Mar2007 ontology report

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Ontology Development & GO Editorial Office Report - March 2007

I. Ontology Development

  • SourceForge
    • Items opened: 88
    • Items closed: 122
      • GO Eds: 50
      • MOD curators: 37 (details in Appendix 1)
      • GO Ed/MOD collaborations: 35 (details in Appendix 2)
    • Items still open: 242
      • assigned, GO Eds: 46
      • assigned, MOD curators: 42
      • unassigned: 154
  • Work on the 'sensu' terms continues; "low-hanging fruit" terms now completed, and smaller groups are tackling the outstanding items. As before, detailed progress reports are available on the wiki (go to the Sensu main page and follow the 'Meeting Notes' link).
  • The meeting with the Harvard/MIT group doing information theory-based GO "engineering" was a big success. There was a good exchange of ideas, and we made plans to continue the collaboration. The first step for GO, which is well under way, is to consider a set of example suggestions and make any ontology changes that look reasonable. More information available on wiki (meeting notes plus managers' call minutes).
  • For links between function and process terms, Chris has tried mining biochemical pathways from Reactome. More details in 28 March managers' call minutes (report from David).
  • Planning continues for the Padua content meeting on muscle. Erika has identified experts and is working with them to set meeting topics and dates.
  • Other content items resolved
    • Protein modification (Jane, John Garavelli)
    • 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)
    • Old plant-related SourceForge items (e.g. gametogenesis) (Jen, Tanya, Donghui)
    • Regulation of process terms - check for consistency with process terms (David, using file from Chris)
    • Erika has begun work on the 'response to drug' terms
    • Erika is trying to investigate how neurogenesis terms and annotations have changed over time

David & Midori have assigned a number of outstanding SourceForge items to GO curators (both GO Eds and MOD curators) based on biological areas of expertise. To continue this work, we need a more complete list of which curators are willing and able to participate in ontology development, and what their biological topics of choice are.

D & M also plan to send an email to the GO list every month to highlight recent ontology development and work coming up in the near future. We hope this will improve communication between "traditional" GO content developers and the rest of the GOC.

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.
    • John is doing lots of work on OBO-Edit 2.0.
    • The revised version of the Bioinformatics Applications Note has been accepted.
  • Software hub group (Jane, Amelia):
    • AmiGO working group (Jane, Amelia)
      • Setting priorities for AmiGO June release
      • AmiGO programming (note: this accounts for much of Amelia's time)
  • Advocacy group (Jane):
    • Considering merging GO and AmiGO home pages; challenging but Amelia is working on mockups
    • Considering ways to improve gohelp response organization
    • Usual gohelp traffic
  • Conferences/meetings
    • GO-MIT (see above)
    • Planning for muscle content meeting (Jen, Erika; see above)
    • TACBAC meeting 11-13th March, Hinxton; see notes on wiki
    • GO demo for masters students at EBI, 19 March (Jen)
    • Manchester Ontogenesis meeting/talk (21-22nd March) (Jane)
    • Genomic disorders meeting 21st-23rd March, Hinxton (Jen attended a half day; not as useful as TACBAC)
  • Anything else
    • mesh2go mapping once again in progress; also working with Dietrich Rebholz-Schumann's group at EBI to develop a tool that will partially automate ontology (etc.) mapping (Jane)
    • IMG mapping in progress (Jane)
    • Jen has set up WebEx accounts, and done a bit of training, e.g. for GOA curators
    • GO Bibliography now has 1320 entries


Appendix 1: MOD curators' SF items
934950 - Eurie
1483728 - David, Erika
1483863 - David, Erika
1501089 - David, Erika
1501514 - David, Erika
1518671 - Eurie
1620478 - Tanya
1630694 - David, Becky
1636093 - David, Val
1666130 - Eurie
1667284 - David, Doug
1667576 - Donghui
1669385 - David, Doug
1670192 - Donghui, Tanya
1672068 - Donghui
1672084 - Donghui
1674164 - David
1674246 - David
1675925 - David, Becky
1676674 - David, Becky, Alex
1679049 - David
1679163 - Donghui
1679392 - Donghui, David, Tanya
1679401 - Donghui
1679406 - Donghui
1679785 - David, Alex
1680043 - Donghui
1680066 - Donghui
1680075 - Donghui
1680079 - Donghui
1680187 - Donghui
1680678 - David
1680707 - David
1680745 - David
1680797 - David
1684437 - David
1687191 - Donghui


Appendix 2: GO Ed-MOD collaboration SF items - MOD curator(s) involved
839253 - Eurie, Val
1003916 - Tanya, Donghui
1370095 - David
1379869 - Eurie, Pascale
1493565 - Eurie, Val
1542601 - Eurie
1585196 - Houg, Rama
1614006 - Karen C, Varsha
1631772 - Petra
1635850 - Karen C
1642843 - Jodi, David
1645569 - Donghui
1648000 - Ruth, Maria
1652533 - Rama, John G
1653166 - Kirill
1653692 - Donghui
1660096 - Donghui
1661774 - Eurie
1661969 - Tanya
1669228 - Alex
1670702 - David, Val
1670707 - David
1672026 - Donghui, Tanya
1674129 - David
1674360 - Alex
1675684 - Rachael
1676054 - Alex
1676208 - Donghui, Peifen, Chris T
1680241 - Donghui
1680932 - Kirill
1681299 - David, Tanya, Rachael
1681629 - Donghui
1687129 - Alex
1688723 - Magdalen (PAMGO), Michelle
1690007 - Rama


(Note: "MOD curator" is shorthand for any non-GO-Ed curator)

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