Ontology meeting 2013-10-10

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Attendees:David H, David OS, Tanya, Becky, Jane, Judy, Heiko, Chris

Minutes:David H.

TG TEMPLATE FOR ORGANELLE PART (LUMEN, MEMBRANE)

We've scheduled to have this done by the end of Q4/13.

The Jira ticket is https://www.ebi.ac.uk/panda/jira/browse/GO-185

Looking at Chris' comments in its sub-task "Verify that all xps for existing organelle part (lumen, membrane) terms are in place" (https://www.ebi.ac.uk/panda/jira/browse/GO-186), what do we need to do here?

Need to be sure that all inferences work using part_of


SCHEDULE SIGNALING CALL

Chris, Becky and ....

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

Oct 28th 8:30AM PDST, 11:30AM EDST, 4:30om GMT

Demo of extension to lego plugin

Chris demonstrates Heiko's new plugin.

XPs for virus terms

virion ; GO:0019012 is a complete infectious extracellular particle. We need a more general 'virus' term to make XPs to. Can we use NCBI taxID:10239 (viruses) in XPs?

NB: IDO (infectious disease ontology) link to NCBI taxID:10239 in their ontology

 virus
 --virion

[1]

Other option is 'virion part ; GO:0044423'.

Where are we up to with work for making a multi-organism template?

We need to be able to define a virus. Use the NCBI taxon ID and CARO.


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?

Yes, broaden the GO term to make a grouping term. Then make the specific terms as children.


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?


Merge and make a new oxaloacetate 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)

Keep the grouping term and then create the children. We will not have a rhea mapping for the parent.


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?

Keep them, define them specifically and ask Rhea to create new reactions.


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?

Ask Rhea if they make separate reactions for different cofactors.


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?

Change to make them map to direction-specific Rhea terms. The Rhea should map to the more generic GO term, ie transporter rather than channel.

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?

Rhea doesn't link back to us yet. Jane will check into this.


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

The parent represents any of them.


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.

Heiko will generate the EC2GO file based on what we have in GO. We will then update the EC2GO references that actually exist in the ontology file. We need to figure out a way to deal EC#s that have a dash in them. For now we should ignore them.


Long term plan for GOCHE terms

What's the plan for the GOCHE terms that are xps between ChEBI chemicals and ChEBI roles?

Next week

Regulation of timing

As per email thread started by Chris.

Next week


EXISTS, TAGGED-INFERRED, NOT-ENTAILED

We need a strategy to deal/work through these. See Jane's comment in email thread "build-go-assert-inferences - Build # 51 - Successful!":

"are the EXISTS, TAGGED-INFERRED, NOT-ENTAILED now being deleted automatically? I think they should be. If we want to check the implications of edits looking through these reports a week later probably isn't a great way to do it - we should use Protege or perhaps we could have a per-commit report in Jenkins?"

next week


Creating a megafile

Can we take the cross products that are currently in the external x-product file that only refer to GO terms and move them into the main file as a first step in creating one editors' file, for example 'capable_of'.

next week