https://wiki.geneontology.org/index.php?title=Managers_20Jun07&feed=atom&action=historyManagers 20Jun07 - Revision history2024-03-28T17:23:02ZRevision history for this page on the wikiMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=Managers_20Jun07&diff=52385&oldid=prevGail at 16:42, 30 June 20142014-06-30T16:42:54Z<p></p>
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<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">[[Category:GO_Managers_Meetings]]</ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Participants: Judy Blake, Eurie Hong, Suzi Lewis, Chris Mungall, Jane Lomax, Jen Deegan (nee Clark), Rex Chisholm<br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Participants: Judy Blake, Eurie Hong, Suzi Lewis, Chris Mungall, Jane Lomax, Jen Deegan (nee Clark), Rex Chisholm<br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Agenda/Chair: Chris Mungall<br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Agenda/Chair: Chris Mungall<br></div></td></tr>
</table>Gailhttps://wiki.geneontology.org/index.php?title=Managers_20Jun07&diff=8942&oldid=prevMidori: New page: Participants: Judy Blake, Eurie Hong, Suzi Lewis, Chris Mungall, Jane Lomax, Jen Deegan (nee Clark), Rex Chisholm<br> Agenda/Chair: Chris Mungall<br> Minutes: Midori Harris == Review Acti...2007-06-20T16:27:50Z<p>New page: Participants: Judy Blake, Eurie Hong, Suzi Lewis, Chris Mungall, Jane Lomax, Jen Deegan (nee Clark), Rex Chisholm<br> Agenda/Chair: Chris Mungall<br> Minutes: Midori Harris == Review Acti...</p>
<p><b>New page</b></p><div>Participants: Judy Blake, Eurie Hong, Suzi Lewis, Chris Mungall, Jane Lomax, Jen Deegan (nee Clark), Rex Chisholm<br><br />
Agenda/Chair: Chris Mungall<br><br />
Minutes: Midori Harris<br />
<br />
== Review Action Items from previous meeting ==<br />
'''Suzi:''' Forward John's versioning write-up to the group<br />
<br />
Done.<br />
<br />
'''Reference Genomes group:''' Review meeting agenda that Rex sent out.<br />
'''Rex:''' Forward reviewed agenda to managers.<br />
<br />
See Ref Gen report below; agenda on its way to managers.<br />
<br />
'''Mike:''' Check with Kara at Princeton about venue for Ref Gen meeting.<br />
<br />
Phone call on Friday to sort this out (Mike, Judy, Kara).<br />
<br />
'''Chris:''' Check with John about OBO-Edit bugs (for GO-Cell cross-products).<br />
<br />
Point was to get next beta (i.e. OBO-Edit 2.0) up and running; first couple beta(s) are out but still rather buggy.<br />
<br />
'''David & Chris:''' Discuss writing a paper on the GO-Cell cross-products.<br />
<br />
Carried over.<br />
<br />
'''Amelia (via Midori):''' Link GO database documentation to main web page.<br />
<br />
Done.<br />
<br />
'''Eurie, Chris, & Jane:''' Continue to follow up on GO Tools compilation & contact with Stefan Goetz.<br />
<br />
Followed up briefly; Stefan's not interested in maintaining his own list; his was a one-off for a paper. Only thing to do is check back when paper is published to make sure we have everything he has.<br />
<br />
'''Rex:''' Find out if Ref Gen annotators are conscientiously submitting new term requests.<br />
<br />
Email sent; a few responses came, and said no problems with request sub per se. Rex asked Pascale to graph request activity; it revealed an early burst and then a decline. Rex is forwarding the data to managers.<br />
<br />
Chris mentioned XML tools to do this sort of mining (but I didn't catch all details).<br />
<br />
'''Jane:''' Put RSS feed information from Colin Batchelor on the wiki. (Note: the action item in the minutes says "Put screenshots on the wiki" but Jane recalled the discussion mentioning Colin's email, not screenshots.)<br />
<br />
Colin's email is now on the wiki.<br />
<br />
Also got clarification from Suzi: "Screenshots" refers to material to go in slides. New action item for Jane.<br />
<br />
<pre><br />
Action: Jane to take screenshots of RSC markup and RSS feeds and <br />
put on wiki for people to use in slides.<br />
</pre><br />
<br />
'''Everyone:''' mention RSC's GO markup and RSS feeds in GO talks.<br />
<br />
Assume that people will do so.<br />
<br />
'''Jane:''' Look into using an RSS feed to post daily ontology changes to the outside world.<br />
<br />
GO website tracker item created.<br />
<br />
'''Ben & Jane:''' Prepare GO workshop for Interactome meeting; Ben will attend.<br />
<br />
Jen will do this, because Jane will be on maternity leave. Jen has talked with Ewan Birney, and the workshop will be joint with Reactome. Dates: Aug 29-Sept 1.<br />
