DBGET Search

DBGET	LinkDB	KEGG2

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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.

1. KEGG Databases in DBGET

Database name Abbre-
viation Content Remark

kegg brite br Functional hierarchies See KEGG BRITE

pathway path KEGG pathways See KEGG PATHWAY

module md KEGG modules

disease ds Human diseases See KEGG DISEASE

drug dr Drugs See KEGG DRUG

orthology ko KEGG orthology See KEGG ORTHOLOGY

genome gn KEGG organisms See KEGG GENES

genes Individual
organisms org
code Gene catalogs in high-quality genomes

dgenes Gene catalogs in draft genomes

egenes Gene catalogs generated as EST contigs

ligand compound cpd Chemical compounds See KEGG LIGAND

glycan gl Glycans

reaction rn Chemical Reactions

rpair rp Reactant pairs

enzyme ec Enzyme nomenclature

expression ex Gene expression profiles Submitted by authors

vgenome vgnm Viral genomes Computationally generated
from RefSeq

vgenes vg Viral gene catalogs

ogenes og Organelle gene catalogs

2. Other DBGET 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

prf prf PRF peptide/protein sequence database PRF

pdb pdb PDB (Protein Data Bank) 3D structure database RCSB

epd epd Eukaryotic promoters ISREC

transfac tf Transcription factors (warning: release of Dec 99) BIOBASE

motifdic prosite ps Protein domains and families ExPASy

blocks bl FHCRC

prodom pd PRABI

prints pr UMBER

pfam pf Sanger

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

litdb lit PRF peptide/protein literature PRF

prosdoc pdoc Prosite literature ExPASy

3. Searchable Databases on the Web

Database name Abbre-
viation Content Original site

insdc genbank Nonredundant database of International Nucleotide Sequence Database Collaboration NCBI

embl 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

go Gene Ontology GO

ipi EBI IPI (reference sequence) database EBI

interpro Protein domains and families EBI

omim Genetic diseases NCBI

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

3dmet 3D structures of natural metabolites 3DMET

drugbank Drug and target information resource DrugBank

ligandbox Ligand data base open and extensible LigandBox

4. Link-only Databases on the Web

The databases in this category can be found in LinkDB

5. PubMed Database

Database name Abbre-
viation Content Original site

pubmed Biomedical literature NCBI

Last updated: July 1, 2009

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