl.obolibrary.org/obo/UBERON_0013398 !
choroidal gland

I think this should be adnexal, but currently part-of the eyeball


Reply to this email directly or view it on GitHub
#1189 (comment)
.

RDruzinsky commented Dec 23, 2015

I believe that the choroidal gland is not really a gland. Rather, it is a
network of vessels associated with the optic nerve. I think that it should
remain a part_of the eye, rather than an adnexal part_of the orbit.

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
druzinsk@uic.edu

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

On Tue, Dec 22, 2015 at 5:27 PM, Chris Mungall notifications@github.com
wrote:

what about

UBERON:0013398 http://purl.obolibrary.org/obo/UBERON_0013398 !
choroidal gland

I think this should be adnexal, but currently part-of the eyeball


Reply to this email directly or view it on GitHub
#1189 (comment)
.

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uberon Dec 27, 2015

On Wed, Dec 23, 2015 at 5:55 PM, Robert Druzinsky notifications@github.com
wrote:

I believe that the choroidal gland is not really a gland. Rather, it is a
network of vessels associated with the optic nerve. I think that it should
remain a part_of the eye, rather than an adnexal part_of the orbit.

Fixed in next release, thanks!

uberon commented Dec 27, 2015

On Wed, Dec 23, 2015 at 5:55 PM, Robert Druzinsky notifications@github.com
wrote:

I believe that the choroidal gland is not really a gland. Rather, it is a
network of vessels associated with the optic nerve. I think that it should
remain a part_of the eye, rather than an adnexal part_of the orbit.

Fixed in next release, thanks!

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