<br />
'''EBI staff:''' take GO flyers and GO newsletter to distribute at ISMB/ECCB.<br />
<br />
All in hand.<br />
<br />
'''Judy:''' Launch a web-based journal club to review relevant publications about GO. <br />
<br />
Not done yet, but demo of alternative to Webex at jax coming up on 29th. Still interested!<br />
<br />
== Individual Manager reports ==<br />
<br />
===Ontology Development===<br />
<br />
* Incremental progress on things reported before:<br />
** David has the cardio meeting in hand.<br />
** Transporter changes to go live July 4.<br />
** Work on RNA processing almost done.<br />
<br />
* Plan to resume work on cross-products, starting with GO-cell when David is back next week; Pascale will also get involved; Chris has beeen doing preparatory work.<br />
<br />
===Outreach===<br />
<br />
* Rama mentioned international meeting on rice genomics; see http://www.isrfg2007.com/.<br />
<br />
Judy - lots of politics; don't know whether we should send someone. Gramene?<br />
<br />
<pre><br />
Action: Jen to ask Pankaj whether anyone from Gramene is going.<br />
</pre><br />
<br />
* Working on SOP flowcharts. Top-level chart (manual vs. ISS, IEA) proving challenging.<br />
::Jane - lots of groups have ESTs.<br />
<br />
<pre><br />
Action: Annotation outreach group to include EST annotation in flowchart.<br />
</pre><br />
<br />
===Software===<br />
<br />
* Improving Obol (relevant to cross-products, above) <br />
* Also see User Advocacy and Reference Genomes<br />
<br />
===Reference Genomes===<br />
<br />
* Phone conf last week very good. Reviewed meeting draft agenda; topics include<br />
** How to identify orthologs<br />
** Metrics and how to use them<br />
** Software to supersede Google spreadsheets<br />
:: Sohel has prototypes<br />
** choosing new genes<br />
:: Midori - EBI Industry Programme may get involved in "druggable genome" effort proposed by some pharmas; resulting gene list may be good Ref Gen fodder. Will keep the managers informed of developments (not much expected before Sept.).<br />
<br />
* More meeting details in agenda (in email and on wiki)<br />
<br />
* Rex sent some metrics on how various groups are doing; there are 209 genes as of June; 1/3 - 1/2 of groups have completed the list.<br />
<br />
* Ref Gen will have monthly phone confs; alternate times so UK & US west coast equally inconvenienced.<br />
<br />
===User Advocacy===<br />
<br />
* Meetings to consider<br />
** CAMDA (http://camda.bioinfo.cipf.es/); Joaquin Dopazo: need to hear more from Joaquin about participants, scope, etc.<br />
** EMBRACE workshop: they have funding, but we need more info about workshop content. General info on EMBRACE: http://www.embracegrid.info/<br />
<br />
* AmiGO 1 development coming on apace; release on target for July.<br />
** Seth has added the map2slim CGI, and it's being tested<br />
<br />
==Meetings==<br />
<br />
* SGD curators going to CSH Yeast Cell Biology meeting; Eurie trying for talk slot on GO.<br />
<br />
* Jane - GO talk at Wellcome Trust Advanced Course on functional genomics on Monday.<br />
<br />
==Collaborations and Interactions, active and new==<br />
==Operations and Procedures==<br />
==Staffing and Personnel==<br />
==Budget issues==<br />
==Publications==<br />
<br />
* Current protocols article update: opted for actual deadline of October 15th (tho it will say Nov. 1 in publisher's sysetm. Judy and Midori will be in touch for content contributions!<br />
<br />
* NAR database issue: we definitely want to do an update. Limit is 4 pages. Ideas:<br />
** AmiGO new features<br />
** Suzi: look at newsletters for ideas<br />
::Judy: good idea -- that will focus on what's new, and give us 4 pages<br />
<br />
* OBO-Edit applications note published.<br />
<br />
* Ideas for standalone papers:<br />
** Ontology content changes (including cross-products).<br />
** Reference Genomes effort.<br />
<br />
==Other Current Topics and Concerns==<br />
<br />
==Next call==<br />
'''July 18''' (the 4th is a holinday in the U.S.), usual time. Agenda: Midori; Minutes: Chris.<br />
<br />
== Summary of Action items ==<br />
<br />
*'''Jane:''' Take screenshots of RSC markup and RSS feeds and put on wiki for people to use in slides.<br />
*'''Jen:''' Ask Pankaj whether anyone from Gramene is going to rice meeting.<br />
*'''Annotation outreach group:''' Include EST annotation in flowchart.<br />
<br />
[[GO_Managers_conference_call_minutes|Back to minutes list]]</div>Midori