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Merging terms Orbit and Orbital cavity #462

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alex-dececchi opened this Issue May 28, 2014 · 5 comments

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alex-dececchi commented May 28, 2014

Given synonymous meaning of the terms "orbit" and "orbital cavity", we suggest we merging them and retain the primary label "orbit".

@RDruzinsky

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RDruzinsky commented May 28, 2014

Wouldn't you rather reserve "orbit" for the bony orbit and "orbital cavity"
as the anatomical space?

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

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On Wed, May 28, 2014 at 1:23 PM, alex-dececchi notifications@github.comwrote:

Given synonymous meaning of the terms "orbit" and "orbital cavity", we
suggest we merging them and retain the primary label "orbit".


Reply to this email directly or view it on GitHubhttps://github.com//issues/462
.

@cmungall

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cmungall commented May 28, 2014

There are actually 3

The cavity is logically distinct, so we would retain this

I actually this that UBERON_2001967 should be merged with orbital cavity or better obsoleted as being confusing. It is named as a region but it's actually classified as an anatomical space (aside: I think all spaces should have "space" "cavity" or similar in their name).

This should be coordinated with ZFA, where many of the UBERON:2xxx terms came from:

  • ZFA:0001410 ! orbital region [DEF: "Anatomical cluster that is a anteriolateral part of the cranium and structurally supports the eye."]
  • ZFA:0005558 ! orbit [DEF: "Anatomical space that is the concavity containing the eye."]
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cmungall commented May 28, 2014

Alex, assigned you since the UBERON:2x term in in ext. I recommend obsoletion

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ANiknejad commented Jul 28, 2014

UBERON_2001967 is still present (not obsoleted) in composite-metazoan.owl
date: 11:07:2014 08:37
thus we have ZFA:0005558 mapped twice: on UBERON:0004867 name: orbital cavity
and on UBERON:2001967 name: orbit

I agree with Chris to obsolete UBERON:2001967

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cmungall commented Jul 28, 2014

Fixed with r4110 in ext.

@cmungall cmungall closed this Jul 28, 2014

cmungall added a commit that referenced this issue Oct 29, 2014

tidied up confusion between orbital regions and ocular regions
UBERON:0001697 has been relabeled from 'orbital region' to 'orbit of skull' to
make its nature as part of the skeleton clear.

The overall partonomy is

```
 ocular region (subdivision of face)
   orbit of skull (skeletal)
   eyebrow
   eye
     eyeball
     eyelid
     lacrimal gland
```

Addresses issue #607
Also related to #462

balhoff pushed a commit to obophenotype/uberon-phenoscape-ext that referenced this issue Feb 29, 2016

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