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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:
CategoryMain commandsRemark
bgetbfindblink
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.

Announcement

PRF, BLOCKS, PRODOM, PRINTS and LITDB in "2. Other DBGET databases" have been discontinued from 28th Fubruary 2014, because we could not update them. We are sorry for any inconveniences.


1. KEGG Databases in DBGET (20+3 databases)

Database name Abbre-
viation
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
egenome egnm EST datasets
mgenome mgnm Metagenomes
genes Complete
genomes
org
code
Gene catalogs in high-quality genomes See KEGG GENES
dgenes   Gene catalogs in draft genomes
egenes EST datasets   Gene catalogs generated as EST contigs
mgenes Metagenomes   Gene catalogs in metagenomes
ligand compound cpd Chemical compounds See KEGG LIGAND
glycan gl Glycans
reaction rn Chemical Reactions
rpair rp Reactant pairs
rclass rc Reaction class
enzyme ec Enzyme nomenclature
disease ds Human diseases See KEGG DISEASE
drug dr Drugs See KEGG DRUG
environ ev Health-related substances See KEGG ENVIRON
  expression ex Gene expression profiles Submitted by authors
vgenome vgnm Viral genomes Computationally
generated from RefSeq
vgenes vg Viral gene catalogs

2. Other DBGET Databases (15 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
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 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
prosdoc pdoc Prosite literature ExPASy

3. Searchable Databases on the Web (22 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
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
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 (99 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: February 27, 2014
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