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DBGET Overview

1. Web of Molecular Biology Databases

DBGET is the backbone retrieval system for all GenomeNet databases including a number of molecular biology databases that are mirrored at the GenomeNet. DBGET is based on a flat-file view of molecular biology databases, where the database is considered as a collection of entries. Because each entry is given a unique entry name (or an accession number) within a database, the molecular biology databases in the world can be retrieved uniformly by the combination of the database name and the entry name:
database:entry
In KEGG an organism is a collection of genes, which may also be considered as a flat-file database. Any gene or gene product (protein or RNA) in KEGG can thus be specified by the combination of the organism name and the gene name:
organism:gene
When two data entries are related in any way, it is customary to incorporate cross-reference information in the molecular biology databases. Examples include links between sequence data and literature data or between amino acid sequence data and nucleotide sequence data. The link information between two entries is a binary relation represented by:
database1:entry1 --> database2:entry2
LinkDB is a collection of all such direct links in the GenomeNet databases as well as indirect links that are computationally obtained by combining multiple links and/or using links in reverse directions.

2. Database Categories

The DBGET/LinkDB system integrates different databases in different ways depending on the availability of mirroring, keyword indexing, and linking. The databases are thus classified into five categories.

CategoryMain commandsRemark
bgetbfindblink
1. KEGG databasesyesyesyesMirrored at GenomeNet
2. Other DBGET databasesyesyesyes
3. Searchable databases on the WebnoyesyesUsed as Web resources
4. Link-only databases on the Webnonoyes
5. PubMed databaseyesnoyes

3. KEGG Databases (Category 1 Databases)

The KEGG databases at GenomeNet are the following. Most of them are daily updated.

DatabaseContentRemark
brite Functional hierarchies and ontologies KEGG BRITE
pathway Pathway maps KEGG PATHWAY
module KEGG modules
disease Human diseases KEGG DISEASE
drug Drugs KEGG DRUG
environ Crude drugs and health-related substances KEGG ENVIRON
orthology KEGG Orthology (KO) groups KEGG ORTHOLOGY
genome KEGG Organisms KEGG GENOME
mgenome Metagenomes
genes Gene catalogs in high-quality genomes KEGG GENES
dgenes Gene catalogs in draft genomes
egenes Gene catalogs as EST contigs
mgenes Gene catalogs in metagenomes
compound Chemical compounds KEGG COMPOUND
glycan Glycans KEGG GLYCAN
reaction Chemical reactions KEGG REACTION
rpair Reactant pairs and chemical transformations
rclass Reaction class
enzyme Enzyme nomenclature
vgenome Viral genomes Computationally generated
from RefSeq
vgenes Viral genes
expression Microarray gene expression profiles Submitted by authors

4. Other DBGET Databases (Category 2 Databases)

Other databases mirrored at GenomeNet are the following.

DatabaseContentOriginal site
refseq refnuc Nucleotide sequences NCBI
refpep Amino acid sequences
uniprot swissprot ExPASy / EBI
trembl
pdb Protein 3D structures RCSB
pdbstr PDB amino acid sequences Kyoto University
epd Eukaryotic promoters ISREC
motifdic prosite Protein domains and sequence motifs ExPASy
pfam Sanger
pmd Protein mutants NIG
aaindex Amino acid indices Kyoto University
carbbank Glycan structures (no longer updated) Teikyou U / U Georgia
prosdoc PROSITE literature ExPASy

5. Searchable Databases on the Web (Category 3 Databases)

The following databases are search-only databases. The actual contents are retrieved from the original sites.

DatabaseContentOriginal site
insdc genbank Nonredundant database of International
Nucleotide Sequence Database Collaboration
NCBI
ddbj NIG
embl EBI
ncbi-gene Entrez Gene database NCBI
unigene UniGene (EST clusters) database NCBI
ensembl Eukaryotic genome annotation database Ensembl
hgnc Human gene nomenclature HGNC
hmdb Human metabolome database HMDB
go Gene Ontology GO
brc-dna Human cDNA Clones RIKEN BRC-DNA
interpro Protein domains and families EBI
omim Genetic diseases NCBI
pubchem PubChem small molecule database NCBI
chebi ChEBI small molecule database EBI
pdb-ccd PDB hemical Component Dictionary PDB
lipidmaps LIPID Metabolites And Pathways Strategy LIPIDMAPS
lipidbank Natural lipids LipidBank
knapsack Plant secondary metabolites KNApSAcK
3dmet 3D structures of natural metabolites 3DMET
drugbank Drug and target information resource DrugBank
ligandbox Ligand data base open and extensible LigandBox
sider Side effect resource SDIER

References

  1. Kanehisa, M.; Linking databases and organisms: GenomeNet resources in Japan. Trends Biochem Sci. 22, 442-444 (1997). [pubmed]
  2. Fujibuchi, W., Goto, S., Migimatsu, H., Uchiyama, I., Ogiwara, A., Akiyama, Y., and Kanehisa, M.; DBGET/LinkDB: an integrated database retrieval system. Pacific Symp. Biocomputing 1998, 683-694 (1997). [pubmed] [pdf]

    (DBGET has a root in the IDEAS package originally developed for GenBank in the early 1980s)
  3. Kanehisa, M., Klein, P., Greif, P., and DeLisi, C.; Computer analysis and structure prediction of nucleic acids and proteins. Nucleic Acids Res. 12, 417-428 (1984). [pubmed] [pdf]
  4. Kanehisa, M.I.; Los Alamos sequence analysis package for nucleic acids and proteins. Nucleic Acids Res. 10, 183-196 (1982). [pubmed] [pdf]

Last updated: June 17, 2011
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Kyoto University Bioinformatics Center