Jan2010 ontology report
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Ontology Development Report - January 2010
I. Ontology Development
- SourceForge
- Items opened: 162
- Items closed: 150 (7 duplicates and 1 invalid item deleted; 1 item "pending")
- Items still open: 291
- assigned: 235
- unassigned: 56
- Completed content items
- Regulates cross-products released into gene_ontology_write.obo and gene_ontology_ext.obo
- Terms added from ASCB - ASCB_2009 (David, Tanya)
- Various SourceForge items
- Content items in progress
- Review of internal cross-product sets such as BP-xp-self and CC-xp-self continues; see plan to add internal cross-products. (Jen, Jane, Midori, Chris, David, Tanya)
- Kidney_Development now under way
- Successful content meeting held January 25, 2010
- Follow-up work in progress
- Further discussion on aligning with ChEBI for cross-products (Midori, Chris, Jane, David, ChEBI curators); also beginning to plan meeting for GO editors to make chemical references in GO internally consistent
- Continuing to add function-process part-of links in gene_ontology_write.obo and gene_ontology_ext.obo (David, Tanya)
- Work continues on overhauling terms related to viruses (Jane)
- Signal transduction overhaul: now seeking comments on new draft of structure and definitions for top terms; Webex session scheduled for February 4th; see Signaling_Meeting_Minutes_January_2010 for latest notes (Jen and experts including Sandra Orchard)
- Extensive work on [taxon triggers]; ontology errors have been corrected; annotation groups have reviewed inconsistencies, and annotations or taxon rules adjusted
- Quality control continues as usual - reports generated by Chris (cronjobs)
- Publications
- GO cross-product manuscript reviewed; revisions in progress (Chris, David, Jane, Midori, Mike Bada)
- Case studies for publication on "revisability" of GO, proposed and coordinated by Sabina Leonelli (Midroi, Jane, Alex, Karen C)
- Continued from November & December:
- Manuscript on Taxon triggers in preparation, to be submitted to BMC Bioinformatics (Jen, Chris)
- Resuming work on manuscript on regulates relations (Jane, Midori, David, Chris, Tanya, maybe other annotators)
- Anything else
- Discussing ways to make ontology editing info (what's been done, when, why, etc.) more readily available to editors, annotators, and users
- GO bibliography has 3105 entries