Ontology meeting 2013-11-07

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Attendees:

Minutes: Paola


Catalytic activity node review at Texas GO meeting?

Spurred by 10/29/13 email to Tanya from Jim:

...
The general issue of substrate specificity and ontology terms seems to be coming up 
in my term requests and I'm wondering if it's something where more general rules 
should be discussed, if they don't already exist.

Also, related to that, there are some very good senior enzymologists here at TAMU 
who have done things like organize enzyme conferences. Maybe we could have some 
consultations during the Spring GO meeting if they are around.

Jim


Template for RESPONSE TO STRESS GO terms

See SF item from Ingrid

Chris says: We have a small ontology of environmental conditions (oxidative stress etc) we use for making logical definitions of these terms. Time to add to production?

Q: What needs to be done next, and where is the environmental condition ontology?

Suggest changing our current definition of stress terms from:

[Term]
id: GO:0034976
name: response to endoplasmic reticulum stress
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production,  gene expression, etc.) as a result of a stimulus indicating endoplasmic reticulum (ER) stress. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen." [GOC:mah]
synonym: "ER stress response" EXACT []
synonym: "response to ER stress" EXACT []
is_a: GO:0033554 ! cellular response to stress

to:

... as a result of a stress stimulus at the endoplasmic reticulum (ER).
... as a result of a stress stimulus acting at the endoplasmic reticulum (ER).
... as a result of a stimulus disrupting the endoplasmic reticulum (ER).

Follow-up: TG TEMPLATE FOR ORGANELLE PART (LUMEN, MEMBRANE)

Chris, David OS and Heiko to report from last week. (see http://wiki.geneontology.org/index.php/Ontology_meeting_2013-10-31#Follow-up:_TG_TEMPLATE_FOR_ORGANELLE_PART_.28LUMEN.2C_MEMBRANE.29)


New OE

Quick run through of new imports and visualization. Any tips to share?


Stemming from question of adding 'luteinizing hormone' in GO

See email thread. Chris says: "GO eds - we will want to switch IDs in the production logical definitions before this, to check the inferences. That's another external ontology imports file - not a big deal. Discuss on thursday?"


GEFs and GAFs

GEF activity is currently a child of 'GTPase regulator activity':

GTPase regulator activity ; GO:0030695
--[isa]guanyl-nucleotide exchange factor activity ; GO:0005085
guanyl-nucleotide exchange factor activity ; GO:0005085 (GEF)
Stimulates the exchange of guanyl nucleotides associated with a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.

Does GEF fit the bill to be a GTPase REGULATOR? GEF alters binding affinity, not the catalytic activity directly. So under normal physiological conditions, it positively regulates GTPase activity, but is it a REGULATOR?

stems from SF ticket from Val





Review of template requests in Jira