June2007 ontology report
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Ontology Development & GO Editorial Office Report - June 2007
I. Ontology Development
- SourceForge
- Items opened: 62
- Items closed: 62
- GO Eds: 42
- MOD curators: 5 (details in Appendix 1)
- GO Ed/MOD collaborations: 15 (details in Appendix 2)
- Items still open: 279
- assigned, GO Eds: 57
- assigned, MOD curators: 49
- unassigned: 173
- Cardiovascular physiology: 1.5 day meeting held at Medical College of Wisconsin; about 100 new terms added, mainly on renal control of blood pressure. Work continues via virtual meetings; file available at go/scratch/gene_ontology_cardio.obo; more detailed description of meeting on wiki: http://gocwiki.geneontology.org/index.php/Cardiovascular_physiology/development
- Other content items resolved
- Disjointness violations in process ontology resolved (Jane and David)
- Some additions/updates for PAMGO (Jane)
- All cellular component terms now defined
- Various small things for SourceForge items
- Other content items in progress
- Ribosomal RNA processing overhaul nearly complete (Harold, Karen C, Ceri)
- Additional incremental progress on sensu terms
- Transporters: draft sent to GO list for comment; will be implemented 1st week July (http://wiki.geneontology.org/index.php?title=Transporters)
- Muscle development: Meeting planned for July 25-26 (http://wiki.geneontology.org/index.php/Muscle_Development).
- More work on cell cycle-related suggestions (Midori, Val, Eurie, Rob)
See monthly report in CVS for ontology statistics.
II. GO Editorial Office activities not represented in part I
- OBO-Edit working group:
- Additional OBO-Edit 2.0 betas released; demos and testing under way
- Software hub group (Jane, Amelia):
- AmiGO working group (Jane, Amelia)
- Continuing development to prepare for next AmiGO 1.0 release
- Discussing various interface options
- Further work on SourceForge tracker submission tool (programmed by Seth; tested by AWG and GO Eds)
- AmiGO working group (Jane, Amelia)
- Advocacy group (Jane):
- Usual gohelp traffic; a few more curators have joined the rota
- Annotation outreach (Jen) (note: much more detail in Jen's group report)
- More work on flowcharts
- Jen has learned the art of UniProt GO annotation from Emily
- Conferences/meetings
- Wellcome Advanced Course: Functional Genomics - talk on "Using GO for analysis of expression data" (Jane)
- Cardio content meeting (David, Simon, experts; see above)
- Planning for muscle content meeting (Jen, Erika; see above)
- Fact-finding on running annotation/ontology development courses at EBI (Jen, for Ruth Lovering & WT grant application)
- Anything else
- IMG mapping: "terms" done; "pathways" in progress (Jane)
- GO Bibliography now has 1451 entries
Appendix 1: MOD curators' SF items 1723713 - David 1728531 - David 1723691 - David, Maria, Val 1730751 - David 1732046 - David Appendix 2: GO Ed-MOD collaboration SF items - MOD curator(s) involved 1578969 - Eurie, Val 1731073 Chris, Melissa 1729186 - Petra 1731477 - Karen C 1734036 - Karen C 1499218 - Sue, Donghui 1741185 - Michelle 1741376 - Matt, David Roos (community expert) 1740879 - David, Louise Dougherty 1742917 - Alex 1728308 - Vladimir Mironov (community expert) 1728275 - Val 1744717 - Val 1728276 - Val 1728279 - Val, Rob, Eurie (Note: "MOD curator" is shorthand for any non-GO-Ed curator)