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obophenotype / human-phenotype-ontology

Ontology for the description of human clinical features
http://obophenotype.github.io/human-phenotype-ontology/
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blue irides #672

Closed pnrobinson closed 8 years ago

pnrobinson commented 8 years ago

Is there a better primary term name that will indicate this is an abnormal phenotype?

pnrobinson commented 8 years ago

After review, I think we should leave the term name as is. Even though there are some genetic disorders characterized by "unexpectedly" blue irides, the phenotype is not abnormal in itself, and to encode the "bundled" situation when one might use this term into the term name would not really be any clearer to users of the HPO not familiar with these diseases.

cmungall commented 8 years ago

I'm not following

"the phenotype is not abnormal in itself"

clearly "blue irises" when used in a general context is not abnormal, but clearly the HPO class is abnormal:

 is_a HP:0000118 ! Phenotypic abnormality
   is_a HP:0000478 ! Abnormality of the eye
    is_a HP:0012372 ! Abnormal eye morphology
     is_a HP:0012374 ! Abnormality of the globe
      is_a HP:0000553 ! Abnormality of the uvea
       is_a HP:0000525 ! Abnormality of the iris
        is_a HP:0008034 ! Abnormal iris pigmentation
         is_a HP:0000635 ! Blue irides ***

nd to encode the "bundled" situation when one might use this term into the term name

no idea what you mean here

pnrobinson commented 8 years ago

I mean that users need to infer we are talking about an „abnormally“ blue iris color from the context, and I cannot think of a way of saying this in the label! -Peter

Von: Chris Mungall [mailto:notifications@github.com] Gesendet: Donnerstag, 17. März 2016 17:47 An: obophenotype/human-phenotype-ontology human-phenotype-ontology@noreply.github.com Cc: Robinson, Peter peter.robinson@charite.de Betreff: Re: [human-phenotype-ontology] blue irides (#672)

I'm not following

"the phenotype is not abnormal in itself"

clearly "blue irises" when used in a general context is not abnormal, but clearly the HPO class is abnormal:

is_a HP:0000118 ! Phenotypic abnormality

is_a HP:0000478 ! Abnormality of the eye

is_a HP:0012372 ! Abnormal eye morphology

 is_a HP:0012374 ! Abnormality of the globe

  is_a HP:0000553 ! Abnormality of the uvea

   is_a HP:0000525 ! Abnormality of the iris

    is_a HP:0008034 ! Abnormal iris pigmentation

     is_a HP:0000635 ! Blue irides ***

nd to encode the "bundled" situation when one might use this term into the term name

no idea what you mean here

— You are receiving this because you modified the open/close state. Reply to this email directly or view it on GitHubhttps://github.com/obophenotype/human-phenotype-ontology/issues/672#issuecomment-197969464

mellybelly commented 8 years ago

see also http://monarch-initiative.blogspot.com/2015/01/how-to-annotate-patients-phenotypic.html

On Mar 17, 2016, at 9:51 AM, Peter Robinson notifications@github.com wrote:

I mean that users need to infer we are talking about an „abnormally“ blue iris color from the context, and I cannot think of a way of saying this in the label! -Peter

Von: Chris Mungall [mailto:notifications@github.com] Gesendet: Donnerstag, 17. März 2016 17:47 An: obophenotype/human-phenotype-ontology human-phenotype-ontology@noreply.github.com Cc: Robinson, Peter peter.robinson@charite.de Betreff: Re: [human-phenotype-ontology] blue irides (#672)

I'm not following

"the phenotype is not abnormal in itself"

clearly "blue irises" when used in a general context is not abnormal, but clearly the HPO class is abnormal:

is_a HP:0000118 ! Phenotypic abnormality

is_a HP:0000478 ! Abnormality of the eye

is_a HP:0012372 ! Abnormal eye morphology

is_a HP:0012374 ! Abnormality of the globe

is_a HP:0000553 ! Abnormality of the uvea

is_a HP:0000525 ! Abnormality of the iris

is_a HP:0008034 ! Abnormal iris pigmentation

is_a HP:0000635 ! Blue irides ***

nd to encode the "bundled" situation when one might use this term into the term name

no idea what you mean here

— You are receiving this because you modified the open/close state. Reply to this email directly or view it on GitHubhttps://github.com/obophenotype/human-phenotype-ontology/issues/672#issuecomment-197969464

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHubhttps://github.com/obophenotype/human-phenotype-ontology/issues/672#issuecomment-197970918

Dr. Melissa Haendel

Associate Professor Ontology Development Group, OHSU Library www.ohsu.edu/library/ontologyhttp://www.ohsu.edu/library/ontology Department of Medical Informatics and Clinical Epidemiology Oregon Health & Science University haendel@ohsu.edu skype: melissa.haendel 503-407-5970 Appointments: Shanez De Silva desilva@ohsu.edu

cmungall commented 8 years ago

But there is no option of talking about HP:0000635 in a non-abnormal context. The hierarchy places it into an abnormal context. Any attempt to use it in a normal context will yield either inconsistencies (on the OWL reasoning level) or confusion (at the human reasoning level: e.g. what are the patient curation guidelines for 'blue irides'? Can I use it for normally blue? Or does it have to be 'markedly' blue?)

