Ontology meeting 2013-12-12

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

Minutes: Paola

START WITH THIS! Review of template requests in Jira

AI: David H and Tanya will check logical defs. for cellular homeostasis terms. If/when they're good enough, they will close the ticket.


Heiko: Update on current state: The x-metazoan file now loads without unsatisfiable classes. Next step move the xps to the main xp file, or wait for the unified file. In both cases the import chain needs an update.

AI (related): David OS: to test the megafile, everyone needs to switch to 64 bits and do some tests. EBIers will do it next Monday. The aim is to switch over in January.


Done, the remaining sub task is a longer work in progress. (That's a list of classes provided by Chris that are currently descendants of 'cell component assembly' but shouldn't be - https://www.ebi.ac.uk/panda/jira/browse/GO-178, assigned to Paola)


AI: David OS will look at the CL side of missing logical defs. AI: Chris and Heiko will investigate importing plant cell terms via extended version of CL.


This one too will need to wait for the megafile.


We recently decided we don't want to add a template for defining intersection terms using capable_of_part_of process, so let's close the ticket. A new ticket is needed for a potential template that allows location as well as function to be defined. David OS to do this.


AI: Chris will generate a list of terms missing logical defs., and Becky will look at them.

Related issues (TG and TG templates)

Tanya requested to highlight the plant templates a bit more. Possible AI for Tanya: let Heiko know what she would like TG to display?

We haven't announced the optional comment field yet. AI: Paola to email Heiko to change the 'Suggested format' slightly (DONE); when this is done, Paola to announce the new feature (DONE).

Support for TG during the holidays, and review of submitted terms during same period:

AI: Heiko and Chris to add some checks/cron jobs;

AI: Jane to alert the users that there will be a delay in approving/committing the terms over the holidays.

ALL ITEMS BELOW ARE BUMPED TO NEXT WEEK

New TG template for 'cell migration'?

Note that 'cell chemotaxis' is_a 'cell migration', which is fine based on their definitions. However, both 'cell chemotaxis' and 'cell migration' terms have logical defs based on alters_location_of, e.g.

[Term]

id: GO:0072676 ! lymphocyte migration

intersection_of: GO:0016477 ! cell migration

intersection_of: alters_location_of CL:0000542 ! lymphocyte

Chris says: "It would be good to use a more generic relation, but this depends on the hierarchy being disjoint with other classes using the same relation with a different genus.."


Drupal documentation for ontology pages

Tanya doing basic formatting, need others to review content.


GO and vesicle nomenclature

Stemming from email thread

Patterns for defining maintenance of location.

Should maintenance of location be a subclass of localization rather than a part? This appears to be consistent with the current textual definition of localiation and would also allow complete automation of new term classification in this branch. Details here: https://www.ebi.ac.uk/panda/jira/browse/GO-232

protein-DNA complexes revisited

We decided some time ago that this was not a useful grouping because it's unclear what constitutes a protein-DNA complex (any protein complex that binds DNA?) making for very tricky manual classification under this term, and we didn't feel it was a useful grouping as this information can be arrived at in other ways. However when I cam eot make the change it became clear that this complex term is referenced in many other process terms e.g. protein-DNA complex assembly, protein-DNA complex remodeling, protein-DNA complex transport, protein-DNA-RNA complex remodeling some of which may be useful, esp the remodeling terms.

Review of Glycolysis work

OBO-Edit 2.3 release

Available at http://sourceforge.net/projects/geneontology/

Please install, test and comment. Paola has used it for everyday commits and it works fine.

Also see http://wiki.geneontology.org/index.php/Ontology_meeting_2013-11-20#Moving_logical_defs_into_the_editors_obo_file (Testing of OE catalogs, Downstream changes)