Mar2007 ontology report
Ontology Development & GO Editorial Office Report - March 2007
I. Ontology Development
- 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).
- Work continues on transporter terms in the function ontology. Details are on the public wiki (http://wiki.geneontology.org/index.php?title=Transporters).
- 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)
- AmiGO working group (Jane, Amelia)
- 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
- Annotation outreach (Jen) (note: much more detail in Jen's group report)
- Flowcharts for annotation procedures in preparation
- Records now available on wiki; see http://gocwiki.geneontology.org/index.php/Text_Version
- 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)