Aims to integrate plant genome-related information from databases (DBs) and the literature. The PGDBj is comprised of three component DBs and a cross-search engine, which provides a seamless search over the contents of the DBs. The three DBs are as follows. (i) The Ortholog DB, providing gene cluster information based on the amino acid sequence similarity. (ii) The Plant Resource DB, integrating the SABRE DB, which provides cDNA and genome sequence resources accumulated and maintained in the RIKEN BioResource Center and National BioResource Projects. (iii) The DNA Marker DB, providing manually or automatically curated information of DNA markers, quantitative trait loci and related linkage maps, from the literature and external DBs. As the PGDBj targets various plant species, including model plants, algae, and crops important as food, fodder and biofuel, researchers in the field of basic biology as well as a wide range of agronomic fields are encouraged to perform searches using DNA sequences, gene names, traits and phenotypes of interest. The PGDBj will return the search results from the component DBs and various types of linked external DBs.

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PGDBj classification

  • Plants

PGDBj specifications

Restrictions to use:
None
Database management system:
MySQL
Data access:
Web user interface
Programming languages:
Javascript, Perl, PHP
Community driven:
No
User data submission:
Not allowed

Publications

  • (Asamizu et al., 2014) Plant Genome DataBase Japan (PGDBj): a portal website for the integration of plant genome-related databases. Plant & cell physiology.
    PMID: 24363285

PGDBj support

Maintainer

Credits

Institution(s)

Department of Plant Genome Research, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan; Center for Transdisciplinary Research, Niigata University, Chuo-ku, Niigata, Japan; LINE Co., Ltd., Tokyo, Japan; RIKEN BioResource Center, Tsukuba, Ibaraki, Japan

Funding source(s)

This work was supported by the Japan Science and Technology Agency (JST) [the Life Science Database Integration Project conducted by the National Bioscience Database Center (NBDC)].

Link to literature

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