We have collected various kind of phenotypes, including those of morphology, responsibility to environmental factors. They are standardized by combination of ontology terms and properties. Phenotypes for morphology are standardized using Plant Ontology (PO) or Trait Ontology (TO), with Phenotype Ontology (PATO). PATO is the vocabulary covering terms of characcteristics such as "large" and "long". PO and TO are the vocabularies covering names of organs and developmental stages. Phenotypes of biochemical characteristics or stress tolerance can be expressed using Gene Ontology (GO), ChEBI etc. Some phenotypes are observed under some specific environements such as "long-day condition". Such phenotypes have links to environmental factors standardized and listed in another class.

Plant Ontology, Phenotype Ontology

Phenotypes mentioned in the presented database, such as "long leaf", can be expressed as combinations of "entity" and "quality". Terms of entities and qualities are expressed with ontology terms, to standardize phenotype information. Entities: Names of organs, tissues, development stages. The vocabulary is defined in Plant Ontology(PO). Qualities: Characteristics, attributes of entities. The vocabulary is defined in Phenotype Ontology(PATO).

Plant Ontology, Phenotype Ontology

List of cDNA in locus

For the five organisms (H. sapiens, M. musculus, D. melanogaster, and A. thaliana, C. elegans) other than O. sativa, cDNA sequences were obtained from UniGene database. For the UniGene cDNAs, we chose those sequences that presumably code for mature protein coding sequences (CDSs) according to the annotation. For O. sativa, a full-length 32 k cDNA clone set and information of coding sequences were obtained from the Laboratory of Gene Expression, Department of Molecular Genetics, National Institute of Agrobiological Sciences (Kikuchi et al., 2003; ftp://cdna01.dna.affrc.go.jp/pub/data/CURRENT).
The genomic sequences of H. sapiens, M. musculus, D. melanogaster, and A. thaliana were obtained from NCBI (ftp://ftp.ncbi.nih.gov/genomes/). The genomic sequences of C. elegans and the draft contigs of O. sativa were obtained from Sanger Center (ftp://ftp.sanger.ac.uk/pub/) and TIGR Institute (ftp://ftp.tigr.org/pub/data/Eukaryotic_Projects/o_sativa/annotaion_dbs/pseudomolecules/version_3.0/), respectively.