https://wiki.geneontology.org/index.php?title=Mar2007_ontology_report&feed=atom&action=historyMar2007 ontology report - Revision history2024-03-28T23:01:43ZRevision history for this page on the wikiMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=Mar2007_ontology_report&diff=19406&oldid=prevMidori: Mar2007 GO Ed report moved to Mar2007 ontology report: consistency with other pages2009-04-02T10:53:48Z<p><a href="/Mar2007_GO_Ed_report" class="mw-redirect" title="Mar2007 GO Ed report">Mar2007 GO Ed report</a> moved to <a href="/Mar2007_ontology_report" title="Mar2007 ontology report">Mar2007 ontology report</a>: consistency with other pages</p>
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</table>Midorihttps://wiki.geneontology.org/index.php?title=Mar2007_ontology_report&diff=8428&oldid=prevMidori: /* II. GO Editorial Office activities not represented in part I */2007-07-03T13:45:35Z<p><span dir="auto"><span class="autocomment">II. GO Editorial Office activities not represented in part I</span></span></p>
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</table>Midorihttps://wiki.geneontology.org/index.php?title=Mar2007_ontology_report&diff=8427&oldid=prevMidori: New page: 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...2007-04-03T10:04:23Z<p>New page: 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...</p>
<p><b>New page</b></p><div>Ontology Development & GO Editorial Office Report - March 2007<br />
<br />
===I. Ontology Development===<br />
*SourceForge<br />
**Items opened: 88<br />
**Items closed: 122<br />
***GO Eds: 50<br />
***MOD curators: 37 (details in Appendix 1)<br />
***GO Ed/MOD collaborations: 35 (details in Appendix 2)<br />
**Items still open: 242<br />
***assigned, GO Eds: 46<br />
***assigned, MOD curators: 42<br />
***unassigned: 154<br />
<br />
*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|Sensu main page]] and follow the 'Meeting Notes' link).<br />
<br />
*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 ([[GO-MIT_meeting_notes|meeting notes]] plus managers' call minutes).<br />
<br />
*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).<br />
<br />
*Work continues on transporter terms in the function ontology. Details are on the public wiki (http://wiki.geneontology.org/index.php?title=Transporters).<br />
<br />
*Planning continues for the Padua content meeting on muscle. Erika has identified experts and is working with them to set meeting topics and dates.<br />
<br />
*Other content items resolved<br />
**Protein modification (Jane, John Garavelli)<br />
**Various small things for SourceForge items<br />
<br />
*Other content items in progress <br />
**Resolving disjointness violations in the process ontology (Jane, using file of violations identified by Chris)<br />
**Old plant-related SourceForge items (e.g. gametogenesis) (Jen, Tanya, Donghui)<br />
**Regulation of process terms - check for consistency with process terms (David, using file from Chris)<br />
**Erika has begun work on the 'response to drug' terms<br />
**Erika is trying to investigate how neurogenesis terms and annotations have changed over time<br />
<br />
David & Midori have assigned a number of outstanding SourceForge items<br />
to GO curators (both GO Eds and MOD curators) based on biological<br />
areas of expertise. To continue this work, we need a more complete<br />
list of which curators are willing and able to participate in ontology<br />
development, and what their biological topics of choice are.<br />
<br />
D & M also plan to send an email to the GO list every month to<br />
highlight recent ontology development and work coming up in the near<br />
future. We hope this will improve communication between "traditional"<br />
GO content developers and the rest of the GOC.<br />
<br />
See monthly report in CVS for ontology statistics.<br />
<br />
<br />
