Aug2007 ontology report
Ontology Development & GO Editorial Office Report - August 2007
I. Ontology Development
- SourceForge
- Items opened: 78
- Items closed: 93
- GO Eds: 58
- MOD curators: 14 (details in Appendix 1)
- GO Ed/MOD collaborations: 21 (details in Appendix 2)
- Items still open: 268
- assigned, GO Eds: 54
- assigned, MOD curators: 48
- unassigned: 166
- Cardiovascular physiology: David has finished meeting follow-up work; file available at go/scratch/gene_ontology_cardio.obo; more detailed information on wiki: http://gocwiki.geneontology.org/index.php/Cardiovascular_physiology/development
- Muscle development: Post-meeting work continues (http://wiki.geneontology.org/index.php/Muscle_Development).
- GO-CL cross-products: Some progress, but further work is now awaiting completion of a major Cell Ontology revision.
- Other content items resolved
- Various small things for SourceForge items
- Other content items in progress
- Quite a bit of progress on sensu terms; plan established to deal with last remaining ones; see http://gocwiki.geneontology.org/index.php/Meeting_Notes_3
- David is working through Chris' file of "regulation of non-process" anomalies; in some cases, new process terms are needed, and in other cases regulation terms need to be moved under regulation of molecular function or regulation of biological quality
- Many synonyms for enzyme activity terms added, derived from EC via Expasy; an update/refinement based on IntEnz is on the way
- Resolwing a few disjoint violations that have cropped up (mainly David, also GO Eds)
- Various SourceForge items
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; new search/filtering interface in progress
- Software hub group (Jane, Amelia):
- AmiGO working group (Jane, Amelia)
- Continuing development to prepare for next AmiGO 1.0 release
- AmiGO working group (Jane, Amelia)
- Advocacy group (Jane):
- Slides for general GOC use (continued)
- August newsletter released
- Usual gohelp traffic
- Annotation outreach (Jen) (note: much more detail in Jen's group report)
- Continuing work on SOPs
- Conferences/meetings
- Interactome Networks in progress (Aug. 30-Sept. 1; Jen, Ben)
- Anything else
- NAR database issue manuscript in progress (content: GO managers; submission: Midori)
- FIGS2GO mapping - about 1000 terms (Jane)
- Parasite book chapter revisions (Jane, with Matt B)
- GO Bibliography now has 1549 entries
Appendix 1: MOD curators' SF items 780275 Harold, Karen C, Ceri 1067017 Harold, Karen C, Ceri 1566692 Harold, Karen C, Ceri 1711527 Donghui 1711561 Donghui 1732986 Donghui 1716772 Donghui 1771261 Donghui 1773245 Donghui 1773281 Donghui 1773295 Donghui 1773312 Donghui 1773238 Tanya 1744496 Tanya Appendix 2: GO Ed-MOD collaboration SF items - MOD curator(s) involved 1322372 Pascale, Val 1759080 Val 1759812 David 1762047 Jodi, Val 1105967 John G 1729099 Harold, Karen C, Peter d'Eustachio 1757389 Val 1450780 transporter wg 1728089 Karen C, Val 1766694 Karen C, Val 1768428 Rama, Val 1767388 Karen C 1770519 Rob 1769547 David 1771167 Rama 1771174 John G 1727804 transporter wg 1778477 Karen C 1778468 Tanya 1744395 Tanya, Jim Hu 1488957 Tanya (Note: "MOD curator" is shorthand for any non-GO-Ed curator)