Ontology meeting 2013-06-06

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Attendees: Paola, Becky, Chris, David, Harold, Heiko, Tanya, Jane, Judy

Minutes: Paola

New TG templates

Have they been tested, can we advertise them already? Or should we test/keep testing?

No, we should test the templates before advertising.

AI: Paola to test the apoptosis template; Tanya to test the plant ones; both to report once done.


Follow-up: metabolism terms

See http://wiki.geneontology.org/index.php/Ontology_meeting_2013-05-30#Metabolism_terms

David, did you pass our thoughts on to Paul T?

David thinks we should bring this up at an annotation call instead, because it's an annotation issue rather than an ontology one.

Jane brought up the related example of MENGO's request for 'hydrogen biosynthesis'. That would be 'molecular hydrogen generation' really. It would be meaningful to have such a class for hydrogen because people may be interested in it, but we wouldn't do it for all by-products. David suggests to add such a term in as a test. 'Methanogenesis' is similar because methane is really a by-product.

AI: Jane to create terms for 'molecular hydrogen generation' and 'methanogenesis'. But they'll be added to a test ontology rather than GO, as we're not sure we'd be able to make all of the inferences in GO yet. Then we'd be able to report to the next GOC meeting.

AI: David to follow-up with Paul T. by replying to his email anyway please, so the PIs know where we stand?

Follow-up: No-longer-inferrable links

See http://wiki.geneontology.org/index.php/Ontology_meeting_2013-05-30#No-longer-inferrable_links

I think we've all looked at the spreadsheet by now - Chris, could you access the file ok?

How do we strategize the necessary actions?

Questions from Becky's set:

  • 2-oxobutyrate: Should ChEBI be changed so 2-oxobutanoic acid is_a short chain fatty acid (see Tanya's suggestion) or should the inferred link deleted (see David's list)?
  • In GO, can we rename 'organic nitrogen' in term names to 'organonitrogen compound' to match the Xref (CHEBI:35352). It seems weird that 'response to cAMP is_a response to organic nitrogen' (organic nitrogen just sounds strange, to me). But 'response to cAMP is_a response to organonitrogen compound' makes more sense.
  • Do we want to distinguish between prohormones and hormones in GO? In ChEBI, ecdysone has_role prohormone, but GO parentage suggests ecdysone is a steroid hormone. Hydroxylation of ecdysone at C-20 forms the hormone ecdysterone(20-hydroxyecdysone).

AI: Becky will ask CHEBI about 2-oxobutyrate.

AI: Becky will change the nitrogen names to match CHEBI.

AI: Becky to look at the ecdysone terms to figure out if they actually refer to 20-hydroxyecdysone.

As for the other 'problematic' links in the spreadsheet:

AI: Tanya will delete all the links marked 'delete'; Tanya and David will look at the 'keep' ones.

AI: For terms where the processes are vesicle mediated, Chris will make that more explicit in the xps.


(Related) part_of is_a (David)

New check for is_a inferences of terms that are already parts.


Follow-up: viable solutions to run reasoner(s) in P4 on go-plus.owl or sub-types of it

Heiko, Chris - Would it be possible to have the explanations along with the weekly inferred links report?


Follow-up: Template for receptor activities

Background: http://wiki.geneontology.org/index.php/Ontology_meeting_2013-05-02#Template_for_receptor_activities

Becky has looked through [1] to check for anomalies, and will remove the mistakes due to synonym mis-catching in ChEBI.

Q1: Receptors in GO are generally split into transport (cargo) receptors that bind to a substrate and internalize it via endocytosis. And signaling receptors which bind to/receive a substrate and pass the signal on within the cell. Do we want to make the differentia more specific (signaling receptor activity ; GO:0038023)?

Q2: Can we have ChEBI roles in the intersections?

[Term]
id: GO:0030594  ! neurotransmitter receptor activity
intersection_of: GO:0004872  ! receptor activity
intersection_of: has_input CHEBI:25512  ! neurotransmitter

For the proteins and peptides (insulin etc), we'd be better off pulling in from protein ontology.

Leave nuclear receptors for now, as these also have parentage in the transcription node.

AI: Becky to add the correct ones to the live XP file. Remember to add the IDs in the correct place, or do the round trip command (ask Chris if it's problematic) to sort them correctly. DONE (10th June).

BUMP TO NEXT WEEK: GO is_a based on ChEBI has_role? (Tanya)

Bringing back the discussion from past meeting. Recent SF request from Peter dE brings it back up . SF item


BUMP TO NEXT WEEK: Missing EC numbers in GO

It seems we don't have the resources to implement a pipeline for these. Shall we wait and see if the new GO Editor can take this on? Shall we discuss this at the next GOC meeting to see how much of a priority it should be?

In the meantime, we can add single terms when requested by curators, cross-referencing to Rhea or asking Rhea to add the reaction if missing.

But can we close the following SF tickets?

https://sourceforge.net/p/geneontology/ontology-requests/9319/ (Becky's - nearly done anyway)

https://sourceforge.net/p/geneontology/ontology-requests/9320/ (Jane's)

https://sourceforge.net/p/geneontology/ontology-requests/9321/ (Paola's)


We never really got to the bottom of handling multi-step reactions. If we create separate GO terms for the subreactions with HAS_PART relationships to the parents, it's tricky to name the sub-reactions. There's no place at the moment where we can take these names. So, do we want to continue just to add one GO term for the overall reaction, stating in the definition that the reaction is multi-step?

BUMP TO NEXT WEEK: Follow-up: template for assembly/disassembly of CC terms

Chris/Heiko, where are we with this?


BUMP TO NEXT WEEK: Organelle vs. macromolecular complex

Stemming from some observations on inferred links in the assembly node, e.g.:

(Added inferred link) GO:0000921 'septin ring assembly' GO:0070925 'organelle assembly'

GO:0000921 'septin ring assembly' also has the is_a parent 'cellular protein complex assembly'. This was added back in 2008 (http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0000921#term=history). However, 'septin ring' only has 'organelle' as ancestor, not 'protein complex'. Should we make 'macromolecular complex' and 'organelle' disjoint?

The proposal would be to have

organelle DisjointWith mm complex


BUMP TO NEXT WEEK: 'Encoded' vs. 'non-encoded' molecules in GO

Stemming from this SF request from Peter: https://sourceforge.net/p/geneontology/ontology-requests/10200/

At the time of writing, I'm waiting for Peter to suggest defs. and placement.


BUMP TO NEXT WEEK: Muscle Fiber vs Muscle cell

[2]

Also see email thread from Chris (subject:muscle fibers in a tangle)

Muscle Issues

  • We need to go through each fiber term and check whether we mean the contractile fiber (CC) or the muscle cell (CL).
  • Should we use the CL naming as default?
  • GO isn't consistent in CC and BP about naming.



BUMP TO NEXT WEEK: Project Management in JIRA

As we likely won't have time to go through this, and we won't have an Editors call next week due to EBI GO Editors interviews, may I suggest that we all look at our tickets and schedule progress on them if necessary.