Ontology meeting 2014-04-17

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Extracellular vesicle terms

See email thread "GO and vesicle nomenclature"

Follow-up: 'colocalizes with' nuclear chromatin

Carried over, see http://wiki.geneontology.org/index.php?title=Ontology_meeting_2014-03-13

Where are we with the planned action items? David OS made a start on this. Transitive?

The latest AI was for David OS to put together a proposal for this, and run it by Tony.

Follow-up on Protege

Are we really ready for Protege? Copied over from previous meetings:

David OS will add examples and tips for GO editing and browsing in Protege on the wiki. Chris has started asking people about the plug-in. The plan is to have a meeting to figure out what kind of progress we can have on that in a reasonable time-frame. We need a write-up of the sort of things that are currently hard for editors to do/render in Protege; things that you can do in OE but can't currently do (or easily do) in Protege. E.g. new terms, searches... rendering in tree views is virtually impossible now. We could have a period where we do things using both tools, but one worry is that some of us may not be able to work with both tools open on a machine that doesn't have loads of memory.

AI for all: For the time being, we can all try using Protege in our normal work flow and report on the difficulties we encounter. Jane made a wiki page and we can all add to it: http://wiki.geneontology.org/index.php/Protege_Feature_Requirements.

AI: DOS to add link to the specs document.

Specs doc is here: https://docs.google.com/document/d/17tph3jwrDGEaa7DyYPOK8HCi2dCDdJxi3VrTWNQpbqc/edit

Alpha version of OBO annotation plugin is here: https://github.com/simonjupp/protege-obo-plugins

The wiki page will be the place to collect use cases, the Google doc will be for specific feature specifications.

Any progress on this?

Follow-up: Reactome ontology mappings

Carried over from April 3rd: Reactome maintain mappings between their processes, reaction etc and GO terms. We have mappings to Reactome in GO, but these are not in sync - one of Amelia's legacies I think. How do we want to handle this? The nuclear option would be just to remove the mappings from the ontology file, or alternatively we could set up a regular job to get the GO-Reactome mappings from their BioPax. Thoughts?

Heiko and Chris will set up a job to make these automatic. Jane will open a Jira ticket.

Where are we with this?

Rest of JIRA issues

Try to review those we didn't get to last time.