Ontology meeting 2014-09-11

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

Minutes: Paola


build-go-assert-inferences - Build # 90 - Still Failing!

Discuss in case it hasn't been solved already:

POTENTIAL REDUNDANT AXIOMS GO:0006606 'protein import into nucleus' part_of 'part_of' GO:0034504 'protein localization to nucleus' is also a simple SubClassOf.

 DOS: No problem I've been fixing in branch. Struggling to finish work on branch to merge back. Have now fixed in the trunk.  
 Assert inferences now passes.  See:  http://build.berkeleybop.org/job/build-go-assert-inferences-report/1120/console

WebProtege

The EBI Editors met with Matt Horridge yesterday. Report.

https://docs.google.com/document/d/1hXZs6V9Ex4zeBhqGjajsEbY50S94O5B1qxxHEghod6o/edit

We suggested to give WebProtege another 6 months before we spend significant time on it.

Transport terms (carried over from last week)

Where are we with these action items?

As discussed at SF jamboree, we will:

1) display existing transport templates in a more user-friendly way;

2) add more templates, e.g. for 'transmembrane import' and 'transmembrane export'; David OS will specify more templates if needed.

We'll then email the GOC to alert curators that they may request new terms, use specific terms rather than generic ones, and move their existing annotations if they wish/can.

AI: Tanya will send Heiko slides of suggested display.

DOS did some work on patterns and they're in the ontology, but not in TG yet. He put them in dead-simple owl/yaml formatting (easy to write and edit).

AI: DOS will make tickets in Jira and point Heiko to these files. These may be easy but some templates will be harder to represent using this format. Heiko will point DOS to examples of other templates (javascript files). DOS will finish documenting the templates we agreed on (import across plasma membrane) and send them to Heiko for review.

NAR paper

We briefly went over the latest draft. Judy and Harold will work on it over the weekend. Val and Jane will write the cell cycle section and will send back by end of the day on Monday (UK time).

exocytosis/endocytosis - relationship to import/export

see https://sourceforge.net/p/geneontology/ontology-requests/10998/#b808

Also see 'endocytic import into cell'

Some terms that seem to refer to exocytosis are not under it. Should all exocytosis be under secretion, or should there be some other relationship between exocytosis and secretion. Could be useful to specify a mechanisms of secretion using some standard relation for differentia; exocytosis is one type of mechanism but there are others.

AI: DOS will look into this further and make a proposal of how to solve this.

Localization and establishment of localization

Top level hierarchy (localization, establishment, maintenance now uses is_a instead of part_of (as previously agreed). This change was useful to get new inferences. But most of the hierarchy under it does not yet follow this pattern - as big job to fix. Will be done when design patterns are in place for all parts of this hierarchy. DOS is working on this.