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InterMine
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<h2 id="supported-data-formats">Supported data formats</h2> <ul><li><a href="/facts/Generic_Model_Organism_Database/gcMmv9gc">Chado</a></li> <li><a href="/facts/General_feature_format/Lh8lDVe4">GFF3</a></li> <li><a href="/facts/FASTA/YetQcbUz">FASTA</a></li> <li><a href="/facts/Gene_Ontology/Grmg6Q8k">GO</a> & gene association files</li> <li><a href="/facts/UniProt/lfDDHjAl">UniProt</a> XML</li> <li>PSI XML (protein interactions, <a href="/facts/Protein_Structure_Initiative/XfxVPDM3">Protein Structure Initiative</a>)</li> <li><a href="/facts/InParanoid/s9JLVXxz">InParanoid</a> orthologs</li> <li><a href="/facts/Ensembl/dEhjvNaA">Ensembl</a></li></ul> <h2 id="clients">Clients</h2> <p>Web clients allow users to access the data programmatically with minimal effort, and are available for <a href="https://search.cpan.org/~intermine/Webservice-InterMine-1.0405/lib/Webservice/InterMine.pm">perl</a>, <a href="https://pythonhosted.org/intermine/">python</a>, <a href="https://rubygems.org/gems/intermine">ruby</a>, <a href="https://alexkalderimis.github.io/imjs/">javascript</a>, <a href="http://intermine.org/intermine/">Java</a>, and <a href="https://github.com/intermine/intermineR">R</a>. Data can also be queried via a <a href="https://play.google.com/store/apps/details?id=org.intermine.app">native Android app</a>. </p> <h2 id="web-application">Web application</h2> <p>The InterMine web application allows creation of custom bioinformatics queries, includes template queries (web forms to run 'canned' queries). Users can upload and operate on lists of data. It is possible to configure/create widgets to analyse lists with graphs and enrichment statistics. </p><p>An admin user can publish new template queries, change report pages and create public lists at any time without any programming. Many aspects of the web app can be configured and branded. </p> <h2 id="current-projects-not-exhaustive-list">Current projects (not exhaustive list)</h2> <p>An up-to-date list of projects can be viewed at the <a href="http://registry.intermine.org/">InterMine Registry</a> </p> <ul><li><a href="/facts/Generic_Model_Organism_Database/gcMmv9gc">Generic Model Organism Database</a></li> <li><a href="http://www.modencode.org">modENCODE</a> <a href="https://web.archive.org/web/20101227221402/http://www.modencode.org/">Archived</a> 2010-12-27 at the <a href="/facts/Wayback_Machine/nmQ3a6JC">Wayback Machine</a></li> <li><a href="http://www.flymine.org">FlyMine</a></li> <li><a href="http://www.humanmine.org">HumanMine</a></li> <li><a href="http://ratmine.mcw.edu">RatMine</a></li> <li><a href="http://yeastmine.yeastgenome.org">YeastMine</a></li> <li><a href="http://targetmine.mizuguchilab.org/">TargetMine</a></li> <li><a href="https://web.archive.org/web/20220617065151/https://mitominer.mrc-mbu.cam.ac.uk/">MitoMiner</a></li> <li><a href="http://www.mousemine.org">MouseMine</a></li> <li><a href="http://zebrafishmine.org/">ZebrafishMine</a></li> <li><a href="http://intermine.wormbase.org/tools/wormmine/begin.do">WormMine</a></li> <li><a href="http://www.cbrc.kaust.edu.sa/indigo/">INDIGO</a></li> <li><a href="https://apps.araport.org/thalemine">ThaleMine</a></li> <li><a href="http://targetmine.mizuguchilab.org/">TargetMine</a></li> <li><a href="https://phytozome.jgi.doe.gov/phytomine/begin.do">PhytoMine</a></li> <li><a href="http://medicmine.jcvi.org">MedicMine</a></li> <li><a href="http://bovinegenome.org/bovinemine/begin.do">BovineMine</a></li> <li><a href="http://hymenopteragenome.org/hymenopteramine/begin.do">HymenopteraMine</a></li> <li><a href="http://mines.legumeinfo.org/soymine/begin.do">SoyMine</a></li> <li><a href="http://mines.legumeinfo.org/beanmine">BeanMine</a></li> <li><a href="http://mines.legumeinfo.org/chickpeamine">ChickpeaMine</a></li> <li><a href="http://intermine.legumefederation.org/legumemine/begin.do">LegumeMine</a></li> <li><a href="http://mines.legumeinfo.org/peanutmine/begin.do">PeanutMine</a></li> <li><a href="http://www.shaare.org.uk/release-1.0/begin.do">Shaare</a></li> <li><a href="http://urgi.versailles.inra.fr/Wheat3BMine/begin.do">Wheat3Bmine</a></li> <li><a href="http://planmine.mpi-cbg.de/planmine/begin.do">PlanMine</a></li> <li><a href="http://urgi.versailles.inra.fr/GrapeMine/begin.do">GrapeMine</a></li> <li><a href="http://urgi.versailles.inra.fr/repetdb">RepetDB</a></li> <li><a href="http://www.xenmine.org/xenmine/begin.do">XenMine</a></li> <li><a href="https://chomine.boku.ac.at/chomine/begin.do">CHOMine</a></li></ul> <h2 id="external-links">External links</h2> <ul><li><a href="http://www.intermine.org">InterMine</a></li> <li><a href="http://www.gen.cam.ac.uk">Department of Genetics, University of Cambridge</a></li> <li><a href="http://www.wellcome.ac.uk/">Wellcome Trust</a></li> <li><a href="http://iodocs.apps.intermine.org/">InterMine API Documentation</a></li></ul> <h2 id="references">References</h2> <ol> <li id="fn:1"><p>"Home". intermine.org. <a href="http://www.intermine.org/" target="_blank">http://www.intermine.org/</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li> <li id="fn:2"><p>Smith, Richard N.; Aleksic, Jelena; et al. (1 December 2012). "InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data". Bioinformatics. 28 (23): 3163–3165. doi:10.1093/bioinformatics/bts577. ISSN 1367-4803. PMC 3516146. PMID 23023984. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3516146" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3516146</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li> </ol>