May2007 ontology report
Ontology Development & GO Editorial Office Report - May 2007
I. Ontology Development
- SourceForge
- Items opened: 91
- Items closed: 71
- GO Eds: 38
- MOD curators: 20 (details in Appendix 1)
- GO Ed/MOD collaborations: 13 (details in Appendix 2)
- Items still open: 280
- assigned, GO Eds: 48
- assigned, MOD curators: 49
- unassigned: 183
- Collaboration with the Harvard/MIT GO Engineering group: A new draft of a manuscript describing the work has been circulating, and will be submitted to Nature Genetics as a Perspectives piece.
- Cardiovascular physiology: file gene_ontology_cardio.obo contains about 50 new terms; organization based on physiology; links to SIMAP to be added. Meeting planned for June. Wiki: http://gocwiki.geneontology.org/index.php/Cardiovascular_physiology/development
- Other content items resolved
- Various small things for SourceForge items
- Other content items in progress
- Ribosomal RNA processing overhaul nearly complete (Harold, Karen C, Ceri)
- A small amount of progress on the sensu and taxon items
- Transporters (http://wiki.geneontology.org/index.php?title=Transporters)
- Muscle development: Meeting planned for last week July (exact dates TBD soon); preparatory editing coordinated by Erika and Jen (http://wiki.geneontology.org/index.php/Muscle_Development).
- Suggestions on cell cycle-related terms from expert in Ghent (via Jane)
- Resolving disjointness violations in the process ontology (Jane and David; almost finished)
See monthly report in CVS for ontology statistics.
II. GO Editorial Office activities not represented in part I
- OBO-Edit working group:
- OBO-Edit 2.0 first beta released
- Bioinformatics Application Note in final throes of publication logistics (actually published as of June 1st)
- Paper on graphical editing in OBO-Edit 2.0 submitted to Bio-ontologies SIG at ISMB
- Software hub group (Jane, Amelia):
- AmiGO working group (Jane, Amelia)
- Continuing development to prepare for June AmiGO (1.0) release
- Prototype of SourceForge tracker submission tool being tested (programmed by Seth; tested by AWG and GO Eds)
- AmiGO working group (Jane, Amelia)
- Advocacy group (Jane):
- May newsletter released
- Some GO web site maintenance (Amelia)
- Usual gohelp traffic (slightly busier than last couple months)
- Annotation outreach (Jen) (note: much more detail in Jen's group report)
- SOP discussions continuing
- New SOP web page available (help from Amelia), with ISS flowchart
- Flowcharts in preparation for IEA and for top-level annotation decisions
- SOP discussions continuing
- Conferences/meetings
- Agro-genomics workshop on plant annotation, Ghent: GO talk and OBO-Edit demo (Jane)
- Planning for cardio content meeting (David, Simon, experts; see above)
- Planning for muscle content meeting (Jen, Erika; see above)
- Anything else
- IMG mapping in progress (Jane)
- GO Bibliography now has 1392 entries
Appendix 1: MOD curators' SF items 856170 - Karen C, Val 1585409 - Karen C, Tanya 1706567 - David 1708418 - Donghui, Karen C 1708446 - Donghui, Karen C 1708896 - Donghui 1710878 - Donghui 1711493 - Donghui 1711867 - David 1718700 - David 1720004 - David 1721422 - David 1722202 - David 1722719 - David 1722869 - David 1723513 - David 1723697 - David 1723705 - David 1725863 - Alex, Petra, Harold 1727948 - Donghui Appendix 2: GO Ed-MOD collaboration SF items - MOD curator(s) involved 1469444 - Alex 1491013 - Chandra, Val, Michelle 1633338 - Harold 1657892 - Karen C 1702938 - Val, community expert 1705071 - Val 1707593 - Tanya, community expert 1708213 - Karen C, Val 1710159 - Cathy Derow (IntAct) 1710724 - Eurie, Val 1714238 - Kirill 1715584 - Ranjana 1717390 - Doug (Note: "MOD curator" is shorthand for any non-GO-Ed curator)