On 17 Mar 2016, at 9:51, Peter Robinson wrote:

I mean that users need to infer we are talking about an „abnormally“ blue iris color from the context, and I cannot think of a way of saying this in the label! -Peter

Von: Chris Mungall [mailto:notifications@github.com] Gesendet: Donnerstag, 17. März 2016 17:47 An: obophenotype/human-phenotype-ontology human-phenotype-ontology@noreply.github.com Cc: Robinson, Peter peter.robinson@charite.de Betreff: Re: [human-phenotype-ontology] blue irides (#672)

I'm not following

"the phenotype is not abnormal in itself"

clearly "blue irises" when used in a general context is not abnormal, but clearly the HPO class is abnormal:

is_a HP:0000118 ! Phenotypic abnormality

is_a HP:0000478 ! Abnormality of the eye

is_a HP:0012372 ! Abnormal eye morphology

 is_a HP:0012374 ! Abnormality of the globe

  is_a HP:0000553 ! Abnormality of the uvea

   is_a HP:0000525 ! Abnormality of the iris

    is_a HP:0008034 ! Abnormal iris pigmentation

     is_a HP:0000635 ! Blue irides ***

nd to encode the "bundled" situation when one might use this term into the term name

no idea what you mean here

— You are receiving this because you modified the open/close state. Reply to this email directly or view it on GitHubhttps://github.com/obophenotype/human-phenotype-ontology/issues/672#issuecomment-197969464

You are receiving this because you commented. Reply to this email directly or view it on GitHub: https://github.com/obophenotype/human-phenotype-ontology/issues/672#issuecomment-197970918

pnrobinson commented 8 years ago

Yes, but blue iris etc is the community accepted label, and given there is no option of talking about this term in a non-abnormal context there should not be a problem….

Von: Chris Mungall [mailto:notifications@github.com] Gesendet: Donnerstag, 17. März 2016 18:53 An: obophenotype/human-phenotype-ontology human-phenotype-ontology@noreply.github.com Cc: Robinson, Peter peter.robinson@charite.de Betreff: Re: [human-phenotype-ontology] blue irides (#672)

But there is no option of talking about HP:0000635 in a non-abnormal context. The hierarchy places it into an abnormal context. Any attempt to use it in a normal context will yield either inconsistencies (on the OWL reasoning level) or confusion (at the human reasoning level: e.g. what are the patient curation guidelines for 'blue irides'? Can I use it for normally blue? Or does it have to be 'markedly' blue?)

On 17 Mar 2016, at 9:51, Peter Robinson wrote:

I mean that users need to infer we are talking about an „abnormally“ blue iris color from the context, and I cannot think of a way of saying this in the label! -Peter

Von: Chris Mungall [mailto:notifications@github.com] Gesendet: Donnerstag, 17. März 2016 17:47 An: obophenotype/human-phenotype-ontology human-phenotype-ontology@noreply.github.com<mailto:human-phenotype-ontology@noreply.github.com> Cc: Robinson, Peter peter.robinson@charite.de<mailto:peter.robinson@charite.de> Betreff: Re: [human-phenotype-ontology] blue irides (#672)

I'm not following

"the phenotype is not abnormal in itself"

clearly "blue irises" when used in a general context is not abnormal, but clearly the HPO class is abnormal:

is_a HP:0000118 ! Phenotypic abnormality

is_a HP:0000478 ! Abnormality of the eye

is_a HP:0012372 ! Abnormal eye morphology

is_a HP:0012374 ! Abnormality of the globe

is_a HP:0000553 ! Abnormality of the uvea

is_a HP:0000525 ! Abnormality of the iris

is_a HP:0008034 ! Abnormal iris pigmentation

is_a HP:0000635 ! Blue irides ***

nd to encode the "bundled" situation when one might use this term into the term name

no idea what you mean here

— You are receiving this because you modified the open/close state. Reply to this email directly or view it on GitHubhttps://github.com/obophenotype/human-phenotype-ontology/issues/672#issuecomment-197969464

You are receiving this because you commented. Reply to this email directly or view it on GitHub: https://github.com/obophenotype/human-phenotype-ontology/issues/672#issuecomment-197970918

— You are receiving this because you modified the open/close state. Reply to this email directly or view it on GitHubhttps://github.com/obophenotype/human-phenotype-ontology/issues/672#issuecomment-197999190