ObservStart

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Genetic and epidemiological resear ... </p> <p><a href="/blog/ObservPaper">(Read more)</a></p> </div> <ul class="metainfo"> <li class="metadates">Posted: <span title="2012-04-06T10:34:21+02:00">13 years ago</span> </li> <li class="metaauthor">Author: <a href="/blog/author/mswertz"><span class="trac-author">Morris Swertz</span></a> </li> <li class="metacategories">Categories: <a href="/blog/category/observ">observ</a> <a href="/blog/category/molgenis">molgenis</a> </li> <li> <a href="/blog/ObservPaper">Comments</a> (0) </li> </ul> </div> <div class="blog-post"> <h1 class="blog-title" id="2012/04/06"><a href="/blog/2012/04/06">CHD7 mutation database published</a> </h1> <div class="blog-body"> <p> We are proud with another <a class="ext-link" href="http://www.chd7.org/"><span class="icon"></span>MOLGENIS for the CHARGE syndrome</a> using <a class="ext-link" href="http://www.observ-om.org"><span class="icon"></span>Observ-OM</a> published in <a class="ext-link" href="http://www.ncbi.nlm.nih.gov/pubmed/22461308"><span class="icon"></span>Human Mutation</a>. CHD7 is a member of the chromodomain helicase DNA- ... </p> <p><a href="/blog/2012/04/06">(Read more)</a></p> </div> <ul class="metainfo"> <li class="metadates">Posted: <span title="2012-04-06T10:26:27+02:00">13 years ago</span> <span class="metaupdated"> (Updated: <span title="2012-04-06T10:31:23+02:00">13 years ago</span>) </span> </li> <li class="metaauthor">Author: <a href="/blog/author/mswertz"><span class="trac-author">Morris Swertz</span></a> </li> <li class="metacategories">Categories: <a href="/blog/category/observ">observ</a> <a href="/blog/category/molgenis">molgenis</a> </li> <li> <a href="/blog/2012/04/06">Comments</a> (0) </li> </ul> </div> </div></div><p> </p> <p> The simple system to format and exchange observation data. </p> <h2 id="Background">Background</h2> <p> Observ-OM is a model capture 'any' phenotype observation lead by <a class="ext-link" href="http://www.gen2phen.org/content/phenotype-modelling"><span class="icon"></span>EU-GEN2PHEN</a>. Our mission mission: store individual and summary level observations in a uniform way to enable harmonization and interoperability of phenotypic and genotypic data across human genetics, model organisms and biobanks. Next to the object model we have an tabular exchange format Observ-TAB and user interfaces, search wizard, <a class="ext-link" href="http://www.ontocat.org"><span class="icon"></span>ontology links</a> and Excel import/export. </p> <p> Status: data model finished and in process of publication for community review. </p> <h2 id="Applications">Applications</h2> <p> View and download Observ-OM applications: </p> <ul><li>the <strong>reference implementation</strong> which is available at <a class="ext-link" href="http://www.ebi.ac.uk/microarray-srv/pheno"><span class="icon"></span>http://www.ebi.ac.uk/microarray-srv/pheno</a> (Adamusiak, Parkinson, GEN2PHEN, Swertz) </li><li>the <strong>xQTL workbench</strong> which is available at <a class="ext-link" href="http://www.xqtl.org"><span class="icon"></span>http://www.xqtl.org</a> (Arends, van der Velde) </li><li>the <strong><a class="wiki" href="/wiki/BiobankCatalog">BiobankCatalog</a></strong> by the <a class="ext-link" href="http://www.nbic.nl/support/task-forces/biobanking/"><span class="icon"></span>NBIC Biobanking Task force</a> (Antonakaki, Enckevoort), <a class="ext-link" href="http://www.lifelines.org"><span class="icon"></span>LifeLines</a> (Lops) and <a class="ext-link" href="http://www.bbmriwiki.nl"><span class="icon"></span>BBMRI-NL</a> (Swertz). </li><li>the <strong><a class="ext-link" href="http://www.animaldb.org"><span class="icon"></span>AnimalDB</a></strong> database for tracking animal observations (Roos) </li><li>the <strong>NGS workbench</strong> for tracking all around next generation sequencing experiment by <a class="ext-link" href="http://www.bbmriwiki.nl"><span class="icon"></span>BBMRI-NL</a> (Dijkstra) </li></ul><h2 id="Sourcecode">Source code</h2> <p> The most recent sourcecode of all these projects is available from SVN at <a class="ext-link" href="http://www.molgenis.org/svn/molgenis_apps/trunk"><span class="icon"></span>http://www.molgenis.org/svn/molgenis_apps/trunk</a> </p> <h2 id="Developers">Developers</h2> <p> Observ-OM and Observ-TAB were developed by: </p> <ul><li><a class="ext-link" href="http://wiki.gcc.rug.nl"><span class="icon"></span>UMC Groningen/GCC</a> (Swertz), </li><li><a class="ext-link" href="http://www.ebi.ac.uk/fg"><span class="icon"></span>EBI Hinxton/FG</a> (Adamusiak, Parkinson), </li><li><a class="ext-link" href="http://www.fimm.fi/"><span class="icon"></span>FIMM Helsinki</a> (Muilu) and </li><li><a class="ext-link" href="http://www.le.ac.uk/ge/pages/staff/staff_pages/brookes.html"><span class="icon"></span>U Leicester</a> (Thorisson, Gollapudi, Brookes) </li><li><a class="ext-link" href="http://www.gen2phen.org/content/phenotype-modelling"><span class="icon"></span>other members of EU-GEN2PHEN</a>. </li></ul><p> Applications using Observ-OM are developed by: </p> <ul><li><a class="ext-link" href="http://www.nbic.nl/support/task-forces/biobanking/"><span class="icon"></span>NBIC Biobanking</a> for <a class="wiki" href="/wiki/BiobankCatalog">BiobankCatalog</a> and <a class="missing wiki">SemanticSearch?</a> (Antonakaki, van Enckevort, Marshall, Swertz), </li><li><a class="ext-link" href="http://www.lifelines.org"><span class="icon"></span>LifeLines</a> for <a class="wiki" href="/wiki/BiobankCatalog">BiobankCatalog</a> (Antonakaki, Lops, Swertz) </li><li><a class="ext-link" href="http://www.bioshare.eu"><span class="icon"></span>BioSHARE</a> for biobank data integration (Chao, Swertz) </li><li><a class="ext-link" href="http://www.bbmriwiki.nl"><span class="icon"></span>BBMRI-NL</a> for <a class="wiki" href="/wiki/BiobankCatalog">BiobankCatalog</a> and <a class="wiki" href="/wiki/NgsWorkbench">NgsWorkbench</a> (Antonakaki, Swertz) </li><li><a class="ext-link" href="http://www.rug.nl/fwn/onderzoek/index"><span class="icon"></span>U Groningen</a> for <a class="ext-link" href="http://www.animaldb.org"><span class="icon"></span>AnimalDB</a> (Roos, Boerema, Swertz) </li></ul></div> <div class="trac-modifiedby"> <span><a href="/wiki/ObservStart?action=diff&version=29" title="Version 29 by Morris Swertz">Last modified</a> <a class="timeline" href="/timeline?from=2012-04-06T10%3A32%3A30%2B02%3A00&precision=second" title="See timeline at 2012-04-06T10:32:30+02:00">13 years ago</a></span> <span class="trac-print">Last modified on 2012-04-06T10:32:30+02:00</span> </div> </div> </div> <script type="text/javascript"> jQuery.loadStyleSheet("/chrome/tracfullblog/css/fullblog.css", "text/css"); 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