Jun2009 ontology report: Difference between revisions
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***Additional progress on [[Cellular_component_processes|Cellular component organization and biogenesis]], in light of internal cross-products | ***Additional progress on [[Cellular_component_processes|Cellular component organization and biogenesis]], in light of internal cross-products | ||
***[[Taxon-GO_Implementation_April_2009_onwards#1st_June|Taxon triggers]] - workflow improved; implementation in progress | ***[[Taxon-GO_Implementation_April_2009_onwards#1st_June|Taxon triggers]] - workflow improved; implementation in progress | ||
***Work on branching organ development (David) | |||
***Electron transport (working group) | ***Electron transport (working group) | ||
***Relationships among multi-organism process regulation terms (Jane, Chris) | ***Relationships among multi-organism process regulation terms (Jane, Chris) | ||
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*OBO-Edit working group: | *OBO-Edit working group: | ||
**See | **See meeting minutes from June [[OEWG_20090602|2]], [[OEWG_20090609|9]], [[OEWG_20090618|18]] and [[OEWG_20090625|25]], and [[OBO-Edit_development_Monthly_Report%2C_June_2009|monthly report]] | ||
*Advocacy/outreach (Jane, Jen) | *Advocacy/outreach (Jane, Jen) |
Latest revision as of 07:14, 10 September 2009
Ontology Development & GO Editorial Office Report - June 2009
I. Ontology Development
- SourceForge
- Items opened: 91
- Items closed: 112 (3 duplicates and one other deleted)
- Items still open: 242
- assigned, GO Eds: 85
- assigned, MOD curators: 103
- unassigned: 54
- Chris visited the EBI GO group on June 10th-11th; the meeting was very productive indeed. The minutes go into more detail, but these are the highlights:
- We're about to test using the has_part relation in a scratch file; Amelia has done draft documentation.
- We worked out a plan to add internal cross-products to the go_write (and therefore also go_ext) file soon. The first ones to go in will be the 'regulates' xps that David & Tanya are working with.
- Content items resolved
- Several SourceForge items resolved
- Content items in progress
- Cross-products - see notes above
- Has_part relationship - see notes above
- Continuing to add function-process part-of links in gene_ontology_write.obo and gene_ontology_ext.obo
- Work continues on overhauling terms related to viruses; mailing list created
- Signal transduction overhaul continuing; content meeting date set (Jen and experts including Sandra Orchard)
- Also continuing
- Additional progress on Cellular component organization and biogenesis, in light of internal cross-products
- Taxon triggers - workflow improved; implementation in progress
- Work on branching organ development (David)
- Electron transport (working group)
- Relationships among multi-organism process regulation terms (Jane, Chris)
- Quality control continues as usual - reports generated by Chris
- Regulation - also see above (David, Tanya)
- Multiple part_of parents (several GO curators, especially Tanya & David)
- Various SourceForge items
- Manuscript in preparation for paper on the regulates relationships on hold due to vacations, meetings, etc. (Midori & Jane so far; David, Chris and Tanya to join in soon)
- Meetings
- Jane gave talk for OBO Foundry meeting (June)
- (Other GO people also attended; they can fill in anything they see fit here.)
- David planning for Society for Developmental Biology meeting (July; poster)
- Jane gave talk for OBO Foundry meeting (June)
- Reminder: plan to retire .ontology file format - see Managers_21Jan09 and GO_Timeline
See monthly report in CVS for ontology statistics.
II. GO Editorial Office activities not represented in part I
- OBO-Edit working group:
- See meeting minutes from June 2, 9, 18 and 25, and monthly report
- Advocacy/outreach (Jane, Jen)
- EBI outreach team planning plant bioinformatics course; Jen contributing GO coverage
- See monthly report
- Meetings
- OBO Foundry meeting June 7-8 (Jane)
- Chris' visit to EBI office (see above)
- Publications
- PAMGO paper "Applying the Gene Ontology in Microbial Annotation" accepted by Trends in Microbiology for publication in July (PAMGO group, plus Jane)
- Anything else
- GO bibliography has 2728 entries