Ontology meeting 2014-12-16
Attendees:
Minutes:
Planning for end of year
Ontology calls: We will not meet on Dec 23rd and 30th. We'll resume on Jan 6th. Paola will be on leave on Jan 5th and 6th, so could someone else please send round agenda and GoToMeeting invite.
AI: Jane to do this.
TG support: Is there going to be support over the holidays? Or should we just 'close' TG and email the GOC?
DECISION: We weill send a general email announcing that there will be no TG support or processing of SF requests over the holidays (dates?) TODO Tanya will dig out last year's mail
SF jamboree
Did Paul T have a chance to discuss possibility of roll-over funding to hold a SF jamboree around end of Feb? Background: http://wiki.geneontology.org/index.php/Ontology_meeting_2014-12-09#Ontology_requests
Need to check with Judy about availability of rollover funding AI: Maybe David H could check with Judy please?
Follow-up: Moving relations from RO to gorel
Where are we with this please? Background: http://wiki.geneontology.org/index.php/Ontology_meeting_2014-12-09#Moving_relations_from_RO_to_gorel
co-incident with and basic inter-organism relations are now in gorel.obo with their own subset tag. AI: DOS to add relations mentioned in multi-organism process paper to RO
Enzyme binding
We agreed to obsolete 'DNA methyltransferase binding' from the TG queue a couple of weeks ago, we need to follow up with a plan for how to handle the existing terms in this branch, and guidance as to whether annotators request these terms. They've asked for us to report back on an annotation call.
(We took a look at this last week, but resolved that we need Chris and Harold on the call to figure this one out properly.)
Still agree: we should not define binding by function of target.
How do we handle legacy terms?
Plan to obsolete Obsolete and shift all up to 'protein binding'
Don't need to obsolete all under 'enzyme binding' as many are legitimate families.
For now - we mark up with a subset to flag for future obsoletion
- once we work out how to deal with all the direct annotations.
Add comment to all flagged to discourage annotation.
We will tolerate X family binding terms - but encourage use of X domain binding where this information is known.
AI for Harold?
Axiomatizing multi-organism processes
We've agreed it's a good idea to try and axiomatize at least some of these terms before I leave. We need to agree which relationship I should use - can I go ahead and use regulates or do we need the more specific regulates_in_other_species?
AI (DONE): add regulates_in_other_organism to RO :DOS:
Note: David Hill suggests defining as a chain relation with occurs_in or has_agent. This won't work for all cases - e.g. effects of viruses. DH: Perhaps another relation for chain? e.g. has_agent ? DS, but still won't be sufficient to record that two organisms involved.
Follow-up on 'old' action items
Everyone please take a look at AIs here: http://wiki.geneontology.org/index.php/Ontology_meeting_2014-11-20
AI for all: please re-read those minutes and mark down any AI that may have slipped our minds because of the Thanksgiving break. (Only the last item on that agenda has been added to Trello.)
Follow-up: 'Response to' terms
Please see AIs here - anything left to do? This is still in place: GO:0097044 'histone H3-K56 acetylation in response to DNA damage' is_a GO:0043200 'response to amino acid'
AI (DONE): DOS to finish moving specific responses from is_a to part_of abstract response to chemical classes. Note: ChEBI have now fixed amino acid derivative is_a amino acid. We still need to clear up the resulting mess. How to do this? Chris suggests a onetime run of ETINE (Exists, tagged, not entailed). But ss this now fixed/safe?! DOS: May also be able to find relationships to delete in Protege by querying for things that have particpant both AA and AA derivative AI?
Follow-up: Protein oligomerization
See discussion from a couple of weeks ago: http://wiki.geneontology.org/index.php/Ontology_meeting_2014-12-02#Protein_oligomerization
We couldn't complete this discussion: "New terms: 'protein heterodimer' and 'protein homodimer' not in GO but PRO? Pragmatically, this might be the best solution."
Paola to report on progress on her action items.
GO:0051259 protein oligomerization: manual experimental annotations, to the term and its is_a children: 946 for 809 proteins; 31.8% MGI, 31.8% UniProtKB, 25.26% RGD (these 3 DBs alone own ~87% annotations) MGI: 206 out of 294 are pre-2010 RGD: 181 out of 239 are pre-2010 UniProtKB: 127 out of 294 are pre-2010
I looked at the 10 oldest UniProtKB annotations and in all cases the gene products are reported to be part of an oligomer. I think the confusion with ‘being involved in the oligomerization process’ may depend on some of these papers detailing characteristics of the domains within the proteins that are responsible for the oligomerization… but this is protein binding.
Could MGI curators please take a look at a sample of their annotations, maybe oldest ones first, and let me know what they think the situation is for these annotations. I can send a spreadsheet if helpful. I’d like to ask the same to RGD curators.
AI: Harold to look into MGI annotations. AI: Paola to ask RGD to do the same. (DONE Dec 23rd) UPDATE (Dec 23rd): Stan confirms that this seems to be the case for RGD annotations also. They'd move their annotations to 'protein complex' or one of its children. He'd agree that obsoleting 'protein oligomerization' and children would be more appropriate than merging them with 'protein complex assembly' as the terms seems to have been misused. What is the situation for MGI annotations? Discussion of oligomer CC terms (they don't exist yet). Harold points out that these terms would be very useful in PRO - (DOS: a way of specifiying closure in genus) AI: Harold (and Chris?) to check with Darren Natale if protein dimer terms could be added in PRO.