lacrimal gland should not be part of skeletal system #607

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cmungall opened this Issue Oct 29, 2014 · 1 comment

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cmungall commented Oct 29, 2014

Incorrect inference caused by being part of 'orbital region'

Caught by @drseb

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cmungall Oct 29, 2014

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May be related to #462

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cmungall commented Oct 29, 2014

May be related to #462

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

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

glands are never parts of the skeletal system.
Fixes issue #607
and prevents further issues of this sort

cmungall added a commit that referenced this issue Nov 17, 2014

This release sees the integration of the following ontologies (in add…
…ition to the existing adult mouse brain atlas, ABA):

 * DHBA - Developing Human Brain Atlas
 * DMBA - Developing Human Brain Atlas
 * HBA - (adult) Human Brain Atlas
 * PBA - (non-human) Primate Brain Atlas

For more details, see:
[Integration-with-neuroanatomical-atlases](https://github.com/obophenotype/uberon/wiki/Integration-with-neuroanatomical-atlases)
and the commits in issue [issue 609](#609)

The new artefacts created are:

 * [uberon-bridge-to-dmba](http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-dmba.owl)
 * [uberon-bridge-to-dhba](http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-dhba.owl)
 * [uberon-bridge-to-hba](http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-hba.owl)
 * [uberon-bridge-to-pba](http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-pba.owl)

Note that at this time, the Allen ontologies are *not* merged into composite-metazoan or composite-vertebrate. A preview is available as:

[composite-brain.obo](http://purl.obolibrary.org/obo/uberon/composite-brain.obo)

This composite ontology includes Uberon with highly specific classes from the Allen ontologies as root nodes or subtrees.

 * neuroanatomy -
     * see [issue 609](#609)
     * Added xrefs for additional Allen ontologies: DHBA, HBA and DMBA
     * Note we retain prefix ABA (though MBA would be consistent with the above)
     * Also added xrefs for Nlx classes not in NIFSTD
     * This release comes with a new ontology, composite-brain.obo
 * Ext (Phenoscape)
    * added internal carotid foramen, added anal fin radial skeleton (series), fix typo in def of supraacetabular buttress [PHENOSCAPE:wd]
 * Other
     * NT: {upper,lower} eyelash. Fixes issue [issue 606](#606) HPO:sk
     * added spatial disjoints: glands are never parts of the skeletal system - Fixes issue [issue 607](#607) and prevents further issues of this sort. HPO:sk
     * tidied up confusion between orbital regions and ocular regions - see notes below
     * Fixed incorrect logical def. Fixes issue [issue 602](#602)
     * fixed typo. closes issue [issue 605](#605)
     * Fixed EMAPA stage/embryo xrefs. Fixes issue [issue 601](#601)

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 now

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