General information of database | |||||||
 Database name | MicrobeDB.jp | ||||||
| Alternative name | - | ||||||
| DOI | 10.18908/lsdba.nbdc01181-000.V002 | ||||||
| Version |
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| Creator | |||||||
| Contact address | 1111 Yata, Mishima, Shizuoka 41-8540, Japan | ||||||
| Database classification | Integrated database of microbiological | ||||||
| Organism | |||||||
| Database description | 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. | ||||||
| Features and manner of utilization of database | 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. | ||||||
| License | CC BY-SA
Detail | ||||||
| Background and funding | Database Integration Coordination Program, National Bioscience Database Center (NBDC), Japan Science and Technology Agency (JST). | ||||||
| Reference(s) | |||||||
Original website information | |||||||
| Database maintenance site | |||||||
| URL of the original website | http://microbedb.jp/ | ||||||
| Operation start date | 2012/12/12/ (version 1) | ||||||
| Last update date | 2017/02/01 | ||||||
| URL of the portal site | http://microbedb.jp/ | ||||||
| Whole data download | - | ||||||
| Referenced database | NCBI RefSeq, INSDC GenBank, INSDC SRA, NBRC, JCM, NCBI BioProject, NCBI BioSample, NCBI Taxonomy, JGI GOLD, UniProt, PubMed | ||||||
| Entry list | Not available | ||||||
| Query search | Available | ||||||
| Web services | Not available | ||||||
| URL of Web services | - | ||||||
| Need for user registration | Not available | ||||||
