Ontology meeting 2015-05-28

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Attendees: Paola, David OS, Tanya, David H, Heiko, Chris

Minutes: Paola

Follow-up: New TG templates

If the export templates are ready, we'll test them, then advertise them along with the ones below:

cellular component binding

cellular component organization




We resolved to change the template for 'cellular component organization' to make 'cellular process' the genus 
(let’s try that, rather than further up the graph, and see what happens). 
Jira ticket: https://www.ebi.ac.uk/panda/jira/browse/GO-327
Once that's done and tested, we can advertise the 5 templates above.
 As for the export templates, David OS is still working on them. He'll check that he has all the relevant info in one ticket.

No more merges

Ref: https://github.com/owlcs/owlapi/issues/317

Obsolete instead and use the replace tag, as discussed in the recent past.

Chris tracked the Protege request here as it's best done as an extension to Jim's plugin: https://github.com/balhoff/obo-actions/issues/1

Any further action item we need to take to make sure this becomes regular practice in GO?

We need a long-term plan to deal with these changes, alert the databases, make sure the infrastructure is up to speed.
David H will ask Harold about MGI expected behavior.
We need to make a detailed proposal and bring it up as a heads-up on an annotation call.
In the meantime, as a short-term solution, we’ll work on the one outlined in the github link above. 
Then we need to test AmiGO load before going live. 
(Related) AI for Chris: remember to prepend all existing obsolete term names with ‘obsolete’ 
(see http://wiki.geneontology.org/index.php/Ontology_meeting_2015-04-23#Follow-up:_Prefixing_of_obsolete_to_label_of_all_obsoletes)

GO-SO issues

Copying from last week:

There are various problems with our use of SO, some of which requires co-ordination with SO dev:

  1. We need a bridge from SO transcript terms -> ChEBI:RNA. In the absence of this, lots of inference is missing. Will the long planned SO molecular save us, or do we need our own bridge axoims?
  2. We need a differentium for recording which RNA metabolic processes are processing (involve maturation). We may be able to do this using terms from SO (see next item), or we could use a similar strategy to the one we use for developmental progression via a 'results in maturation of' relation. (We may, in fact, need a combination of these).
  3. We use the SO terms nRNA, ncRNA and its children as if they refer to both mature and immature states of transcripts. In fact, according to SO they refer to the mature state. To align with SO properly we would need to review usage and use alternative SO terms where available. SO has an additional set of terms for primary transcripts, but no terms for immature. Primary transcript refers only to before splicing so no terms for intermediate state after splcing and before other modifications involved in maturation such as capping and polyadenylation for mRNA. Need to discuss possibilities of adding these with SO.

DOS organising meeting with Karen Elibeck. Who wants to be involved?

AI: organise a meeting with Mike Bada and Karen Eilbeck. David OS and Chris will be involved. 
AI: David OS will make a doodle poll.
We need a formal way to refer to transcript maturation; it’s all manual right now. 
It would be nice if we could do it by referring to the participating transcript, but maybe that’s a bit too complicated. 
Otherwise use results_in_maturation_of - currently it’s used strictly in development; could it be expanded? 
No, that may lead to too many unwanted inferences. 
We probably need a whole new relation to refer to transcript maturation. 
AI: come up with a new relation. Do that in discussion with SO.

Intersections vs. relationships in children of 'protein complex'

(David OS to elaborate) To avoid mis-classification of protein complexes that may have the same function or be involved in the same process, we need to retrospectively check all children of 'protein complex' that have intersections (not relationships!) with capable_of function links and capable_of_part_of process links. David OS prepared a list:

list of protein complexes with EC def + axiom linking to MF/BP

 Send list to Harold

part_of vs has_part in export from nucleus

dph-All of the named RNAs that are exported from the nucleus are exported as part of RNP complexes. In the ontology we had asserted that the RNA export has_part RNP export. This seemed backwards to me since the RNA is part of the RNP. I reversed these relations to make the RNA transport part_of the RNP transport.

 DPH to look at how this works for protein complexes, LDLs etc.
 If we go all the way with this then we should add the property chain transport o has_part -\> transports. But this may be too strong.  Leave use of this pattern up to editor discretion?

transcription repressor/activator naming

Ruth has a proposal which needs general review https://sourceforge.net/p/geneontology/ontology-requests/11716/

Here's a less radical solution: https://sourceforge.net/p/geneontology/ontology-requests/11712/#482e

AI: DOS to go ahead with conservative name change, letting GO know about change.
AI: DPH to read and coment on Ruth's proposal.

X dependent process & involved in (bumped to next week)

We have many X-dependent process terms. My initial reading of the names and definitions of these terms was that the X must be upstream, but typically X (implicitly) is treated as part of the process that depends on it, as shown by the large number of cases of term of the form X involved in X dependent process Y. This may be a good thing, but perhaps could be made clearer with some design patterns.

Prompted by: https://sourceforge.net/p/geneontology/ontology-requests/11713/#a397