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<a id="top"></a> <div id="siteNotice"></div> <div class="mw-indicators"> </div> <h1 id="firstHeading" class="firstHeading mw-first-heading"><span class="mw-page-title-main">Manager 6Oct10</span></h1> <div id="bodyContent" class="vector-body"> <div id="siteSub" class="noprint">From GO Wiki</div> <div id="contentSub"><div id="mw-content-subtitle"></div></div> <div id="contentSub2"></div> <div id="jump-to-nav"></div> <a class="mw-jump-link" href="#mw-head">Jump to navigation</a> <a class="mw-jump-link" href="#searchInput">Jump to search</a> <div id="mw-content-text" class="mw-body-content mw-content-ltr" lang="en" dir="ltr"><div class="mw-parser-output"><div id="toc" class="toc" role="navigation" aria-labelledby="mw-toc-heading"><input type="checkbox" role="button" id="toctogglecheckbox" class="toctogglecheckbox" style="display:none" /><div class="toctitle" lang="en" dir="ltr"><h2 id="mw-toc-heading">Contents</h2><span class="toctogglespan"><label class="toctogglelabel" for="toctogglecheckbox"></label></span></div> <ul> <li class="toclevel-1 tocsection-1"><a href="#Present:"><span class="tocnumber">1</span> <span class="toctext">Present:</span></a></li> <li class="toclevel-1 tocsection-2"><a href="#Discussion_topics"><span class="tocnumber">2</span> <span class="toctext">Discussion topics</span></a></li> <li class="toclevel-1 tocsection-3"><a href="#Annotation"><span class="tocnumber">3</span> <span class="toctext">Annotation</span></a> <ul> <li class="toclevel-2 tocsection-4"><a href="#Evidence_Proposal"><span class="tocnumber">3.1</span> <span class="toctext">Evidence Proposal</span></a></li> </ul> </li> <li class="toclevel-1 tocsection-5"><a href="#Ref_Genome"><span class="tocnumber">4</span> <span class="toctext">Ref Genome</span></a> <ul> <li class="toclevel-2 tocsection-6"><a href="#Possible_paper_(Kara)"><span class="tocnumber">4.1</span> <span class="toctext">Possible paper (Kara)</span></a></li> </ul> </li> <li class="toclevel-1 tocsection-7"><a href="#Ontology_Development"><span class="tocnumber">5</span> <span class="toctext">Ontology Development</span></a></li> <li class="toclevel-1 tocsection-8"><a href="#Software"><span class="tocnumber">6</span> <span class="toctext">Software</span></a></li> </ul> </div> <h2><span class="mw-headline" id="Present:">Present:</span></h2> <p>David, Judy, Suzi, Paul S, Paul T, Chris, Jane, Pascale, Kara </p> <h2><span class="mw-headline" id="Discussion_topics">Discussion topics</span></h2> <h2><span class="mw-headline" id="Annotation">Annotation</span></h2> <ul><li>Updating annotation documentation</li> <li>Set a date for a regular conf call every other Monday to reduce Doodle polls</li> <li>Working on 'chain of evidence' (need a better name for this - includes much more than chain of evidence - context, background info, multiple annotation inference etc).</li></ul> <h3><span class="mw-headline" id="Evidence_Proposal">Evidence Proposal</span></h3> <p><a rel="nofollow" class="external free" href="http://gocwiki.geneontology.org/index.php/Chain_of_Evidence">http://gocwiki.geneontology.org/index.php/Chain_of_Evidence</a> </p> <h2><span class="mw-headline" id="Ref_Genome">Ref Genome</span></h2> <ul><li>Discussing how to set priorities for ref genome - tree annotations for specific families. Scalable? Could do a few hundred trees before grant.</li> <li>Biocuration meeting next week.</li></ul> <h3><span id="Possible_paper_.28Kara.29"></span><span class="mw-headline" id="Possible_paper_(Kara)">Possible paper (Kara)</span></h3> <p>I was asked to do a write-up on PPOD in for a chapter on inferring evolutionary relationships in Current Protocols in Bioinformatics (www.currentprotocols.com), due November 15. </p><p>However, it occurred to me that we could instead use this as a forum for the phylogenetic-based annotation, specifically the <a rel="nofollow" class="external text" href="http://amigo-sven.princeton.edu/cgi-bin/amigo/phylotree?mode=cluster&key=PTHR10000&dbname=PantherDB">Annotation Tracker</a> that we have been working on, which can end up as a really handy portal to this project for the general community (in addition to us using this as an internal tool). To do this, we'd need to: </p><p>1) be comfortable rolling this out in production to the general public. This would just require a little clean-up (eg hiding the "Not in DB" fields), and adding some additional info to make it more useful to general users. </p><p>2) provide a way for users to query the phylotree pages in a useful way. One idea: from the Gene Product Search Results, we just add a link under the Ref Genome