Request "upper central primary incisor tooth" #602

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drseb opened this Issue Oct 28, 2014 · 6 comments

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drseb commented Oct 28, 2014

I couldn't find this class. Probably should be defined as:
'incisor tooth' and (part_of some 'upper jaw region') and (part_of some 'primary dentition') and (in_central_side_of some 'incisor region of dentition')

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cmungall Oct 28, 2014

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I think we just need to add to the import closure? It's in uberon
already:

[Term]
id: UBERON:0018593
name: upper central primary incisor tooth
synonym: "upper central deciduous incisor tooth" EXACT [FMA:84216]
synonym: "upper primary tooth A" EXACT [FMA:84216]
intersection_of: UBERON:0018597 ! upper primary incisor tooth
intersection_of: in_central_side_of UBERON:0018645 ! incisor region of 
dentition
xref: FMA:84216 ! Upper central primary incisor tooth
def: "A upper primary canine tooth that is in_the_central_side_of a 
dentition." [OBOL:automatic]

On 28 Oct 2014, at 7:13, Sebastian wrote:

I couldn't find this class. Probably should be defined as:
'incisor tooth' and (part_of some 'upper jaw region') and (part_of
some 'primary dentition') and (in_central_side_of some 'incisor region
of dentition')


Reply to this email directly or view it on GitHub:
#602

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cmungall commented Oct 28, 2014

I think we just need to add to the import closure? It's in uberon
already:

[Term]
id: UBERON:0018593
name: upper central primary incisor tooth
synonym: "upper central deciduous incisor tooth" EXACT [FMA:84216]
synonym: "upper primary tooth A" EXACT [FMA:84216]
intersection_of: UBERON:0018597 ! upper primary incisor tooth
intersection_of: in_central_side_of UBERON:0018645 ! incisor region of 
dentition
xref: FMA:84216 ! Upper central primary incisor tooth
def: "A upper primary canine tooth that is in_the_central_side_of a 
dentition." [OBOL:automatic]

On 28 Oct 2014, at 7:13, Sebastian wrote:

I couldn't find this class. Probably should be defined as:
'incisor tooth' and (part_of some 'upper jaw region') and (part_of
some 'primary dentition') and (in_central_side_of some 'incisor region
of dentition')


Reply to this email directly or view it on GitHub:
#602

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drseb Oct 28, 2014

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Thanks. Note that I didn't find it because the requested class is not a subclass of "upper primary incisor tooth", which IMHO has not a single subclass. (I use full uberon at the moment; will mireot later)

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drseb commented Oct 28, 2014

Thanks. Note that I didn't find it because the requested class is not a subclass of "upper primary incisor tooth", which IMHO has not a single subclass. (I use full uberon at the moment; will mireot later)

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cmungall Oct 28, 2014

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Reopening until we get the correct inferences

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cmungall commented Oct 28, 2014

Reopening until we get the correct inferences

@cmungall cmungall reopened this Oct 28, 2014

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RDruzinsky Oct 29, 2014

I know that, in theory, homology should not enter into this, but I think
that it would be very cool if we could find a way to link homologous teeth
across mammals. For example, the central incisor in a rodent is not the
same tooth, neither in a developmental nor an evolutionary sense, as a
central incisor in a human. Any ideas on how to add this information?

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

Office: 312-996-0406
Lab: 312-996-0629
Website: www.peerj.com/RobertDruzinsky

On Tue, Oct 28, 2014 at 6:59 PM, Chris Mungall notifications@github.com
wrote:

Reopened #602 #602.


Reply to this email directly or view it on GitHub
#602 (comment).

I know that, in theory, homology should not enter into this, but I think
that it would be very cool if we could find a way to link homologous teeth
across mammals. For example, the central incisor in a rodent is not the
same tooth, neither in a developmental nor an evolutionary sense, as a
central incisor in a human. Any ideas on how to add this information?

