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Standard terms for annotating mammalian phenotypic data
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IMPC terms #1426

Closed obophenotype-user closed 9 years ago

obophenotype-user commented 11 years ago

From: Luis Santos l.santos@har.mrc.ac.uk Date: Tuesday, October 8, 2013 9:46 AM To: Cynthia Smith cynthia.smith@jax.org Cc: "wranglers@mousephenotype.org" wranglers@mousephenotype.org Subject: MP terms request

Dear Cynthia,

I am writing you following a request for the addition of some MP terms. We are stumbling upon what terms to add for two different procedures, and would like your suggestions. One is Eye morphology (here: https://www.mousephenotype.org/impress/protocol/94), where MP terms are missing for Corneal Sclerization IMPC_EYE_080_001 and Iris transilumination IMPC_EYE_082_001, and we would like to suggest “abnormal corneal sclerization” and “abnormal iris transilumination”. The other one is plethysmography, in the ICS pipeline (here: https://www.mousephenotype.org/impress/protocol/112/10). Seeing as the test challenges all the mice with lipopolysaccharides (LPS), causing them to experience bronchoconstriction as a spontaneous reaction, the centre is asking to add 'abnormal/increased/decreased' bronchoconstriction MPs to the enhanced pause parameter (Enhanced pause (Penh)ICS_CHL_003_001), so that differences can be detected. Are there more appropriate terms, and if not, would it be ok to add these?

Thank you for your attention to this matter.

Best regards, Luis Santos

Skype: luis-snt l.santos@har.mrc.ac.uk wranglers@mousephenotype.org Data Wrangler - MRC Harwell Mammalian Genetics Unit Harwell Science and Innovation Campus Oxfordshire OX11 0RD, UK

Reported by: cindyJax

Original Ticket: obo/mammalian-phenotype-requests/1426

obophenotype-user commented 11 years ago

Original comment by: cindyJax

obophenotype-user commented 11 years ago

Hi Luis, et al-

As always, we are happy to add what you need.

1) corneal sclerization -

I was considering the precise meaning of the phrase "corneal sclerization" , but I am presuming this is the same as the more common term sclerocornea:

New term added:

Sclerocornea [MP:0012121]

a congenital anomaly of the eye in which partial or complete corneal opacity is present and resembles the sclera, with no clear boundary between these structures.

Please let me know if this is not the case. "corneal sclerization" was added as a synonym.

2) New term added:

abnormal iris transillumination [MP:0012122]

any anomaly in the radial light dispersion pattern of the iris when a focused light beam is passed through it; dispersion pattern anomalies are indicative of abnormalities in iris pigment distribution and for the presence of glaucoma, atrophy and/or infection

3) enhanced pause parameter: I think in your case, you want a term more like "abnormal bronchoconstrictive response". In your challenge parameter, the bronchoconstriction in response to LPS is expected in controls; any change in the normal response to the challenge, measured by plethysmography is what is being recorded. We do have bronchoconstriction [MP:0001945] but this is used for cases where this phenotype is observed in the absence of any provocation challenge.

New terms added: abnormal bronchoconstrictive response [MP:0012123] anomaly in the expected bronchoconstrictive response to provocation challenge with lipopolysaccharide, bradykinin, histamine or other antigen/allergen or agent, as measured by plethysmography

increased bronchoconstrictive response [MP:0012124] enhanced or greater decreased bronchoconstrictive response [MP:0012125] reduced or reduction

These changes should appear on the MGI site within a week, and to other ontology resource sites shortly after that. Please let us know if you need anything else.

Original comment by: cindyJax