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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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NTR: Alkalemia #4503

Closed callahantiff closed 5 years ago

callahantiff commented 5 years ago

NTR: Alkalemia

Parent: HP:0004360 Acid-base homeostasis

For LOINC Code: 11558-4 pH of Blood

Biocurator ID for loinc2hpo: UCDenver:tjcallahan

LCCarmody commented 5 years ago

According to Merck manual https://www.merckmanuals.com/professional/endocrine-and-metabolic-disorders/acid-base-regulation-and-disorders/acid-base-disorders, below are the definitions. We have both Acidosis and Alkalosis. Should this be a child of alkalosis? @pnrobinson Acidemia is serum pH < 7.35. Alkalemia is serum pH > 7.45. Acidosis refers to physiologic processes that cause acid accumulation or alkali loss. Alkalosis refers to physiologic processes that cause alkali accumulation or acid loss.

LCCarmody commented 5 years ago

Sorry, just noticed this ticket. https://github.com/obophenotype/human-phenotype-ontology/issues/736

pnrobinson commented 5 years ago

Yes, this is correct. But could we please add PMIDs to support the definitions. This one might work https://www.ncbi.nlm.nih.gov/pubmed/28232934

callahantiff commented 5 years ago

Thanks @LCCarmody for referencing that issue, I'm sorry I did not include that in the original post. I also realized I have not been including definitions. I will try to work back through the recent posts and suggest definitions with PMIDs.

LCCarmody commented 5 years ago

That's fine. I'll work on the sources. Just want to make sure that you are okay with it being a child of Alkalosis

callahantiff commented 5 years ago

Absolutely, that makes sense to me!

pnrobinson commented 5 years ago

Possible they should be sibs?

LCCarmody commented 5 years ago

I guess because the definition of Alkalosis is defined as "Depletion of acid or accumulation base in the body fluids." in HP, alkalemia, a high pH in serum would be a subclass. I will put it either way

The logical definition of Alkalosis is: 'has part' some ('increased amount' and ('inheres in' some (base and ('part of' some 'bodily fluid'))) and ('has modifier' some abnormal))

I was thinking of below for Alkemia: 'has part' some ('increased amount' and ('inheres in' some (base and ('part of' some 'blood serum'))) and ('has modifier' some abnormal))

pnrobinson commented 5 years ago

see #736

pnrobinson commented 5 years ago

added term and log def