July2007 ontology report
Ontology Development & GO Editorial Office Report - July 2007
I. Ontology Development
- SourceForge
- Items opened: 77
- Items closed: 72
- GO Eds: 35
- MOD curators: 12 (details in Appendix 1)
- GO Ed/MOD collaborations: 25 (details in Appendix 2)
- Items still open: 285
- assigned, GO Eds: 53
- assigned, MOD curators: 51
- unassigned: 181
- Cardiovascular physiology: Meeting follow-up work continuing via virtual meetings; 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: Meeting held in Padova, July 25-26 (http://wiki.geneontology.org/index.php/Muscle_Development). About 80-90 new terms added to gene_ontology_cardio.obo file; post-meeting work in progress. A report will go on the wiki soon.
- GO-CL cross-products: Work has resumed with a webex session held July 26th. Notes on wiki at http://wiki.geneontology.org/index.php/XP:Meetings#2007.2F07.2F26_:_GO-CL_XPs.2C_next_steps; also see http://wiki.geneontology.org/index.php/Logical_Definitions and BBOP Obol wiki.
- Other content items resolved
- Transporters: High-level changes committed (also see below)
- Ribosomal RNA processing overhaul committed (http://gocwiki.geneontology.org/index.php/RNA_processing; Harold, Karen C, Ceri)
- Various small things for SourceForge items
- Other content items in progress
- Additional incremental progress on sensu terms
- Transporters: Work on more specific terms, definitions, etc. to resume at end of summer (http://wiki.geneontology.org/index.php?title=Transporters)
- 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; demos and testing under way
- Prioritizing additional features for OBO-Edit 2.0
- 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):
- Standards for GO tools
- Slides for general GOC use
- August newsletter in progress
- Usual gohelp traffic
- Annotation outreach (Jen) (note: much more detail in Jen's group report)
- User categories - descriptions
- Grant proposal in preparation for immunology (Wellcome Trust)
- Conferences/meetings
- Muscle content meeting (Jen, Erika, Midori; see above)
- Anything else
- IMG mapping (Jane):
- IMG functional roles mapping COMPLETE (~2000 terms mapped, ~200 new GO function terms)
- IMG pathways (500 terms) to commence 6th August
- metacyc2go update; about 140 new terms (Midori)
- Search-and-replace script for ontology editing (Jen)
- GO Bibliography now has 1491 entries
- IMG mapping (Jane):
Appendix 1: MOD curators' SF items 1427800 - David, Doug 1745015 - David 1747859 - David 1749719 - David 1751918 - David 1752858 - Doug 1756987 - David 1757574 - David 1757663 - David 1758842 - David 1760941 - Karen C 1761459 - David Appendix 2: GO Ed-MOD collaboration SF items - MOD curator(s) involved 1233407 - Val, transporter wg 1566704 - Chris T 1621572 - Pascale 1660496 - Karen C, Dianna 1707310 - Michelle, Peter 1719897 - Karen C, Val 1723313 - Alex 1727367 - Val 1739177 - Alex 1741102 - Tom Walk (expert) 1746983 - Val, Harold 1747347 - Doug 1747820 - Susan 1748527 - Doug 1752006 - Alex, Susan 1752079 - Val 1752095 - Val 1752111 - Val 1753438 - Val 1753808 - Karen, Rama 1754690 - Val, Rama 1755770 - Pascale 1756236 - Karen C, Val 819299 - Eurie, Val 973913 - Karen C, Val (Note: "MOD curator" is shorthand for any non-GO-Ed curator)