Ontology meeting 2013-12-12
Attendees: Jane, Paola, David H, David OS, Harold, Heiko, Becky, Tanya, Chris
Minutes: Paola
START WITH THIS! Review of template requests in Jira
- https://www.ebi.ac.uk/panda/jira/browse/GO-58 homeostasis xps
AI: David H and Tanya will check logical defs. for cellular homeostasis terms. If/when they're good enough, they will close the ticket.
- https://www.ebi.ac.uk/panda/jira/browse/GO-168 TermGenie templates with UBERON
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.
- https://www.ebi.ac.uk/panda/jira/browse/GO-177 assembly/disassembly of CC
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)
- https://www.ebi.ac.uk/panda/jira/browse/GO-181 cell differentiation
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.
- https://www.ebi.ac.uk/panda/jira/browse/GO-185 organelle part (lumen, membrane)
This one too will need to wait for the megafile.
- https://www.ebi.ac.uk/panda/jira/browse/GO-204 Protein Complex by activity
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.
- https://www.ebi.ac.uk/panda/jira/browse/GO-240 TermGenie template for receptor activity
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)