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

Office: 312-996-0406
Lab: 312-996-0629
Website: www.peerj.com/RobertDruzinsky

On Tue, Oct 28, 2014 at 6:59 PM, Chris Mungall notifications@github.com
wrote:

Reopened #602 #602.


Reply to this email directly or view it on GitHub
#602 (comment).

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If someone wants to provide a set of homology mappings, @fbastian and @ANiknejad will add it to the homology table.

There is a problem here analogous to digits, in which the referents used in the homology assertions are often ambiguous and/or have homology assumptions built in. E.g. for digits we decided that "digit 3" did not always mean the 3rd digit, but that it meant the digit homologous to digit 3 in a pentadactyl autopod, and it was OK to build in homology where it's uncontroversial and not liable to cause confusion (e.g. humans, horses). If there was either controversy or confusion, e.g. aves with the whole 1+2+3=2+3+4 dev frameshift we opted to make aves-specific classes with names used in the taxon (e.g. alular digit).

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cmungall commented Oct 29, 2014

If someone wants to provide a set of homology mappings, @fbastian and @ANiknejad will add it to the homology table.

There is a problem here analogous to digits, in which the referents used in the homology assertions are often ambiguous and/or have homology assumptions built in. E.g. for digits we decided that "digit 3" did not always mean the 3rd digit, but that it meant the digit homologous to digit 3 in a pentadactyl autopod, and it was OK to build in homology where it's uncontroversial and not liable to cause confusion (e.g. humans, horses). If there was either controversy or confusion, e.g. aves with the whole 1+2+3=2+3+4 dev frameshift we opted to make aves-specific classes with names used in the taxon (e.g. alular digit).

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 cmungall closed this Feb 15, 2015

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RDruzinsky Feb 16, 2015

I would be interested in doing this, but it will take time. Also, the
homologies are different in different mammalian taxonomic groups, so it's
complicated.

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

Office: 312-996-0406
Lab: 312-996-0629
Website: www.peerj.com/RobertDruzinsky

On Tue, Oct 28, 2014 at 9:39 PM, Chris Mungall notifications@github.com
wrote:

If someone wants to provide a set of homology mappings, @fbastian
https://github.com/fbastian and @ANiknejad
https://github.com/ANiknejad will add it to the homology table.

There is a problem here analogous to digits, in which the referents used
in the homology assertions are often ambiguous and/or have homology
assumptions built in. E.g. for digits we decided that "digit 3" did not
always mean the 3rd digit, but that it meant the digit homologous to digit
3 in a pentadactyl autopod, and it was OK to build in homology where it's
uncontroversial and not liable to cause confusion (e.g. humans, horses). If
there was either controversy or confusion, e.g. aves with the whole
1+2+3=2+3+4 dev frameshift we opted to make aves-specific classes with
names used in the taxon (e.g. alular digit).


Reply to this email directly or view it on GitHub
#602 (comment).

I would be interested in doing this, but it will take time. Also, the
homologies are different in different mammalian taxonomic groups, so it's
complicated.

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

Office: 312-996-0406
Lab: 312-996-0629
Website: www.peerj.com/RobertDruzinsky

On Tue, Oct 28, 2014 at 9:39 PM, Chris Mungall notifications@github.com
wrote:

If someone wants to provide a set of homology mappings, @fbastian
https://github.com/fbastian and @ANiknejad
https://github.com/ANiknejad will add it to the homology table.

There is a problem here analogous to digits, in which the referents used
in the homology assertions are often ambiguous and/or have homology
assumptions built in. E.g. for digits we decided that "digit 3" did not
always mean the 3rd digit, but that it meant the digit homologous to digit
3 in a pentadactyl autopod, and it was OK to build in homology where it's
uncontroversial and not liable to cause confusion (e.g. humans, horses). If
there was either controversy or confusion, e.g. aves with the whole
1+2+3=2+3+4 dev frameshift we opted to make aves-specific classes with
names used in the taxon (e.g. alular digit).


Reply to this email directly or view it on GitHub
#602 (comment).

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