<div class="main"><div><p><span style="font-size: 15px;"><font style="font-size: 15px;">The<em> Arabidopsis thaliana</em> phenome is the whole set of characteristics expressedin response to genomic, environmental and experimental factors of the mostmajor experimental plant. The huge variety of published data have beenaccumulated, which is an indispensable resource to improve plant omics studiesboth on basic and applied research fields. It is also important to linkinformation of bioresources such as mutant lines to the phenome to improveexperimental research. Inconstancy among them however has inhibited theireffective application. We developed the new <em>Arabidopsis</em>Phenome Database integrating two novel databases. One is the “<a href="http://database.riken.jp/db/arabidopsis_mutant_phenome">RIKEN PhenomeIntegration of <em>Arabidopsis</em> Mutants</a>”, that allows researchers to search mutants developed in RIKEN accordingto their interests in specified phenotypes to find useful materials for theirexperimental research. The other, the “<a href="http://database.riken.jp/db/curated_plant_phenome">Database of Curated Plant Phenome</a>” focusingon the <em style="mso-bidi-font-style:normal">Arabidopsis</em> phenome collectedby human curation of published papers, is designed to realize easily both phenotype-to-genomeand genome-to-phenotype association studies.<br><br></font></span></p><h3 style="border-left: 5px solid #535d09; color: #535d09; text-indent: 5px; margin-bottom: 5px; background: none repeat scroll 0% 0% #eff7b1;"><font style="font-size: 15px;">Manual <br></font></h3><font style="font-size: 15px;"><strong><br><a href="http://scinets.org/item/cria255s6i">The guide of integrated plant phenome databases</a></strong><br><br>Download <a href="/item/RIA00143~swf~tutorial_plant_phenome_db-Dg-doi.pdf">PDF file</a> : last updated <span style="font-size:9.0pt" lang="EN-US">10 July 2013</span><br><br><br><h3 style="border-left: 5px solid #535d09; color: #535d09; text-indent: 5px; margin-bottom: 5px; background: none repeat scroll 0% 0% #eff7b1;">RIKEN Phenome Integration of Arabidopsis mutants</h3><br><p>RIKEN has developed mutants of <em>Arabidopsis thaliana</em> using various methods.</p><ul><li><a href="/item/cria37u1i">RIKEN Activation tagging line </a></li><li><a href="/item/cria61u1i">RIKEN Arabidopsis Fox-hunting line</a></li><li><a href="/item/cria278u1i">Ds transposon line</a></li></ul><p>The presented database covers phenotypes of the developed mutants, which are standardized by two ontologies, <a href="/item/cria131u9011i ">Plant Ontology(PO)</a> and <a href="/item/cria135u1i">Phenotipic Quality Ontology(PATO)</a>.</p><p>Each of <a href="/item/cria143u2i">observation data</a> is accompanied by hyperlinks to original phenome databases and ontologies (see <a href="/sw/download/ria143i%7Eswf%7Eold_phenotype_rdf_small.jpg">Fig</a>), and users can easily refer to related information.</p> <br><br><h3 style="border-left: 5px solid #535d09; color: #535d09; text-indent: 5px; margin-bottom: 5px; background: none repeat scroll 0% 0% #eff7b1;">Literature Curated Arabidopsis Phenome<br></h3><strong><br><br></strong><strong>This literature curation covers <em>Arabidopsis</em> phenotypes collected by careful human curation of published papers.</strong><br><br>We collected 823 phenotype-gene relationships of varied types of <em>Arabidopsis thaliana </em>phenotypes, such as those for morphology, seed productivity, responsibility to environment, etc. Each phenotype is standardized using six public ontologies. Users can perform efficient searches of genetic data with phenotypic keywords.<br><br><p>Each of <a href="/item/cria224u3i"> standardized phenotypes</a> has links to responsive genes (TAIR Locus Identifier) and PubMed.</p></font></div></div> The RIKEN integrated database of mammals 理研哺乳類統合プロジェクト