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Map additional Allen Brain ontologies #609

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cmungall opened this issue Nov 1, 2014 · 4 comments
Closed

Map additional Allen Brain ontologies #609

cmungall opened this issue Nov 1, 2014 · 4 comments
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neuro

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@cmungall
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cmungall commented Nov 1, 2014

Previously we only mapped ABA as the others were not available in structured form.

Others now available in JSON:

  • pba - primate
  • hba - human
  • dhba - developing human
  • dmba - developing mouse
cmungall added a commit that referenced this issue Nov 1, 2014
@cmungall
convert allen json to obo. See http://help.brain-map.org/display/api/…
8f9643a 
…Atlas+Drawings+and+Ontologies#AtlasDrawingsandOntologies-StructuresAndOntologies. Addresses issue #609
cmungall added a commit that referenced this issue Nov 1, 2014
@cmungall
targets for making and aligning Allen ontologies. Issue #609
36a60dc
cmungall added a commit that referenced this issue Nov 1, 2014
@cmungall
Initial align of DMBA. Issue #609
d40d068
cmungall added a commit that referenced this issue Nov 1, 2014
@cmungall
Adding missing from PBA. Issue #609
7b105a2
cmungall added a commit that referenced this issue Nov 1, 2014
@cmungall
Initial align of HBA. Issue #609
98b0c6b
cmungall added a commit that referenced this issue Nov 1, 2014
@cmungall
Initial align of DHBA. Issue #609
11d4e35
@cmungall
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cmungall commented Nov 1, 2014

TODO: check alignments using reasoning

cmungall added a commit that referenced this issue Nov 17, 2014
@cmungall
Xrefs and NTs for #609
45b8068
cmungall added a commit that referenced this issue Nov 17, 2014
@cmungall
This release sees the integration of the following ontologies (in add…
5fdabce 
…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
@cmungall
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Request from Terri Gilbert: https://twitter.com/uberanat/status/529806366437679104

"What's the chance you could use our structure_id instead of our acronym?"

cmungall added a commit that referenced this issue Nov 28, 2014
@cmungall
additional alignment. Issue #609
110b7e8
cmungall added a commit that referenced this issue Dec 19, 2014
@cmungall
Mapped DHBA xrefs from acronyms to IDs. Issue #609
38a09b4
cmungall added a commit that referenced this issue Dec 19, 2014
@cmungall
Mapped HBA, DMBA, PBA xrefs from acronyms to IDs. Issue #609
405c4e2
cmungall added a commit that referenced this issue Dec 19, 2014
@cmungall
Mapped DMBA, PBA xrefs from acronyms to IDs. Issue #609. Note: revert…
853b5f3 
…ed previous attempt at this, will do HBA separately
cmungall added a commit that referenced this issue Dec 19, 2014
@cmungall
Mapped HBA xrefs from acronyms to IDs. Issue #609. Note: reverted pre…
41ea4d8 
…vious attempt at this, which erroneously mapped to lateral subtypes
cmungall added a commit that referenced this issue Dec 19, 2014
@cmungall
issue #609
a1f4510
cmungall added a commit that referenced this issue Dec 19, 2014
@cmungall
Mapped HBA xrefs from acronyms to IDs. Issue #609. Remaining lateral …
8140603 
…structures that have no lateral-neutral counterpart
@cmungall
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todo: map ABA to MBA.

the following can't be mapped:

xref: ABA:CTX1-6b ! Cerebral cortex, layers 1-6b
xref: ABA:CTX1 ! Cerebral cortex, layer 1
xref: ABA:CTX2 ! Cerebral cortex, layer 2
xref: ABA:CTX3 ! Cerebral cortex, layer 3
xref: ABA:CTX4 ! Cerebral cortex, layer 4
xref: ABA:CTX5 ! Cerebral cortex, layer 5
xref: ABA:CTX6 ! Cerebral cortex, layer 6
xref: ABA:SNI ! Substantia nigra, lateral part

cmungall added a commit that referenced this issue Dec 19, 2014
@cmungall
Mapped ABA to MBA. Issue #609.
6f8b51d
@dosumis
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dosumis commented Dec 19, 2014

Great to see this progress. May be worth taking to Allen about their plans
for tracking neuron classes.
On 1 Nov 2014 01:24, "Chris Mungall" notifications@github.com wrote:

Previously we only mapped ABA as the others were not available in
structured form.

Others now available in JSON:

  • pba - primate
  • hba - human
  • dhba - developing human
  • dmba - developing mouse

—
Reply to this email directly or view it on GitHub
#609.

cmungall added a commit that referenced this issue Dec 19, 2014
@cmungall
new MBA alignment (was ABA). Issue #609.
94d3d0d
cmungall added a commit that referenced this issue Dec 19, 2014
@cmungall
new MBA alignment (was ABA). Issue #609.
157d160
cmungall added a commit that referenced this issue Dec 19, 2014
@cmungall
new MBA alignment (was ABA). Issue #609.
f799485
@cmungall cmungall added the neuro label Feb 15, 2015
@cmungall cmungall mentioned this issue Feb 15, 2016
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