Ontology meeting 2014-07-31

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Attendees: Paola, Harold, Heiko, Tanya, David OS, Chris, Jane

Minutes: Paola

Importing SO

We're still using CHEBI for some RNA logical defs - isn't it time we switched to SO? I needed something to define miRNA transport but no miRNA in CHEBI (although they do have many RNA types). See also this ticket: [1]

Some time ago, Chris, Karen, Colin and Mike Bada started working on a molecular sequence ontology (MSO). Lately progress has been slow. However, in principle there's no reason not to use what is in place so far; at least we could get the inferences right, and it would provide us with some structure. MSO is importing RNA terms from ChEBI at the moment, though ChEBI may not be the best solution for RNAs in the long run.

AI: Chris will email them to check on the status of the MSO, and see if we can start using that as an import file.

Is 'telomere maintenance via semi-conservative replication' a subclass of 'cellular homeostasis'?

Stemming from latest assert inferences job. Root is 'telomere maintenance' subclass of 'anatomical structure homeostasis'. Just double-checking that we're all ok with this as it sounds a bit weird, telomere being an anatomical structure.

It does sound biologically unintuitive to others too, but this overall classification was implicitly agreed upon some time ago. David OS: a solution may be to tweak CARO (the Common Anatomy Reference Ontology). In CARO, anatomical entity is the most general class, and that includes spaces. A structure is a connected thing that has mass. Under that are cell and cell part.

AI: David OS will add to the agenda for the next CARO meeting (to be held in September) to try and have a class at an intermediate level between cell and anatomical structure.

Review of Jira tickets (continued from last week)

We got as far as GO-198 included.

Stemming from the Rhea Jira tickets: Colin is developing a reaction ontology, broader than Rhea, and trying to map Rhea into it. His slides are at the bottom of this page: http://www.ebi.ac.uk/seqdb/confluence/display/ONT/Ontology+Workshops+2014

Brief report on PAINT jamboree

Tanya takes notes of ontology questions and then gets back to PAINTers (see SAM email). Lesson: we should continue to send ontology developers to PAINT meetings and calls, and in general keep explaining ontology stuff to a wider GO audience outside the editors group. Also we could make sure that one of us is always present at the bimonthly PAINT call.

AI: Tanya asked to move the PAINT call to the same time as the annotation call, but on alternate weeks. Waiting for feedback (only one - negative - answer at the time of writing).

Plan work for SF jamboree

Review and assign mini-projects, etc. Jane added a label 'jamboree' to ticket(s) of hers that she'd like us to discuss at the jamboree.

Aim is to get numbers down. We need to go through mini-projects, but is that the best use of the jamboree?

AI: We all need to take some time prior to the jamboree to comprehensively review tickets. Use the jamboree tag. Everyone to pick up their problem items, the ones that need input from others, whether for knowledge or for streamlining strategies. Then we'll work on them in rotation, say 1-2 a day from each editor.