Mapping problem for EMAPA:16033, EMAPA:16037, EMAPA:31865 #601

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fbastian opened this Issue Oct 28, 2014 · 1 comment

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These EMAPA terms are anatomical structures (e.g., "8-cell stage embryo"), but they are mapped to developmental stages (e.g., UBERON:0007236 "8 cell stage"). They are just embryos with particular start and end stages.

@cmungall cmungall closed this Oct 29, 2014

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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fbastian Aug 29, 2016

The problem is still present in last composite-metazoan, e.g.:

[Term]
id: UBERON:0000106
name: zygote stage
...
xref: EMAPA:16033

The problem is still present in last composite-metazoan, e.g.:

[Term]
id: UBERON:0000106
name: zygote stage
...
xref: EMAPA:16033

@fbastian fbastian reopened this Aug 29, 2016

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