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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

XREFS	GENE	UNIPROT	ENSEMBL
Affy ID	no	no	Yes
Agilent ID	no	no	Yes
ApiDB_CryptoDB ID	Yes	no	no
BioCyc ID	no	Yes	no
BuruList ID	no	Yes	no
CCDS ID	no	no	Yes
CYGD ID	no	Yes	no
CleanEx ID	no	Yes	no
CodeLink ID	no	no	Yes
DIP ID	no	Yes	no
DisProt ID	no	Yes	no
DrugBank ID	no	Yes	no
EC Number	no	Yes	no
ECO2DBASE ID	no	Yes	no
EchoBASE ID	no	Yes	no
EcoCyc ID	Yes	no	no
EcoGene ID	no	Yes	no
Ensembl Gene ID	Yes	no	Yes
Ensembl Transcript ID	no	Yes	no
FlyBase Gene ID	Yes	Yes	Yes
FlyBase Protein ID	no	no	Yes
FlyBase Transcript ID	no	no	Yes
GO - Biological Process	no	Yes	Yes
GO - Cellular Component	no	Yes	Yes
GO - Molecular Function	no	Yes	Yes
GenBank Nucleotide Accession	no	Yes	Yes
GenBank Protein Accession	no	no	Yes
Gene ID	Yes	Yes	Yes
Gene Symbol	no	Yes	no
GeneDB_Spombe ID	no	Yes	no
GeneFarm ID	no	Yes	no
GenomeReviews ID	no	Yes	no
H-Inv Locus ID	no	Yes	no
HAMAP ID	no	Yes	no
HGNC ID	Yes	Yes	Yes
HPA ID	no	Yes	no
HPRD ID	Yes	no	no
IMGT/GENE-DB ID	Yes	no	Yes
IMGT/LIGM-DB ID	no	no	Yes
IPI ID	no	no	Yes
Illumina ID	no	no	Yes
InterPro ID	Yes	Yes	Yes
KEGG Gene ID	no	Yes	no
KEGG Pathway ID	no	Yes	no
LegioList ID	no	Yes	no
Leproma ID	no	Yes	no
ListiList ID	no	Yes	no
MEROPS ID	no	Yes	Yes
MGI ID	Yes	Yes	Yes
MIM ID	no	Yes	Yes
MaizeGDB ID	no	Yes	no
MypuList ID	no	Yes	no
Orphanet ID	no	Yes	no
PANTHER ID	no	Yes	no
PBR ID	Yes	no	no
PDB ID	no	Yes	Yes
PIR ID	no	Yes	no
PIRSF ID	no	Yes	Yes
PRINTS ID	no	Yes	Yes
PROSITE ID	no	Yes	no
PeroxiBase ID	no	Yes	no
Pfam ID	no	Yes	Yes
PharmGKB ID	no	Yes	no
PhotoList ID	no	Yes	no
PptaseDB ID	no	Yes	no
ProDom ID	no	Yes	no
PseudoCAP ID	no	Yes	no
RATMAP ID	Yes	no	no
REBASE ID	no	Yes	no
RGD ID	Yes	Yes	Yes
Reactome ID	no	Yes	no
RefSeq Protein Accession	no	Yes	Yes
RefSeq mRNA Accession	no	no	Yes
Rfam ID	no	no	Yes
SGD ID	Yes	Yes	Yes
SMART ID	no	Yes	Yes
SagaList ID	no	Yes	no
StyGene ID	no	Yes	no
SubtiList ID	no	Yes	no
TAIR ID	Yes	Yes	no
TIGRFAMs ID	no	Yes	Yes
TubercuList ID	no	Yes	no
UCSC ID	no	no	Yes
UniGene ID	no	Yes	Yes
UniProt Accession	Yes	Yes	no
UniProt Entry Name	Yes	Yes	Yes
UniProt Protein Name	no	Yes	no
VEGA Gene ID	no	no	Yes
VEGA Protein ID	no	no	Yes
VEGA Transcript ID	no	no	Yes
WormBase Gene ID	Yes	Yes	no
WormPep Protein ID	no	no	Yes
WormPep Transcript ID	no	Yes	no
Xenbase ID	Yes	no	no
ZFIN ID	Yes	Yes	Yes
dbSNP ID	no	no	Yes
dictyBase ID	no	Yes	no
miRBase ID	no	no	Yes