Jul2009 ontology report
Ontology Development & GO Editorial Office Report - July 2009
I. Ontology Development
- SourceForge
- Items opened: 86
- Items closed: 68 (3 duplicates deleted)
- Items still open: 257
- assigned, GO Eds: 92
- assigned, MOD curators: 115
- unassigned: 50
- Content items resolved
- The has_part relation has been implemented in the CC ontology (and will soon be used in BP also).
- Background
- Documentation is available (thanks to Amelia)
- SF item on spliceosomes for which new terms have been added, using has_part
- Several SourceForge items resolved
- The has_part relation has been implemented in the CC ontology (and will soon be used in BP also).
- Content items in progress
- The plan to add internal cross-products to the go_write (and therefore also go_ext) file is in progress.
- Work has begun on terms for kidney development
- New terms from SDB meeting (see below)
- Evaluating new link suggestions and mismatches from ChEBI cross-products
- Continuing to add function-process part-of links in gene_ontology_write.obo and gene_ontology_ext.obo
- Work continues on overhauling terms related to viruses
- Signal transduction overhaul is going very well; see Signaling_Meeting_Minutes_July_2009 for latest notes (Jen and experts including Sandra Orchard)
- Also continuing
- Additional progress on Cellular component organization and biogenesis, in light of internal cross-products
- Taxon triggers; currently moving "sensu" information from synonyms to definitions (see notes for latest)
- Work on branching organ development (David)
- Quality control continues as usual - reports generated by Chris
- Regulation - also see above (David, Tanya)
- Multiple part_of parents (several GO curators, especially Tanya & David)
- Various SourceForge items
- Manuscript in preparation for paper on the regulates relationships should resume soon (Midori & Jane so far; David, Chris and Tanya to join in)
- Considering publication options for cross-product paper (extended version of ICBO xp work noted below)
- Meetings
- ICBO, Buffalo, NY July 20-23
- Cross-product talk and paper (Chris et al.); see http://precedings.nature.com/documents/3496/version/1
- OBO-Edit demos (Amina, David OS)
- David and Tanya attended the Society for Developmental Biology meeting (San Francisco, July 23-27), and have begun adding ontology terms based on discussions with other participants. They expect to add about 50-100 terms.
- Organization under way for September GOC and SAB meetings
- ICBO, Buffalo, NY July 20-23
- Reminder: plan to retire .ontology file format August 1st - see Managers_21Jan09 and GO_Timeline
See monthly report in CVS for ontology statistics.
II. GO Editorial Office activities not represented in part I
- OBO-Edit working group:
- OBO-Edit 2.1 beta released for testing
- See meeting minutes from July 1 and 16, and monthly report
- ICBO presentations (see above)
- Advocacy/outreach (Jane, Jen)
- See monthly report
- Anything else
- GO bibliography has 2797 entries