New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Map additional Allen Brain ontologies #609

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

Comments

Projects
None yet
2 participants
@cmungall
Member

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

This comment has been minimized.

Show comment
Hide comment
@cmungall

cmungall Nov 1, 2014

Member

TODO: check alignments using reasoning

Member

cmungall commented Nov 1, 2014

TODO: check alignments using reasoning

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

This comment has been minimized.

Show comment
Hide comment
@cmungall

cmungall Nov 20, 2014

Member

Request from Terri Gilbert: https://twitter.com/uberanat/status/529806366437679104

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

Member

cmungall commented Nov 20, 2014

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 added a commit that referenced this issue Dec 19, 2014

Mapped DMBA, PBA xrefs from acronyms to IDs. Issue #609. Note: revert…
…ed previous attempt at this, will do HBA separately

cmungall added a commit that referenced this issue Dec 19, 2014

Mapped HBA xrefs from acronyms to IDs. Issue #609. Note: reverted pre…
…vious attempt at this, which erroneously mapped to lateral subtypes

cmungall added a commit that referenced this issue Dec 19, 2014

cmungall added a commit that referenced this issue Dec 19, 2014

Mapped HBA xrefs from acronyms to IDs. Issue #609. Remaining lateral …
…structures that have no lateral-neutral counterpart
@cmungall

This comment has been minimized.

Show comment
Hide comment
@cmungall

cmungall Dec 19, 2014

Member

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
Member

cmungall commented Dec 19, 2014

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

@dosumis

This comment has been minimized.

Show comment
Hide comment
@dosumis

dosumis Dec 19, 2014

Contributor

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.

Contributor

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.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment