DBGET Search

DBGET	LinkDB	KEGG2

DBGET is an integrated database retrieval system for major biological databases, which are classified into five categories:

Category Main commands Remark

bget bfind blink

1. KEGG databases in DBGET yes yes yes Mirrored at GenomeNet

2. Other DBGET databases yes yes yes

3. Searchable databases on the Web no yes yes Used as Web resources

4. Link-only databases on the Web no no yes

5. PubMed database yes no yes

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 (18+1 databases)

Database name Abbre-
viation Content Remark

kegg pathway path KEGG pathways KEGG PATHWAY

brite br Functional hierarchies KEGG BRITE

module md KEGG modules KEGG MODULE

orthology ko KEGG orthology KEGG ORTHOLOGY

genes Organisms org
code Genes in KEGG organisms KEGG GENES

Viruses vg Genes in viruses category

Vpept vp Mature peptides in viruses

Addendum ag Genes in addendum category

genome gn KEGG organisms and selected viruses KEGG Organism

mgenes Gene catalogs in metagenomes KEGG Metagenomes

mgenome mgnm Metagenomes

ligand compound cpd Chemical compounds KEGG LIGAND

glycan gl Glycans

reaction rn Chemical Reactions

rclass rc Reaction class

enzyme ec Enzyme nomenclature

network ne Network elements KEGG NETWORK

variant hsa_var Human gene variants

disease ds Human diseases KEGG DISEASE

drug dr Drugs KEGG DRUG

dgroup dg Drug groups

expression ex Gene expression profiles Submitted by authors

2. Other DBGET Databases (19 databases)

Database name Abbre-
viation 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 OM-RGC: Ocean microbial reference gene catalog EMBL

rg002 IGC: Integrated reference catalog of the human gut microbiome BGI / EMBL

rg003 MATOU: Marine Atlas of Tara Oceans Unigenes Tara Oceans

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 (19 databases)

Database name Abbre-
viation 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

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

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

knapsack Secondary metabolite database KNApSAcK

hmdb Human metabolome database HMDB

ligandbox Ligand data base open and extensible LigandBox

sider Side effect resource SIDER

4. Link-only Databases on the Web (85 databases)

The databases in this category can be found in LinkDB

5. PubMed Database

Database name Abbre-
viation Content Original site

pubmed pmid Biomedical literature NCBI

Last updated: July 7, 2021

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