- About this database
The Arabidopsis thaliana phenome 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 Arabidopsis Phenome Database integrating two novel databases. One is the “RIKEN Phenome Integration of Arabidopsis Mutants”, 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 “Database of Curated Plant Phenome” focusing on the Arabidopsis phenome collected by human curation of published papers, is designed to realize easily both phenotype-to-genome and genome-to-phenotype association studies.
- RIKEN Phenome Integration of Arabidopsis mutants
RIKEN has developed mutants of Arabidopsis thaliana using various methods.
The presented database covers phenotypes of the developed mutants, which are standardized by two ontologies, Plant Ontology(PO) and Phenotipic Quality Ontology(PATO).
Each of observation data is accompanied by hyperlinks to original phenome databases and ontologies (see Fig), and users can easily refer to related information.
- Literature Curated Arabidopsis Phenome
This 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.