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obophenotype / uberon

An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology
http://obophenotype.github.io/uberon/
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Term request: Superclasses for "diastema between central incisors" #687

Closed drseb closed 9 years ago

drseb commented 9 years ago

Can you add general classes for "diastema between incisors", "diastema between teeth", "diastema between primary teeth", without the restriction on the central incisors.

I would need this for the definition of HPO classes such as "Widely-spaced incisors", "Abnormal spaced incisors", "Widely spaced teeth" etc.

Thanks, Sebastian

This is related to: https://github.com/obophenotype/uberon/commit/3a05ee21e60e707392adc55c3692d7089367509e

cmungall commented 9 years ago

Ah, I thought I got all the ones required for HPO but missed the primary teeth one.

hierarchy seems a bit weird no?

         is_a HP:0000692 ! Misalignment of teeth [DEF: "Abnormal alignment, positioning, or spacing of the teeth, i.e., `misaligned` (PATO:0001654) `teeth` (FMA:12516)."]
          is_a HP:0000687 ! Widely spaced teeth ***  [DEF: "Increased spaces (diastemata) between most of the teeth in the same dental arch."]
           is_a HP:0006313 ! Widely spaced primary teeth [DEF: "Increased space between the primary teeth. Note this phenotype should be distinguished from increased space due purely to microdontia."]
          is_a HP:0000699 ! Diastema ***  [DEF: "Increased space between two adjacent teeth in the same dental arch."]
           is_a HP:0001566 ! Widely-spaced maxillary central incisors [DEF: "Increased distance between the `maxillary central permanent incisor tooth` (FMA:55722)."]

also feel free to re-open tickets

RDruzinsky commented 9 years ago

Calling a diastema a "misalignment" is a very human-centric approach.

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, Apr 14, 2015 at 10:13 AM, Chris Mungall notifications@github.com wrote:

Ah, I thought I got all the ones required for HPO but missed the primary teeth one.

hierarchy seems a bit weird no?

     is_a HP:0000692 ! Misalignment of teeth [DEF: "Abnormal alignment, positioning, or spacing of the teeth, i.e., `misaligned` (PATO:0001654) `teeth` (FMA:12516)."]
      is_a HP:0000687 ! Widely spaced teeth ***  [DEF: "Increased spaces (diastemata) between most of the teeth in the same dental arch."]
       is_a HP:0006313 ! Widely spaced primary teeth [DEF: "Increased space between the primary teeth. Note this phenotype should be distinguished from increased space due purely to microdontia."]
      is_a HP:0000699 ! Diastema ***  [DEF: "Increased space between two adjacent teeth in the same dental arch."]
       is_a HP:0001566 ! Widely-spaced maxillary central incisors [DEF: "Increased distance between the `maxillary central permanent incisor tooth` (FMA:55722)."]

also feel free to re-open tickets

— Reply to this email directly or view it on GitHub https://github.com/obophenotype/uberon/issues/687#issuecomment-92897773.

drseb commented 9 years ago

@cmungall Yes, I start to work on this part now.

@RDruzinsky Might be true, but I guess you are referring to the HP-IDs posted before and these refer to the Human Phenotype Ontology. Do you agree that a diastema is a "misalignment of teeth" in humans?

RDruzinsky commented 9 years ago

@SKöhler I suppose that most dentists would call a diastema a misalignment in humans.

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, Apr 14, 2015 at 10:22 AM, Sebastian Köhler <notifications@github.com

wrote:

@cmungall https://github.com/cmungall Yes, I start to work on this part now.

@RDruzinsky https://github.com/RDruzinsky Might be true, but I guess you are referring to the HP-IDs posted before and these refer to the Human Phenotype Ontology. Do you agree that a diastema is a "misalignment of teeth" in humans?

— Reply to this email directly or view it on GitHub https://github.com/obophenotype/uberon/issues/687#issuecomment-92905831.

cmungall commented 9 years ago

The uberon class has primary label 'diastema' and is intended to be neutral. We could call it 'interdental space' if less likely to conflict with HPO and it's value judgements.

btw, I use 'diastema' as singular and 'diastemata' as plural, but I have seen 'diastem' used before which sounded odd. Know the correct usage @RDruzinsky ?

cmungall commented 9 years ago

@drseb I think I see why HPO has the two branches now. 'Widely spaced teeth' is essentially a mereological sum of abnormal diastemata in a single quadrant, whereas 'Diastema' is a single abnormal diastema between exactly two teeth?

RDruzinsky commented 9 years ago

Diastema is the proper term and we should use it. It is a neutral term.

You are correct with regard to the singular and plural terms.

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, Apr 14, 2015 at 10:31 AM, Chris Mungall notifications@github.com wrote:

The uberon class has primary label 'diastema' and is intended to be neutral. We could call it 'interdental space' if less likely to conflict with HPO and it's value judgements.

btw, I use 'diastema' as singular and 'diastemata' as plural, but I have seen 'diastem' used before which sounded odd. Know the correct usage @RDruzinsky https://github.com/RDruzinsky ?

— Reply to this email directly or view it on GitHub https://github.com/obophenotype/uberon/issues/687#issuecomment-92911418.