line that links to the correct phylotree page. </p><p>Note that, at least at this point, we don't expect this to be the main face of the project, rather it would be at least one hook in for people to explicitly see the phylogenetic-based annotations in one place, can see our progress, etc. </p> <ul><li>Hold off until we have a better idea how users can navigate tree-inferred annotations</li></ul> <ul><li>ACTIOM: load ancestral annots into labs</li></ul> <h2><span class="mw-headline" id="Ontology_Development">Ontology Development</span></h2> <ul><li>Ruth emailed to request some ontology development meetings - Judy will forward email</li> <li>GOCHE completion - in time for grant? Paper probably be finished in time for renewal in Jan 2011, implementation some time later.</li> <li>Becky started on Friday - working on signaling</li> <li>BP x BP cross-products to be implemented soon (processes involved in other processes)</li> <li>Taxon paper should be published by now - BMC Bioinformatics</li></ul> <h2><span class="mw-headline" id="Software">Software</span></h2> <ul><li>AmiGO 1.8 out soon</li> <li>OBO-Edit 2.1 - addresses outstanding bugs. There will be another maintenance release - 2.2 - before freeze.</li> <li>Have money for 3 one-year positions - Berkeley position filled, two still available at Stanford.</li></ul>    </div> <div class="printfooter" data-nosnippet="">Retrieved from "<a dir="ltr" href="https://wiki.geneontology.org/index.php?title=Manager_6Oct10&oldid=52318">https://wiki.geneontology.org/index.php?title=Manager_6Oct10&oldid=52318</a>"</div></div> <div id="catlinks" class="catlinks" data-mw="interface"><div id="mw-normal-catlinks" class="mw-normal-catlinks"><a href="/Special:Categories" title="Special:Categories">Category</a>: <ul><li><a href="/Category:GO_Managers_Meetings" title="Category:GO Managers Meetings">GO Managers Meetings</a></li></ul></div></div> </div> </div> <div id="mw-navigation"> <h2>Navigation menu</h2> <div id="mw-head"> <nav id="p-personal" class="vector-menu mw-portlet mw-portlet-personal vector-user-menu-legacy" aria-labelledby="p-personal-label" role="navigation" > <h3 id="p-personal-label" class="vector-menu-heading " > <span class="vector-menu-heading-label">Personal tools</span> </h3> <div class="vector-menu-content"> <ul class="vector-menu-content-list"><li id="pt-login" class="mw-list-item"><a href="/index.php?title=Special:UserLogin&returnto=Manager+6Oct10" title="You are encouraged to log in; however, it is not mandatory [o]" accesskey="o"><span>Log in</span></a></li></ul> </div> </nav> <div id="left-navigation"> <nav id="p-namespaces" class="vector-menu mw-portlet mw-portlet-namespaces vector-menu-tabs vector-menu-tabs-legacy" aria-labelledby="p-namespaces-label" role="navigation" > <h3 id="p-namespaces-label" class="vector-menu-heading " > <span class="vector-menu-heading-label">Namespaces</span> </h3> <div class="vector-menu-content"> <ul class="vector-menu-content-list"><li id="ca-nstab-main" class="selected mw-list-item"><a href="/Manager_6Oct10" title="View the content page [c]" accesskey="c"><span>Page</span></a></li><li id="ca-talk" class="new mw-list-item"><a href="/index.php?title=Talk:Manager_6Oct10&action=edit&redlink=1" rel="discussion" title="Discussion about the content page (page does not exist) [t]" accesskey="t"><span>Discussion</span></a></li></ul> </div> </nav> <nav id="p-variants" class="vector-menu mw-portlet mw-portlet-variants emptyPortlet vector-menu-dropdown" aria-labelledby="p-variants-label" role="navigation" > <input type="checkbox" id="p-variants-checkbox" role="button" aria-haspopup="true" data-event-name="ui.dropdown-p-variants" class="vector-menu-checkbox" aria-labelledby="p-variants-label" /> <label id="p-variants-label" aria-label="Change language variant" class="vector-menu-heading " > <span class="vector-menu-heading-label">English</span> </label> <div class="vector-menu-content"> <ul class="vector-menu-content-list"></ul> </div> </nav> </div> <div id="right-navigation"> <nav id="p-views" class="vector-menu mw-portlet mw-portlet-views vector-menu-tabs vector-menu-tabs-legacy" aria-labelledby="p-views-label" role="navigation" > <h3 id="p-views-label" class="vector-menu-heading " > <span class="vector-menu-heading-label">Views</span> </h3> <div class="vector-menu-content"> <ul class="vector-menu-content-list"><li id="ca-view" class="selected mw-list-item"><a href="/Manager_6Oct10"><span>Read</span></a></li><li id="ca-viewsource" class="mw-list-item"><a href="/index.php?title=Manager_6Oct10&action=edit" title="This page is protected.
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