Nov2006 ontology report
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Ontology Development & GO Editorial Office Report - November 2006
I. Ontology Development A. SourceForge 1. Items opened 91 2. Items closed 97 a. GO Eds 53 b. MOD curators 38* c. GO Ed/MOD collaborations 6** 3. Items still open a. assigned, GO Eds 74 b. assigned, MOD curators 22 c. unassigned 174 *details in Appendix 1 **details in Appendix 2 B. Considerable progress on is_a-complete biological process (mainly David, Jane, Jen, Midori, Tanya; occasional contributions from other curators on specific questions). Much more detail is available on the internal wiki: http://gocwiki.geneontology.org/index.php/Isa-complete_BP. There is also a Google spreadsheet of outstanding tasks and questions. C. Collaboration with Jonathan Liu, MIT: David has pointed Jonathan to the is_a-complete file. David & Midori commented on the most recent set of suggestions; as noted in the last managers' call, "too specific" terms tend to need work, whereas "too general" terms often serve some ontology-organization purpose. David will suggest to Jonathan that he compare different versions of the is_a-complete file to see how the analysis results change. D. Erika's work on 'response to drug' revamp also documented on wiki: http://gocwiki.geneontology.org/index.php/Response_to_drug E. Other content items resolved 1. High-level cellular component terms (Jane) 2. Usual small things for diverse SF items F. Other content items in progress 1. Damaged DNA binding terms (Midori, with RefGen group, esp. Varsha & Eurie) 2. Cardiac muscle terms, round 2 (Jen, with Varsha) 3. Specific cytokine/interleukin production terms (Midori, Alex, Evelyn) 4. General and specific transcription (Karen C, Midori, Val) 5. Synaptic transmission (David) 6. Several DNA repair items (Eurie) See monthly report in CVS for ontology statistics. II. GO Editorial Office activities not represented in part I A. OBO-Edit working group: 1. OBO-Edit 1.1 beta testing near completion; target release date Dec. 14 2. Reviews received for Bioinformatics Application Note manuscript; Chris & John will respond to editors 3. obomerge testing continues; also relevant to is_a-complete ontology work (Jane) B. AmiGO working group (Jane, Amelia): 1. Finalizing new look (Amelia) 2. Documentation/user guide for next release C. Software hub group (Jane, Amelia): 1. AmiGO 2.0 features D. Advocacy group (Jane): 1. November newsletter sent 2. GOhelp list a little bit more active than in Oct. E. Annotation outreach (Jen) (note: may overlap with Jen's group report) 1. Aspergillus Annotation Jamboree (also see meetings) 2. More progress populating outreach database 3. Annotation SOP for wiki F. Conferences/meetings 1. Aspergillus Annotation Jamboree, Copenhagen (Jen) 2. Topic contributions for Jan. 2007 GOC meeting G. Anything else 1. mesh2go mapping (Jane) 2. GO Bibliography now has 1146 entries Appendix 1: MOD curators' SF items 1237491 - Erika 1240327 - Erika 1459883 - Erika 1511520 - David 1569577 - Karen C 1573845 - David 1575421 - David 1584578 - David 1587343 - David 1588923 - Donghui 1588926 - Donghui 1588927 - Donghui 1588931 - Donghui 1588993 - Donghui 1589002 - Donghui 1589006 - Donghui 1589008 - Donghui 1589417 - Donghui 1589420 - Donghui 1589483 - Donghui 1589610 - Donghui 1595911 - Donghui 1589668 - Donghui 1589666 - Donghui 1589662 - Donghui 1589604 - Donghui 1589600 - Donghui 1589286 - David 1589469 - Donghui 1604808 - Donghui 1604814 - Donghui 1604823 - Donghui 1604827 - Donghui 1604835 - Donghui 1604874 - Donghui 1604902 - Donghui 1604923 - Donghui 1605436 - David Appendix 2: GO Ed-MOD collaboration SF items - MOD curator(s) involved 907476 - Val 1493227 - Pascale 1567822 - Alex 1569608 - Kimberly 1587325 - Emily, David, Rama 1595591 - David (Note: "MOD curator" is shorthand for any non-GO-Ed curator)