Feb2007 ontology report
Ontology Development & GO Editorial Office Report - February 2007
I. Ontology Development
- Items opened: 84
- Items closed: 94
- GO Eds: 30
- MOD curators: 23 (details in Appendix 1)
- GO Ed/MOD collaborations: 41 (details in Appendix 2)
- Items still open: 277
- assigned, GO Eds: 50
- assigned, MOD curators: 79
- unassigned: 198
- Work on the 'sensu' terms is well under way; changes are being made "live," i.e. in gene_ontology_edit.obo rather than in a separate ontology file. Detailed progress reports are available on the wiki (go to the Sensu main page and follow the 'Meeting Notes' link).
- Planning & preparation continue for the meeting on the collaboration with Jonathan Liu et al. at MIT.
- Plans are firming up for ceating links between function and process terms. We'll start with metabolic pathways, and have our biochemically inclined curators start identifying links (using available resources such as Reactome) in parallel with Chris and Amelia sorting out the actual relationship to be used. More details available on the wiki and in manager conf call notes.
- Work has begun on transporter terms in the function ontology. Details are on the public wiki (http://wiki.geneontology.org/index.php?title=Transporters).
- Other content items resolved
- PAMGO content changes (Jane, Amelia, PAMGO curators; there's a press release: http://www.eurekalert.org/pub_releases/2007-02/vt-ulf022707.php)
- Various small things for SourceForge items
- Other content items in progress
- Resolving disjointness violations in the process ontology (Jane, using file of violations identified by Chris)
- Protein modification (Jane, John Garavelli)
- Regulation of process terms - check for consistency with process terms (David, using file from Chris)
David & Midori have looked over the outstanding SourceForge items, and are ready to start assigning many of them to GO curators (both GO Eds and MOD curators) based on biological areas of expertise.
We have implemented the first part of our nascent system for crediting community experts who contribute to ontology development: one abstract has been added to the GO_REFs file (CCNS meeting), another is in the works (immunology), and a syntax has been established for citing them. Additional info is in manager call minutes and on the GO list.
See monthly report in CVS for ontology statistics.
II. GO Editorial Office activities not represented in part I
- OBO-Edit working group:
- OBO-Edit 1.1 beta testing continues; a few more bugs have been fixed.
- A (slightly) revised manuscript for the applications note has been submitted to Bioinformatics, along with a response to reviewers' comments.
- Software hub group (Jane, Amelia):
- AmiGO working group (Jane, Amelia)
- AmiGO now running on faster servers, and from new URL, http://amigo.geneontology.org
- Setting priorities for feature additions
- Interface and search enhancements in progress
- Testing ongoing (features, interface, bug fixes, etc)
- AmiGO working group (Jane, Amelia)
- Advocacy group (Jane):
- February newsletter is out
- Tool requirments document in preparation
- Meetings calendar on internal wiki
- Usual gohelp traffic
- Annotation outreach (Jen) (note: much more detail in Jen's group report)
- Flowcharts for annotation procedures in preparation
- Metrics likewise
- GO-MIT (see aboeve)
- Planning for muscle content meeting (Jen, Erika)
- Signaling meeting at Sanger - Jen attended
- Anything else
- GO Bibliography now has 1281 entries
- Jen has helped Erika get software set up
Appendix 1: MOD curators' SF items 1604888 - Donghui, Tanya 1644804 - Donghui 1644819 - Donghui 1644838 - Donghui 1644868 - Donghui 1646949 - David 1649857 - David 1650780 - Becky 1653574 - Donghui 1653971 - David, Becky 1654525 - Harold, Rama 1659249 - David 1659952 - Donghui 1660958 - Donghui 1661017 - Donghui, Tanya 1661597 - David 1661624 - David 1661722 - David 1664533 - Harold 1665537 - David 1666457 - David Appendix 2: GO Ed-MOD collaboration SF items - MOD curator(s) involved 1378881 - David, Karen P, Pascale 1400564 - Chris T 1431082 - Melissa 1432177 - Nick Thomson 1516347 - Martha Arnaud 1526200 - Karen C 1562205 - Many, including David, Tanya, Michelle 1636063 - Several, including Evelyn, Emily, Val, Karen C 1643043 - Julie 1645488 - John Garavelli 1646580 - Rama 1646614 - Rama, Val 1647142 - Alex 1647347 - David, Tanya 1647477 - Rama, Kimberly 1647990 - Maria 1648258 - Rama, Michelle 1649153 - Michelle 1649617 - David 1650586 - PAMGO curators 1650742 - Maria, Rama 1650749 - Alex, Karen C 1652331 - Rama 1652350 - Rama 1652475 - Jodi 1653399 - Harold 1653490 - Rama, Becky, Val 1653493 - Rama 1653518 - Rama, Becky 1653565 - Donghui 1654108 - Rama, Val 1654151 - Becky 1655351 - David, Melissa 1656404 - Karen C 1658303 - Alex 1658320 - Harold 1660872 - Alex 1660877 - Alex 1660880 - Donghui 1660897 - Alex 1665398 - Alex 1665539 - Alex 1669228 - Alex (Note: "MOD curator" is shorthand for any non-GO-Ed curator)