#131 New term request: amylase

[Nicole Vasilevsky]

New term request for amylase (a generic form)
Definition: amylase is an enzyme in the blood, which helps digest glycogen and starch. It is produced mainly in the pancreas and salivary glands.

This term is needed for a logical definition in the Human Phenotype Ontology: HP_0410282 'Abnormal circulating amylase level'

[Darren Natale]

Hi Nicole,
Before we create the term you need, I'll need to have a clarification. When you say " a generic form" do you mean a generic-to-humans versions (that combines, say, human alpha amylase and human beta amylase), or do you mean fully generic, as in "any protein from any organism with amylase activity" (which would include from yeasts, bacteria, etc)?

[Nicole Vasilevsky]

Hi Darren,
I meant generic-to-humans form, thank you!
Best,
Nicole

--
Nicole Vasilevsky, PhD

Research Assistant Professor
Translational and Integrative Sciences Labhttps://tislab.org/
Oregon Clinical & Translational Research Institute
Department of Medical Informatics & Clinical Epidemiology
Oregon Health & Science University

Email: vasilevs@ohsu.edu

Skype: nicolevasilevsky

From: Darren Natale darren_natale@users.sourceforge.net
Reply-To: "[pro-obo:term-requests]" 131@term-requests.pro-obo.p.re.sourceforge.net
Date: Tuesday, January 29, 2019 at 11:28 AM
To: "[pro-obo:term-requests]" 131@term-requests.pro-obo.p.re.sourceforge.net
Subject: [pro-obo:term-requests] #131 New term request: amylase

Hi Nicole,
Before we create the term you need, I'll need to have a clarification. When you say " a generic form" do you mean a generic-to-humans versions (that combines, say, human alpha amylase and human beta amylase), or do you mean fully generic, as in "any protein from any organism with amylase activity" (which would include from yeasts, bacteria, etc)?

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[term-requests:#131]https://sourceforge.net/p/pro-obo/term-requests/131/ New term request: amylase

Status: open
Group:
Labels: new term request
Created: Mon Jan 28, 2019 08:17 PM UTC by Nicole Vasilevsky
Last Updated: Mon Jan 28, 2019 08:17 PM UTC
Owner: nobody

New term request for amylase (a generic form)
Definition: amylase is an enzyme in the blood, which helps digest glycogen and starch. It is produced mainly in the pancreas and salivary glands.

This term is needed for a logical definition in the Human Phenotype Ontology: HP_0410282 'Abnormal circulating amylase level'

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[Darren Natale]

Hi Nicole,

I have made two classes based on this request. The one you want is PR:000049996. Note that these were defined using activity as the basis rather than evolution (which is how we usually define PRO terms of this type). I did it this way because I presume you are interested in measureable amylase, and so far as I can tell, the measurement is one of activity rather than something like proteomics. Please let me know if I'm mistaken!

Note also that these terms won't appear in the downloadable version of PRO until the next release. They will, however, still resolve to a destination page immediately.

[Term]
id: PR:000049995
name: active alpha-amylase isozyme
def: "A protein that has alpha-amylase activity." [PRO:DAN]
comment: Category=family. Note: The enzymatic activity corresponds to EC 3.2.1.1. This class refers only to functional enzymes; that is, those with measurable activity.
synonym: "fam:AMY" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000000001 ! protein
intersection_of: has_function GO:0004556 ! alpha-amylase activity

[Term]
id: PR:000049996
name: active alpha-amylase isozyme (human)
def: "An active alpha-amylase isozyme in human." [PRO:DAN]
comment: Category=organism-family. Requested by=HPO. Note: The enzymatic activity corresponds to EC 3.2.1.1. This class refers only to functional enzymes; that is, those with measurable activity. The isozymes are produced by the salivary glands (the identical AMY1A, AMY1B, and AMY1C genes) and the pancreas (AMY2A and AMY2B genes).
synonym: "fam:hAMY" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000049995 ! active alpha-amylase isozyme
intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens