SourceForge meeting 2013-10-09

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ATTENDEES

Jane, Becky, David O-S, David H, Tanya


WRAP-UP: Equivalent classes for Acid/Base transport and transport activity

Anything missing for this item? http://wiki.geneontology.org/index.php/Ontology_meeting_2013-09-26#Bumped_from_last_week:_Equivalent_classes_for_Acid.2FBase_transport_and_transport_activity

(Moved from editors' call)

AI: Tanya to make tickets, and assign to Harold.


Stemming from missing metabolism xps: quinone cofactor vs. quinone

We have the following terms in GO that lack xps:

GO:0042375 quinone cofactor metabolic process

GO:0042378 quinone cofactor catabolic process

GO:0045426 quinone cofactor biosynthetic process

No informative definition, no PMID reference.

Would 'quinone cofactor' belong in CHEBI?

I (Paola) asked ChEBI and Gareth replied:

"The problem with quinone cofactor is that it conflates within its name a structural term (is_a quinone) with a role term (has_role cofactor), which I gather is not really allowed in OWL. Although we do have some analogous conflated terms in the ChEBI ontology, we are trying to get rid of them, rather than add to them!"

Makes sense. Then how does 'quinone cofactor metabolic process' differ from 'quinone metabolic process'? Should I simply merge the former into the latter? Same for catabolism and biosynthesis. The only publication supporting manual experimental annotations to 'quinone cofactor metabolic process' is http://europepmc.org/abstract/MED/10514444, and I can't see it would disagree with my assumption, but I'm not an expert.

On a related note, we also have a MF term GO:0030580 'quinone cofactor methyltransferase activity' defined as 'Catalysis of the transfer of a methyl group from S-adenosylmethionine during the synthesis of quinone cofactors such as ubiquinone (coenzyme Q), menaquinone (vitamin K2), plastoquinone and phylloquinone (vitamin K1).'. So the 'quinone cofactor' differentia here doesn't strictly refer to the MF - maybe we should rename the term as 'methyltransferase activity involved in quinone biosynthetic process'? But I haven't looked at the children/annotations in detail.


From the 'quinone cofactor metabolism' terms, it's unclear whether it's referring to a quinone that is acting as a cofactor. Or whether it's metabolism of a cofactor that works alongside a quinone.

The 'quinone cofactor metabolism' terms are not children of 'quinone metabolism' terms.

It looks like the quinone cofactor refer to chemicals that are derivatives of quinone.

AI: Ask ChEBI to add 'cofactor' roles to all the child terms of 'cofactor metabolic process'. DONE: https://sourceforge.net/p/chebi/curator-requests/2212/

AI: Merge 'quinone cofactor metabolism' into 'quinone metabolism' terms. DONE.

Obsolete 'regulation of transcription during mitosis' and kids?

Issue brought up by Val. SF item

Annotations (all evidence codes) are to:

negative regulation of transcription from RNA polymerase II promoter during mitosis (71) + -

regulation of transcription during mitosis (28) + -

positive regulation of transcription from RNA polymerase II promoter during mitosis (19) + -

positive regulation of transcription on exit from mitosis (7) + -

positive regulation of transcription on exit from mitosis, from RNA polymerase II promoter (2) + -

positive regulation of transcription during mitosis (1) + -


AI: GO ahead and obsolete


New children for protein complexes? transmembrane transporters / drug exporters

Stems from this SF request from Birgit: http://sourceforge.net/p/geneontology/ontology-requests/10420/

We need a TG template to add in complexes defined based on their function. The capable_of templates are in the XP file, so we're nearly there.

AI: David H ask Heiko to add a template: protein complex capable of MF.