Mar2009 ontology report
Ontology Development & GO Editorial Office Report - March 2009
I. Ontology Development
- SourceForge
- Items opened: 108
- Items closed: 94
- Note: Due to changes in SourceForge's tracker system, the breakdown of SF items resolved by MOD curators, GO editorial office curators, and MOD-GOed collaborations cannot easily be determined for March 2009. Midori has submitted a feature request to have the relevant feature (ability to sort closed items by close date) restored, but there has been no response so far. From April onwards, a workaround would be possible but would take a lot more time.
- Items still open: 272
- assigned, GO Eds: 85
- assigned, MOD curators: 127
- unassigned: 60
The main thing for March, of course, has been preparation for and participation in the GO Consortium meeting in Eugene, Oregon. A progress report prepared for the meeting is available.
- Presented at meeting:
- Timeline and pipeline, current and planned
- MF-MF and MF-BP regulates links live in gene_ontology_ext.obo (Chris, David, Tanya, Jane)
- Quality control - see wiki and slides
- Lung development and branching morphogenesis - see wiki and slides
- Biological Signaling - see wiki and slides
- Cellular component organization and biogenesis - see wiki and slides
- Internal cross-products (see links below; add slide link when available)
- Proposal to add process-specific function terms - see discussion on wiki (part of work in progress, just before ontology development discussion topics) and slides
- Also see ontology development discussion topics for notes and links on:
- Location-specific process terms
- Chaperones
- Response to stimulus
- Wiki links to terms in ontology files, tools, etc.
- Content items resolved
- Several 'activator' and 'inhibitor' terms obsolete for consistency with obsolete function terms
- Several SourceForge items resolved
- Content items in progress (much the same as last month)
- Additional work on cross-products within GO -- see Category:Internal_Cross_Products and Editors_cross-product_implementation_plan (David, Midori, Jane, Jen, Chris, Tanya)
- Signal transduction overhaul continuing, as is content meeting planning (Jen, David, experts)
- external experts identified; new proposal drafted
- Signaling wiki page reorganized
- mailing list created
- Planning continues for small content meeting for prokaryotic electron transport (Rob Gunsalus, working with Jen and rest of electron transport WG)
- Cellular component organization and biogenesis almost done
- Quality control reports generated by Chris (ongoing work)
- Regulation - also see above (David, Tanya)
- Multiple part_of parents (several GO curators, especially Tanya & David)
- Various SourceForge items
- Publications
- Agreed to contribute a chapter on ontology development approaches used in GO, for book entitled Knowledge-Based Bioinformatics: From Analysis to Interpretation, edited by Marco Ramoni and Gil Alterovitz (our GO Engineering collaborators) (David, Tanya, Chris, Judy, maybe others as needed)
- Reminder: plan to retire .ontology file format - see Managers_21Jan09 and GO_Timeline
See monthly report in CVS for ontology statistics.
II. GO Editorial Office activities not represented in part I
- Amelia at Berkeley
- OBO-Edit working group:
- OBO-Edit 2 release candidate now being tested, bugs fixed, etc. Release planned for April 7, 2009.
- Colin Batchelor has joined working group
- monthly report available
- Advocacy/outreach
- Highlight: News feed available for testing at http://ash.lbl.gov/drupal/
- See monthly report for more
- Meetings
- GOC meeting (see above)
- Biocurator meeting preparation
- "Clackpoint" VOIP software trial (OBO-Edit working group meeting)
- Anything else
- GO bibliography has 2575 entries
Appendix 1: MOD curators' SF items NOT AVAILABLE FOR MARCH 2009 Appendix 2: GO Ed-MOD collaboration SF items - MOD curator(s) involved NOT AVAILABLE FOR MARCH 2009 (Note: "MOD curator" is shorthand for any non-GO-Ed curator)