Database Description
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Database name
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MicrobeDB.jp
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Alternative name
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- | ||||||
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DOI
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10.18908/lsdba.nbdc01181-000.V002 |
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Version
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Creator
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Creator Name
Ken Kurokawa*  
Creator Affiliation
Center for Information Biology, National Institute of Genetics
Literature Search
Creator Name
Yasukazu Nakamura
Creator Affiliation
Center for Information Biology, National Institute of Genetics
Literature Search
Creator Name
Ikuo Uchiyama
Creator Affiliation
National Institute for Basic Biology
Literature Search
Creator Name
Hiroshi Mori
Creator Affiliation
Center for Information Biology, National Institute of Genetics
Literature Search
Creator Name
Takatomo Fujisawa
Creator Affiliation
Center for Information Biology, National Institute of Genetics
Literature Search
Creator Name
Hirokazu Chiba
Creator Affiliation
National Institute for Basic Biology
Literature Search
Creator Name
Nozomi Yamamoto
Creator Affiliation
School of Life Science, Tokyo Institute of Technology
Creator Name
Shinya Suzuki
Creator Affiliation
School of Life Science, Tokyo Institute of Technology
Creator Name
Hiroyo Nishide
Creator Affiliation
National Institute for Basic Biology
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Contact address
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1111 Yata, Mishima, Shizuoka 41-8540, Japan National Institute of Genetics Center for Information Biology Ken Kurokawa E-mail: 
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Database classification
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Integrated database of microbiological |
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Organism
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Database description
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MicrobeDB.jp is an integrated database of several microbiological datasets (e.g., genes, taxa, and environments) using semantic web technology with a gene/genome -centric approach. |
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Features and manner of utilization of database
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MicrobeDB.jp version 2 (doi: 10.18908/lsdba.nbdc01181-000.V002) is an updated version of MicrobeDB.jp version 1 (doi: 10.18908/lsdba.nbdc01181-000.V001). Since version 1 contains microbial genome, ortholog, metagenome, and culture collection data that were obtained before 2013, we updated these data with reorganizing RDF data structures. Microbial environmental ontology and other ontologies were also updated. These ontologies were used for annotation of the data. The data format of MicrobeDB.jp version 2 are RDF and OWL. Users can use these data by (i) loading the data to Triplestore, and (ii) searching the data using SPARQL. |
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License
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CC BY-SA Detail | ||||||
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Background and funding
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Database Integration Coordination Program, National Bioscience Database Center (NBDC), Japan Science and Technology Agency (JST).
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Reference(s)
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-
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| Original website information | |||||||
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Database maintenance site
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URL of the original website
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http://microbedb.jp/ | ||||||
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Operation start date
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2012/12/12/ (version 1) | ||||||
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Last update date
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2017/02/01 | ||||||
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URL of the portal site
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http://microbedb.jp/ | ||||||
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Whole data download
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- | ||||||
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Referenced database
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NCBI RefSeq, INSDC GenBank, INSDC SRA, NBRC, JCM, NCBI BioProject, NCBI BioSample, NCBI Taxonomy, JGI GOLD, UniProt, PubMed |
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Entry list
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Not available | ||||||
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Query search
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Not available | ||||||
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Web services
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Not available | ||||||
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URL of Web services
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- | ||||||
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Need for user registration
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Not available | ||||||