#11536 MP cellular metabolic process

[Valerie Wood]

missing cellular metabolic process parentage (have only metabolci process, but appear to be cellular?)

positive regulation of Rho GTPase activity
iron-sulfur cluster assembly
gene expression
regulation of Ras protein signal transduction (or possibly a parent)

[Pascale Gaudet]

Hi Val,

To be consistent with https://sourceforge.net/p/geneontology/ontology-requests/11253/
should we not remove the 'metabolic process' parent of positive regulation of Rho GTPase activity?

Pascale

[Valerie Wood]

would that work though? I thought we were saying that they were metabolic but not catabolic? (This suggestion would mean that the parentage of catalytic activity could not be metabolic)

v

[Pascale Gaudet]

My understanding was that none of this was 'metabolism'. Or else all cellular processes are types of cellular metabolism ?

There was also discussion to narrow the definition of metabolism to be something more like http://en.wikipedia.org/wiki/Metabolism

For me it seems logical to remove signaling from metabolism, but there may be instances I am not thinking about.
A good rule of thumb may be that a term should either be 'catabolic process' or 'biosynthetic process'; if it falls in between then it probably doesn't belong. What do you think ?

Pascale

[Valerie Wood]

I'm not sure.

GTPase activity could not be is_a catalytic activity because catalytic activity is part of a metabolic process. I can't see a way around this.....

[Pascale Gaudet]

sure, but here you are talking about 'regulation of'. Shouldn't regulation be outise metabolism ?

[Valerie Wood]

Ah I guess so. Will wait for Eds. to comment...

[Paola Roncaglia]

Hi Val and Pascale,

Wrt Pascale’s question on parentage of positive regulation of Rho GTPase activity, I’ll defer to Tanya as she’s been working on general Ras GTPase terms. I’ll add a comment on her related SF ticket, https://sourceforge.net/p/geneontology/ontology-requests/10426/

Wrt the broader issue of redefining metabolism, I’ll ask David H if there’s a ticket somewhere to collate discussions on this. (I looked in SF, Jira and Trello, but I think this has been going on via email only so far.)

So far for ‘positive regulation of Rho GTPase activity’ and ‘regulation of Ras protein signal transduction’ (or possibly a parent) in Val’s original request.

As for the other two missing links:

I’m fine with making ‘iron-sulfur cluster assembly’ is_a ‘cellular metabolic process’. I looked at a couple of references and haven’t found any evidence that this process ever occurs e.g. at tissue level rather than cellular level, e.g. in blood plasma. So I’ll add the link unless there are any comments.

As for ‘gene expression’ being is_a ‘cellular metabolic process’, I think this will also be fine to add. At first I was concerned about its child ‘viral gene expression’. But ‘viral process’ has ‘cellular process’ as its ancestor, so we’re good. I’ll add this link when I add the one above.

Thanks,

Paola

[David Hill]

Just one quick comment on metabolism. I don't think it will only include biosynthesis and catabolism. There are clearly cases where biochemicals are metabolized, but are not broken down or built into something else. Examples of this can be seen in the necessary parts of some of the children of specific types of glycolysis (glycerol to glycerone phosphate metabolic process).

[Tanya Berardini]

RE: positive regulation of Rho GTPase activity, this has been merged into 'positive regulation of GTPase activity'

http://amigo.geneontology.org/amigo/term/GO:0043547

Is this still an issue for that term?