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Ontology Development & GO Editorial Office Report - February 2009

===I. Ontology Development===
*SourceForge
**Items opened: 84
**Items closed: 91
***GO Eds: 50
***MOD 11 (details in Appendix 1)
***GO Ed/MOD collaborations: 50 (details in Appendix 2)
**Items still open: 258
***assigned, GO Eds: 86
***assigned, MOD curators: 115
***unassigned: 57

*Content items resolved
**MF-MF and MF-BP regulates links live in gene_ontology_ext.obo (Chris, David, Tanya, Jane)
***For more information, see the [[Jan2009_ontology_report|January ontology development report]] and the [[Managers_21Jan09|January 21st managers' call minutes]]
**More PAMGO terms (Jane)
**Several SourceForge items resolved

*Content items in progress
**Additional work on cross-products within GO -- see [[:Category:Internal_Cross_Products]] and [[Editors_cross-product_implementation_plan]] (David, Midori, Jane, Jen, Chris, Tanya)
**Signal transduction overhaul continuing, as is content meeting planning; latest notes at [[Signaling_Meeting_Minutes_April_2008_-]] (Jen, David)
**Planning continues for small content meeting for prokaryotic electron transport (Rob Gunsalus, working with Jen and rest of electron transport WG)
**Quality control reports generated by Chris (ongoing work)
***Regulation - also see above (David, Tanya)
***Multiple part_of parents (several GO curators, especially Tanya & David)
**Various SourceForge items

*Publications
**Paper from muscle content meeting published (meeting participants, especially Erika, Jen, Giorgio Valle)
::[http://www.ncbi.nlm.nih.gov/pubmed/19178689?dopt=Abstract| PubMed abstract] [http://www.biomedcentral.com/1755-8794/2/6| full text]

*[http://wiki.geneontology.org/index.php/Ontology_publishing_pipeline_2009| Ontology publishing pipeline] revised
**New checks to be put in place -- see go/software/utilities/check-obo-for-standard.release.pl

*Reminder: plan to retire .ontology file format - see [[Managers_21Jan09]]

See monthly report in CVS for ontology statistics.

===II. GO Editorial Office activities not represented in part I===
*Amelia at Berkeley

*OBO-Edit working group:
**OBO-Edit 2 testing -- considerable progress working through testing task list for 2.0 release; plans for final testing and WG sign-off in mid-March
**Also see [http://wiki.geneontology.org/index.php/OBO-Edit_development_Monthly_Report%2C_February_2009| report]

*Advocacy/outreach
**Meeting with Mauno Vihinen to discuss his plan for a mutation ontology. Introduced him to Karen Eilbeck to follow up. (Jen)
**Also see [http://wiki.geneontology.org/index.php/Outreach_February_2009_Report| report]
**Usual gohelp traffic

*Meetings
**Content meeting planning (see above)

*Publications
**Muscle paper (see above)

*Anything else
**GO bibliography has 2544 entries

<pre>
Appendix 1: MOD curators' SF items
2513373 David, Tanya
2523951 David, Tanya
2531604 David, Tanya
2545211 David, Tanya
2565393 Tanya
2568753 David, Tanya
2569392 Tanya
2569613 Tanya
2573254 Tanya
2589176 Tanya
2617157 Harold


Appendix 2: GO Ed-MOD collaboration SF items - MOD curator(s) involved
1806214 Colin
1853360 Val, David
1866852 Colin
1993246 Erika, Paolo Laveder (community expert)
2012346 Julie, Rama
2018086 Julie
2067787 Karen C, Val
2374080 David, Tanya
2391140 Kate
2510017 David
2526210 David, Tanya
2528641 electron transport wg
2528656 Tanya
2550022 Karen C
2560505 transport wg
2573002 Val
2586582 Kate
2590374 John Garavelli
2593252 Maria
2593300 Maria
2593745 Harold
2593932 Alex
2597089 Julie, Rama
2597296 Alex
2597333 Alex
2606668 Harold
2611474 Alex
2625065 Alex
2631894 Doug
2632430 Kate
2637136 Tanya


(Note: "MOD curator" is shorthand for any non-GO-Ed curator)
</pre>

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