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Term request: Superclasses for "diastema between central incisors" #687

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drseb opened this Issue Apr 14, 2015 · 7 comments

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drseb commented Apr 14, 2015

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: 3a05ee2

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cmungall Apr 14, 2015

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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

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cmungall commented Apr 14, 2015

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

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RDruzinsky Apr 14, 2015

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


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#687 (comment).

RDruzinsky commented Apr 14, 2015

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
#687 (comment).

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@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?

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drseb commented Apr 14, 2015

@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?

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RDruzinsky Apr 14, 2015

@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
#687 (comment).

RDruzinsky commented Apr 14, 2015

@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
#687 (comment).

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cmungall Apr 14, 2015

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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 ?

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cmungall commented Apr 14, 2015

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 ?

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@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?

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cmungall commented Apr 14, 2015

@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?

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RDruzinsky Apr 14, 2015

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
#687 (comment).

RDruzinsky commented Apr 14, 2015

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
#687 (comment).

cmungall added a commit that referenced this issue Apr 15, 2015

@cmungall cmungall closed this Apr 30, 2015

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