bioDBnet: Documentation: Database Cross References

Cross references from various databases at ABCC

Some of the databases downloaded at ABCC come with extensive cross references to other databases. bioDBnet makes use of these tables for various conversions and also in dbFind to find the type of any given identifier.

Below is a list of the major databases and their cross references that are used in bioDBnet

XREFSGENEUNIPROTENSEMBL
Affy IDnonoYes
Agilent IDnonoYes
Allergome CodenoYesno
ApiDB_CryptoDB IDYesnono
BioCyc IDnoYesno
CCDS IDnonoYes
CYGD IDnoYesno
CleanEx IDnoYesno
CodeLink IDnonoYes
DIP IDnoYesno
DisProt IDnoYesno
DrugBank Drug IDnoYesno
DrugBank Drug NamenoYesno
EC NumbernoYesno
EchoBASE IDnoYesno
EcoGene IDYesYesno
Ensembl Gene IDYesnoYes
Ensembl Protein IDnonoYes
Ensembl Transcript IDnoYesYes
FlyBase Gene IDYesYesYes
FlyBase Protein IDnonoYes
FlyBase Transcript IDnonoYes
GO - Biological ProcessnoYesYes
GO - Cellular ComponentnoYesYes
GO - Molecular FunctionnoYesYes
GenBank Nucleotide AccessionnoYesYes
GenBank Protein AccessionnonoYes
Gene IDYesYesYes
Gene SymbolnoYesno
Gene Symbol ORFnoYesno
GeneFarm IDnoYesno
H-Inv Locus IDnoYesno
HAMAP IDnoYesno
HGNC IDYesYesYes
HPA IDnoYesno
HPRD IDYesnono
IMGT/GENE-DB IDYesnono
Illumina IDnonoYes
InterPro IDYesYesYes
KEGG Gene IDnoYesno
KEGG Pathway IDnoYesno
KEGG Pathway InfonoYesno
LegioList IDnoYesno
Leproma IDnoYesno
MEROPS IDnoYesYes
MGI IDYesYesYes
MIM IDnoYesYes
MaizeGDB IDnoYesno
Orphanet IDnoYesno
PANTHER IDnoYesno
PBR IDYesnono
PDB IDnoYesYes
PIR IDnoYesno
PIRSF IDnoYesYes
PRINTS IDnoYesYes
PROSITE IDnoYesYes
PeroxiBase IDnoYesno
Pfam IDnoYesYes
PharmGKB Gene IDnoYesno
PptaseDB IDnoYesno
ProDom IDnoYesno
PseudoCAP IDnoYesno
REBASE IDnoYesno
RGD IDYesYesYes
Reactome IDnoYesno
RefSeq Protein AccessionnoYesYes
RefSeq mRNA AccessionnonoYes
RefSeq ncRNA AccessionnonoYes
Rfam IDnonoYes
SGD IDYesYesYes
SMART IDnoYesYes
TAIR IDYesYesno
TCDB IDnoYesno
TIGRFAMs IDnoYesYes
TubercuList IDnoYesno
UCSC IDnoYesYes
UniGene IDnoYesYes
UniProt AccessionYesYesYes
UniProt Entry NamenoYesno
UniProt Protein NamenoYesno
VEGA Gene IDnonoYes
VEGA Protein IDnonoYes
VEGA Transcript IDnonoYes
VectorBase Gene IDYesnono
WormBase Gene IDYesYesYes
WormPep Protein IDnonoYes
XenBase Gene IDYesYesno
ZFIN IDYesYesYes
dictyBase IDnoYesno
miRBase IDnonoYes