Ontology meeting 2014-01-09
Attendees:DavidH, DavidOS, Becky, Paola, Jane, Harold, Heiko, Chris, Tanya
Minutes: Tanya
Do we have roll-over funds for a meeting?
If yes, dates that work for all editors and are before the end of February are Feb. 5th and 6th - i.e. 4 weeks from today.
Chris mentioned that "Heiko and I need a lot of advance notice to inform the DOE we are traveling - preferably 6 weeks but we can get get dispensation for 4."
If we do have funding, are we still in time to arrange this meeting (presumably in Hinxton - Chris said he's traveling to Switzerland around those dates)?
no money yet, if we get it, everyone MOVE!
Drupal documentation for ontology pages
Tanya doing basic formatting, need others to review content. Drupal pages
Tanya figured out how to format the Drupal pages so that they resemble the original ones as much as possible. As this was/is time consuming, she offered to do the formatting work for all the ontology-related pages, and we'll then split the pages among editors to check the validity of their content.
GO and vesicle nomenclature
Stemming from email thread
Action: wait and see
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
DavidOS has worked on this quite a bit, trying to establish consistency. Will put slides up which summarize changes. Check existing transport annotations, try pombe ones. For editing, would need to branch both main file and xp file. Or wait for megafile. Action: ?
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.
Not as easy at it seemed. Jane to talk to Birgit to get list of complexes and see if we can use that as a basic framework.
Review of Glycolysis work
Current files are in experimental directory (obo and owl) Glycolysis Glycolysis complete Check out. More progress made. Has part axioms not sufficient, need has input/has output relationships.
Readiness for megafile
Are all branches merged in? Can we set a date for making the switch?
Test Megafile with 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)
Jane/David – load only, let’s just go ahead and see what happens! Test when DavidH is in CA. Need to test megafile in Protégé as well. Conversion to OWL should work seamlessly. Test suite? Watch out for lattice-y look (Graphviz viewer may explode) Will load more slowly. Should get better, the pain will be good for you. Have a script? Chris will think about. Chris will put a catalog file in the editors directory.
Incoming slew of catalytic activity children from PlantCyc/Metacyc
New catalytic activity terms – MANY 100 or so Metacyc reactions not in GO Metacyc2GO mapping will also be updated. Requests will come in March. Will BioPax facilitate new term addition? Probably. Could put under ‘catalytic activity’ and classify later. Does Metacyc have xrefs to Rhea?