===II. GO Editorial Office activities not represented in part I===<br />
<br />
*OBO-Edit working group:<br />
**OBO-Edit 1.1 beta testing continues; a few more bugs have been fixed.<br />
**John is doing lots of work on OBO-Edit 2.0.<br />
**The revised version of the Bioinformatics Applications Note has been accepted.<br />
<br />
*Software hub group (Jane, Amelia):<br />
**AmiGO working group (Jane, Amelia)<br />
***Setting priorities for AmiGO June release<br />
***AmiGO programming (note: this accounts for much of Amelia's time)<br />
<br />
*Advocacy group (Jane):<br />
**Considering merging GO and AmiGO home pages; challenging but Amelia is working on mockups<br />
**Considering ways to improve gohelp response organization<br />
**Usual gohelp traffic<br />
<br />
*Annotation outreach (Jen) (note: much more detail in Jen's group report)<br />
**Flowcharts for annotation procedures in preparation<br />
**Records now available on wiki; see http://gocwiki.geneontology.org/index.php/Text_Version<br />
<br />
*Conferences/meetings<br />
**GO-MIT (see above)<br />
**Planning for muscle content meeting (Jen, Erika; see above)<br />
**TACBAC meeting 11-13th March, Hinxton; see [[Therapeutic_Applications_of_Computational_Biology_and_Chemistry_2007|notes on wiki]]<br />
**GO demo for masters students at EBI, 19 March (Jen)<br />
**Manchester Ontogenesis meeting/talk (21-22nd March) (Jane)<br />
**Genomic disorders meeting 21st-23rd March, Hinxton (Jen attended a half day; not as useful as TACBAC)<br />
<br />
*Anything else<br />
**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)<br />
**IMG mapping in progress (Jane)<br />
**Jen has set up WebEx accounts, and done a bit of training, e.g. for GOA curators<br />
**GO Bibliography now has 1320 entries<br />
<br />
<br />
<pre><br />
Appendix 1: MOD curators' SF items<br />
934950 - Eurie<br />
1483728 - David, Erika<br />
1483863 - David, Erika<br />
1501089 - David, Erika<br />
1501514 - David, Erika<br />
1518671 - Eurie<br />
1620478 - Tanya<br />
1630694 - David, Becky<br />
1636093 - David, Val<br />
1666130 - Eurie<br />
1667284 - David, Doug<br />
1667576 - Donghui<br />
1669385 - David, Doug<br />
1670192 - Donghui, Tanya<br />
1672068 - Donghui<br />
1672084 - Donghui<br />
1674164 - David<br />
1674246 - David<br />
1675925 - David, Becky<br />
1676674 - David, Becky, Alex<br />
1679049 - David<br />
1679163 - Donghui<br />
1679392 - Donghui, David, Tanya<br />
1679401 - Donghui<br />
1679406 - Donghui<br />
1679785 - David, Alex<br />
1680043 - Donghui<br />
1680066 - Donghui<br />
1680075 - Donghui<br />
1680079 - Donghui<br />
1680187 - Donghui<br />
1680678 - David<br />
1680707 - David<br />
1680745 - David<br />
1680797 - David<br />
1684437 - David<br />
1687191 - Donghui<br />
<br />
<br />
Appendix 2: GO Ed-MOD collaboration SF items - MOD curator(s) involved<br />
839253 - Eurie, Val<br />
1003916 - Tanya, Donghui<br />
1370095 - David<br />
1379869 - Eurie, Pascale<br />
1493565 - Eurie, Val<br />
1542601 - Eurie<br />
1585196 - Houg, Rama<br />
1614006 - Karen C, Varsha<br />
1631772 - Petra<br />
1635850 - Karen C<br />
1642843 - Jodi, David<br />
1645569 - Donghui<br />
1648000 - Ruth, Maria<br />
1652533 - Rama, John G<br />
1653166 - Kirill<br />
1653692 - Donghui<br />
1660096 - Donghui<br />
1661774 - Eurie<br />
1661969 - Tanya<br />
1669228 - Alex<br />
1670702 - David, Val<br />
1670707 - David<br />
1672026 - Donghui, Tanya<br />
1674129 - David<br />
1674360 - Alex<br />
1675684 - Rachael<br />
1676054 - Alex<br />
1676208 - Donghui, Peifen, Chris T<br />
1680241 - Donghui<br />
1680932 - Kirill<br />
1681299 - David, Tanya, Rachael<br />
1681629 - Donghui<br />
1687129 - Alex<br />
1688723 - Magdalen (PAMGO), Michelle<br />
1690007 - Rama<br />
<br />
<br />
(Note: "MOD curator" is shorthand for any non-GO-Ed curator)<br />
</pre></div>Midori