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DBGET is an integrated database retrieval system for major biological databases, which are classified into five categories:
CategoryMain commandsRemark
1. KEGG databases in DBGETyesyesyesMirrored 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
Databases in the third category are integrated for keyword seach, but the actual data are to be obtained from the original sites. Databases in the fourth category are available only in the LinkDB system. PubMed is a link-only database, but the bget page is generated using the NCBI service in order to better integrate with KEGG and other DBGET databases. DBGET search targets are described on this page.

1. KEGG Databases in DBGET (17+1 databases)

Database name Abbre-
Content Remark
kegg pathway path KEGG pathways See KEGG PATHWAY
brite br Functional hierarchies See KEGG BRITE
module md KEGG modules See KEGG MODULE
orthology ko KEGG orthology See KEGG ORTHOLOGY
genomes genome gn KEGG organisms See KEGG GENOME
mgenome mgnm Metagenomes
genes Complete
Gene catalogs in high-quality genomes See KEGG GENES
mgenes Metagenomes   Gene catalogs in metagenomes
ligand compound cpd Chemical compounds See KEGG LIGAND
glycan gl Glycans
reaction rn Chemical Reactions
rclass rc Reaction class
enzyme ec Enzyme nomenclature
network ne Network elements See KEGG NETWORK
variant hsa_var Human gene variants
disease ds Human diseases See KEGG DISEASE
drug dr Drugs See KEGG DRUG
dgroup dg Drug groups
environ ev Health-related substances See KEGG ENVIRON
  expression ex Gene expression profiles Submitted by authors

2. Other DBGET Databases (20 databases)

Database name Abbre-
Content Original site
refseq refnuc rs rsnt NCBI Reference Sequence Database NCBI
refpep rsaa
uniprot swissprot up sp UniProt (Universal Protein Resource) protein sequence database SIB / EBI
trembl tr
refgene rg001 rg OM-RGC: Ocean microbial reference gene catalog EMBL
rg002 IGC: Integrated reference catalog of the human gut microbiome BGI / EMBL
egenes   Gene catalogs generated as EST contigs Kyoto
egenome egnm EST datasets
pdb pdb PDB (Protein Data Bank) 3D structure database RCSB
epd epd Eukaryotic promoters ISREC
motifdic prosite ps Protein domains and families ExPASy
pfam pf EBI
ncbi-cdd ncbi-cdd NCBI
pmd pmd Protein mutants DDBJ
aaindex aaindex1 aax1 Amino acid indices Kyoto
aaindex2 aax2
aaindex3 aax3
pdbstr pdbstr Protein sequences generated from PDB Kyoto
carbbank ccsd Carbohydrate structures Teikyo U /
U Georgia
prosdoc pdoc Prosite literature ExPASy

3. Searchable Databases on the Web (23 databases)

Database name Abbre-
Content Original site
insdc genbank gb Nonredundant database of International Nucleotide Sequence Database Collaboration NCBI
embl emb EBI
ddbj   DDBJ
ncbi-gene   NCBI Entrez Gene database NCBI
unigene   NCBI UniGene (EST clusters) database NCBI
ensembl   Eukaryotic genome annotation database Ensembl
hgnc   Human gene nomenclature HGNC
brc-dna   RIKEN BRC cDNA Cloned Library RIKEN BRC
brc-epd   RIKEN BRC cDNA Cloned Library for Plants
go   Gene Ontology GO
interpro   Protein domains and families EBI
omim   Genetic diseases OMIM
pubchem   NCBI PubChem (small molecules) database NCBI
chebi   EBI ChEBI (small molecules) database EBI
pdb-ccd   PDB Chemical Component Dictionary PDB
lipidmaps   LIPID Metabolites And Pathways Strategy LIPIDMAPS
lipidbank   Molecular information on natural lipids LipidBank
knapsack   Secondary metabolite database KNApSAcK
hmdb   Human metabolome database HMDB
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 SIDER

4. Link-only Databases on the Web (89 databases)

The databases in this category can be found in LinkDB

5. PubMed Database

Database name Abbre-
Content Original site
pubmed pmid Biomedical literature NCBI

Last updated: June 15, 2015
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