Ontology meeting 2013-10-10

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Attendees:

Minutes:


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


TG TEMPLATE FOR ORGANELLE PART (LUMEN, MEMBRANE)

https://www.ebi.ac.uk/panda/jira/browse/GO-185

Just so we don't forget that we've 'promised' we'd do this by the end of Q4/13.


SCHEDULE SIGNALING CALL

Chris, Becky and ....

Tag on to end of an upcoming Thursday ontology call? Sooner would be good.


ENZYME REACTIONS/RHEA MAPPINGS

For the 1 RHEA mapping on >1 GO term, there's several common themes:


1/ GO definition (and EC reaction) are specific, but the EC comments suggest a broad substrate range: 

adenosine-phosphate deaminase activity ; GO:0047623
Catalysis of the reaction: AMP + H2O = IMP + NH3.
EC:3.5.4.17
Acts on 5'-AMP, ADP, ATP, NAD+ and adenosine, in decreasing order of activity. The bacterial  enzyme also acts on the deoxy derivatives.
RHEA:14780 was mapped to GO:0047623 & GO:0003876, which currently have same definitions.

ACTION?: Broaden GO term, and make it a parent (currently a sibling) to the AMP deaminase, ATP deaminase, adenosine deaminase etc terms?


2/ Two GO terms which differ on substrate specificity: 

malate dehydrogenase (decarboxylating) activity ; GO:0004471
EC:1.1.1.39
Catalysis of the reaction: (S)-malate + NAD+ = pyruvate + CO2 + NADH + H+. Does not decarboxylate oxaloacetate.

malate dehydrogenase (oxaloacetate-decarboxylating) activity ; GO:0016619
EC:1.1.1.38
Catalysis of the reaction: (S)-malate + NAD+ = pyruvate + CO2 + NADH + H+. Also decarboxylates oxaloacetate.

Both map to RHEA:12656

ACTION: Merge GO:0004471 & GO:0016619, and create a separate term for oxaloacetate decarboxylation. Map EC:1.1.1.38 to the merged term and the oxaloacetate decarboxylation term?


3/ EC term catalyses two reactions (normally two separate substrates): 

D-glutamate(D-aspartate) oxidase activity ; GO:0047819
EC:1.4.3.15
Reaction: (1) D-glutamate + H2O + O2 = 2-oxoglutarate + NH3 + H2O2
(2) D-aspartate + H2O + O2 = oxaloacetate + NH3 + H2O2

ACTION?: Do we want to keep GO:0047819 for EC mapping or should it be obsoleted and EC:1.4.3.15 added to both the individual reactions?

  • D-glutamate oxidase activity ; GO:0047821 (EC:1.4.3.7) (RHEA:10031: was also mapped to GO:0047819)
  • D-aspartate oxidase activity ; GO:0008445 (EC:1.4.3.1)


4/ GO terms/EC numbers only differ in co-factors and/or substrate-specificity. 

aldehyde dehydrogenase (FAD-independent) activity ; GO:0033727
EC:1.2.99.7
Catalysis of the reaction: an aldehyde + H2O + acceptor = a carboxylate + reduced acceptor.
Comments: The enzyme from Desulfovibrio sp. does not contain FAD.

aldehyde dehydrogenase (pyrroloquinoline-quinone) activity ; GO:0047113
Catalysis of the reaction: an aldehyde + acceptor + H2O = a carboxylate + reduced acceptor.
http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/2/99/3.html
Comments: A quinoprotein. Wide specificity; acts on straight-chain aldehydes up to C10, aromatic aldehydes, glyoxylate and glyceraldehyde.

carboxylate reductase activity ; GO:0047770
Catalysis of the reaction: an aldehyde + acceptor + H2O = a carboxylate + reduced acceptor.
EC:1.2.99.6
Comments: A tungsten protein. Methyl viologen can act as acceptor. In the reverse direction, non-activated acids are reduced by reduced  viologens to aldehydes, but not to the corresponding alcohols.

RHEA:13884 mapped to all 3 GO terms.

ACTION: Merge all 3 GO terms, and have 3 EC mappings to that one GO term?


5/ Terms differ only in cofactor: 

phosphoglucomutase activity (alpha-D-glucose-1,6-bisphosphate-dependent) ; GO:0004614
5.4.2.2
Catalysis of the reaction: alpha-D-glucose 1-phosphate = alpha-D-glucose 6-phosphate.

phosphoglucomutase (glucose-cofactor) activity ; GO:0047468
Catalysis of the reaction: glucose-1-phosphate = glucose-6-phosphate; using D-glucose as a cofactor.
5.4.2.5

ACTION: Is the cofactor enough difference to warrant two separate (currently sibling) terms?


QUESTION: The exporting/importing transporter terms are still mapped to the two-directional Rhea terms (e.g. hydrogen-exporting ATPase activity ; GO:0036442, RHEA:20855). Do we want to change these to the uni-directional Rhea mapping?

QUESTION: Where do current RHEA:GO mappings come from? RHEA or GO? If I remove mappings at the GO end, do I need to contact Rhea to remove the GO mappings their end?

QUESTION: IUBMB have confirmed that NAD(P) means the enzyme can use BOTH NAD and NADP. Do we want to keep the three GO terms as siblings in GO? glutamate dehydrogenase (NAD+) activity ; GO:0004352 glutamate dehydrogenase (NADP+) activity ; GO:0004354 glutamate dehydrogenase [NAD(P)+] activity ; GO:0004353

Propagating RHEA EC xrefs to GO

RHEA xrefs to EC are more up-to-date than ours, can we do an automatic pass to update all of our EC xrefs where we have a RHEA xref? We will need to check how they handle partial ECs though, I think it's different to how GO does it.

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