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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.


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 (20 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
lipidbank   Molecular information on natural lipids LipidBank
knapsack   Secondary metabolite database KNApSAcK
hmdb   Human metabolome database HMDB
3dmet   3D structures of natural metabolites 3DMET
ligandbox   Ligand data base open and extensible LigandBox
sider   Side effect resource SIDER

4. Link-only Databases on the Web (98 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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