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Ontology for the description of human clinical features
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NTR: Gonadal biopsy: seminiferous tubules obstructed or decreased size and number (Lab: pathology: biopsies & morphology) #9187

Open pnrobinson opened 1 year ago

pnrobinson commented 1 year ago

New term request Gonadal biopsy: seminiferous tubules obstructed or decreased size and number (elthat_100924023534): Part of dysgenetic gonads UMLS: 1968705

pnrobinson commented 1 year ago

@MagoWyr -- where should this term go?

MagoWyr commented 1 year ago

Diesen Term wuerde ich gar nicht benutzen. Ich weiss nicht, was damit gemeint ist. Eine Obstruktion der Tubuli ist das Gegenteil von Tubuli, die "decreased size and number" aufweisen. Ich wuerde empfehlen diesen Term zu streichen.

From: Peter Robinson @.> Sent: 19 July 2023 12:46 To: obophenotype/human-phenotype-ontology @.> Cc: Margot Wyrwoll @.>; Mention @.> Subject: Re: [obophenotype/human-phenotype-ontology] NTR: Gonadal biopsy: seminiferous tubules obstructed or decreased size and number (Lab: pathology: biopsies & morphology) (Issue #9187)

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@MagoWyrhttps://github.com/MagoWyr -- where should this term go?

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pnrobinson commented 1 year ago

@MickeySegal the recommendation of Dr Margot Wyrwoll, University of Muenster, is that we rethink this because obstruction of the tubuli is not the same as decreased size/number -- possibly this is a bundled phenotype. Could you provide more context?

MickeySegal commented 1 year ago

I reviewed our uses of this term, and typical was https://www.ncbi.nlm.nih.gov/books/NBK1547/ "decreased size and number of seminiferous tubules". So I took out the obstruction part from our term, though I don't know if small refers to length or width; the latter might be consistent with obstruction.

pnrobinson commented 4 months ago

@MagoWyr according to https://www.ncbi.nlm.nih.gov/books/NBK1547/

Dysgenetic testis (decreased size and number of seminiferous tubules, reduced number or absence of germ cells, peritubular fibrosis, and hyperplasia of Leydig cells)

We have the existing term Testicular dysgenesis HP:0008715 -- would this be an adequate annotation here?

MagoWyr commented 4 months ago

Hi Peter, yes, dysgenetic testis and testicular dysgenesis are the same. However, the term testicular dysgenesis is much more common and is also used on the page you cited below in the form of gonadal dysgenesis. Best, Margot

From: Peter Robinson @.> Sent: 08 May 2024 17:40 To: obophenotype/human-phenotype-ontology @.> Cc: Margot Wyrwoll @.>; Mention @.> Subject: Re: [obophenotype/human-phenotype-ontology] NTR: Gonadal biopsy: seminiferous tubules obstructed or decreased size and number (Lab: pathology: biopsies & morphology) (Issue #9187)

This email was sent to you by someone outside the University. You should only click on links or attachments if you are certain that the email is genuine and the content is safe.

@MagoWyrhttps://github.com/MagoWyr according to https://www.ncbi.nlm.nih.gov/books/NBK1547/

Dysgenetic testis (decreased size and number of seminiferous tubules, reduced number or absence of germ cells, peritubular fibrosis, and hyperplasia of Leydig cells)

We have the existing term Testicular dysgenesis HP:0008715https://hpo.jax.org/app/browse/term/HP:0008715 -- would this be an adequate annotation here?

— Reply to this email directly, view it on GitHubhttps://github.com/obophenotype/human-phenotype-ontology/issues/9187#issuecomment-2100977425, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A7RYGVKBZ7XOHUWAYPUC6C3ZBJIPHAVCNFSM6AAAAAAS2JFJZCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMBQHE3TONBSGU. You are receiving this because you were mentioned.Message ID: @.***>

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.

MickeySegal commented 4 months ago

Testicular dysgenesis HP:0008715 is a macroscopic observation. The intention here was to describe a biopsy.