{"id":155,"date":"2015-05-13T11:54:35","date_gmt":"2015-05-13T02:54:35","guid":{"rendered":"http:\/\/jphenome.info\/?page_id=155"},"modified":"2023-08-04T14:54:46","modified_gmt":"2023-08-04T05:54:46","slug":"aboutarabidopsisphenome","status":"publish","type":"page","link":"https:\/\/jphenome.info\/?page_id=155","title":{"rendered":"\u30b7\u30ed\u30a4\u30cc\u30ca\u30ba\u30ca\u30d5\u30a7\u30ce\u30fc\u30e0\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u306b\u3064\u3044\u3066"},"content":{"rendered":"<p><a title=\"Projects\" href=\"https:\/\/jphenome.info\/?page_id=646\">Projects<\/a>\u00a0&gt;\u00a0<a title=\"Arabidopsis Phenome Database\" href=\"https:\/\/jphenome.info\/?page_id=95\">\u30b7\u30ed\u30a4\u30cc\u30ca\u30ba\u30ca\u30d5\u30a7\u30ce\u30fc\u30e0\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9<\/a>\u00a0&gt;\u00a0about this database<\/p>\n<ul>\n<li><strong>About this database<br \/>\n<\/strong>The<em>\u00a0Arabidopsis thaliana<\/em>\u00a0phenome is the whole set of characteristics expressed in response to genomic, environmental and experimental factors of the most major experimental plant. The huge variety of published data have been accumulated, which is an indispensable resource to improve plant omics studies both on basic and applied research fields. It is also important to link information of bioresources such as mutant lines to the phenome to improve experimental research. Inconstancy among them however has inhibited their effective application. We developed the new\u00a0<em>Arabidopsis<\/em>\u00a0Phenome Database integrating two novel databases. One is the \u201c<a title=\"RIKEN Phenome Integration of Arabidopsis mutants\" href=\"http:\/\/metadb.riken.jp\/metadb\/db\/SciNetS_ria143i\" target=\"_blank\" rel=\"noopener\">RIKEN Phenome Integration of\u00a0<em>Arabidopsis<\/em>\u00a0Mutants<\/a>\u201d, that allows researchers to search mutants developed in RIKEN according to their interests in specified phenotypes to find useful materials for their experimental research. The other, the \u201c<a title=\"Plant Phenome\" href=\"http:\/\/metadb.riken.jp\/metadb\/db\/SciNetS_ria224i\" target=\"_blank\" rel=\"noopener\">Database of Curated Plant Phenome<\/a>\u201d focusing on the\u00a0<em>Arabidopsis<\/em>\u00a0phenome collected by human curation of published papers, is designed to realize easily both phenotype-to-genome and genome-to-phenotype association studies.<\/li>\n<\/ul>\n<ul>\n<li><strong>Manual<\/strong><br \/>\nIn preparation<\/li>\n<\/ul>\n<ul>\n<li><strong>RIKEN Phenome Integration of Arabidopsis mutants<\/strong><br \/>\nRIKEN has developed mutants of\u00a0<em>Arabidopsis thaliana<\/em>\u00a0using various methods.<\/p>\n<ul>\n<ul>\n<li><a title=\"RIKEN Arabidopsis Activation tagging line\" href=\"http:\/\/metadb.riken.jp\/metadb\/db\/SciNetS_ria37i\" target=\"_blank\" rel=\"noopener\">RIKEN Activation tagging line\u00a0<\/a><\/li>\n<li><a title=\"FOX Hunting\" href=\"http:\/\/metadb.riken.jp\/metadb\/db\/SciNetS_ria61i\" target=\"_blank\" rel=\"noopener\">RIKEN Arabidopsis Fox-hunting line<\/a><\/li>\n<li><a title=\"DS tag line\" href=\"http:\/\/metadb.riken.jp\/metadb\/db\/SciNetS_ria278i\" target=\"_blank\" rel=\"noopener\">Ds transposon line<\/a><\/li>\n<\/ul>\n<\/ul>\n<p>The presented database covers phenotypes of the developed mutants, which are standardized by two ontologies,\u00a0<a href=\"https:\/\/database.riken.jp\/item\/cria131u9011i\">Plant Ontology(PO)<\/a>\u00a0and\u00a0<a href=\"https:\/\/database.riken.jp\/item\/cria135u1i\">Phenotipic Quality Ontology(PATO)<\/a>.<br \/>\nEach of\u00a0<a title=\"observation of Arabidopsis phenotype\" href=\"http:\/\/metadb.riken.jp\/metadb\/db\/SciNetS_ria143i\/http:\/\/metadb.riken.jp\/db\/SciNetS_ria143i\/cria143u1i\" target=\"_blank\" rel=\"noopener\">observation data<\/a>\u00a0is accompanied by hyperlinks to original phenome databases and ontologies (see\u00a0<a title=\"fig\" href=\"https:\/\/jphenome.info\/wp-content\/uploads\/2015\/05\/old_phenotype_rdf_small.jpg\" target=\"_blank\" rel=\"noopener\">Fig<\/a>), and users can easily refer to related information.<\/li>\n<li><strong>Literature Curated Arabidopsis Phenome<\/strong><br \/>\nThis literature curation covers Arabidopsis phenotypes collected by careful human curation of published papers.We collected 823 phenotype-gene relationships of varied types of Arabidopsis thaliana 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.Each of standardized phenotypes has links to responsive genes (TAIR Locus Identifier) and PubMed.<\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Projects\u00a0&gt;\u00a0\u30b7\u30ed\u30a4\u30cc\u30ca\u30ba\u30ca\u30d5\u30a7\u30ce\u30fc\u30e0\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u00a0&gt;\u00a0about this database About this database The\u00a0Arabidopsis thaliana\u00a0phenome &hellip; <a href=\"https:\/\/jphenome.info\/?page_id=155\" class=\"more-link\"><span class=\"screen-reader-text\">&#8220;\u30b7\u30ed\u30a4\u30cc\u30ca\u30ba\u30ca\u30d5\u30a7\u30ce\u30fc\u30e0\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u306b\u3064\u3044\u3066&#8221; \u306e<\/span>\u7d9a\u304d\u3092\u8aad\u3080<\/a><\/p>\n","protected":false},"author":3,"featured_media":0,"parent":0,"menu_order":1,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_seopress_robots_primary_cat":"","_seopress_titles_title":"","_seopress_titles_desc":"","_seopress_robots_index":"","_locale":"ja","_original_post":"155","footnotes":""},"class_list":["post-155","page","type-page","status-publish","hentry","ja"],"_links":{"self":[{"href":"https:\/\/jphenome.info\/index.php?rest_route=\/wp\/v2\/pages\/155","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/jphenome.info\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/jphenome.info\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/jphenome.info\/index.php?rest_route=\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/jphenome.info\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=155"}],"version-history":[{"count":13,"href":"https:\/\/jphenome.info\/index.php?rest_route=\/wp\/v2\/pages\/155\/revisions"}],"predecessor-version":[{"id":1409,"href":"https:\/\/jphenome.info\/index.php?rest_route=\/wp\/v2\/pages\/155\/revisions\/1409"}],"wp:attachment":[{"href":"https:\/\/jphenome.info\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=155"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}