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Data

This page lists all data sources loaded along with the date the data was downloaded and related publication. NOTE: All external links open in a new window.

Data CategoryOrganismDataSourcePubMedNote
Gene Bos taurus NCBI Genes (RefSeq) NCBI Bos taurus Annotation Release 106 (ARS-UCD1.2) O'Leary et al - PubMed 26553804 NCBI FTP
Bubalus bubalis NCBI Bubalus bubalis Annotation Release 101 (UOA_WB_1) NCBI FTP
Canis lupus familiaris NCBI Canis lupus familiaris Annotation Release 105 (CanFam3.1) NCBI FTP
Capra hircus NCBI Capra hircus Annotation Release 102 (ARS1) NCBI FTP
Equus caballus NCBI Equus caballus Annotation Release 103 (EquCab3.0) NCBI FTP
Felis catus NCBI Felis catus Annotation Release 104 (Felis_catus_9.0) NCBI FTP
Gallus gallus NCBI Gallus gallus Annotation Release 104 (GRCg6a) NCBI FTP
Homo sapiens NCBI Homo sapiens Annotation Release 109 (GRCh38.p12) NCBI FTP
Mus musculus NCBI Mus musculus Annotation Release 106 (GRCm38.p6) NCBI FTP
Ovis aries NCBI Ovis aries Annotation Release 101 (Oar_v3.1) NCBI FTP
Rattus norvegicus NCBI Rattus norvegicus Annotation Release 106 (Rnor_6.0) NCBI FTP
Sus scrofa NCBI Sus scrofa Annotation Release 106 (Sscrofa11.1) NCBI FTP
Bos taurus Ensembl Genes Ensembl Release 95 Cunningham et al - PubMed 30407521 Ensembl Download
Canis lupus familiaris Ensembl Release 95 Ensembl Download
Capra hircus Ensembl Release 95 Ensembl Download
Equus caballus Ensembl Release 95 Ensembl Download
Felis catus Ensembl Release 95 Ensembl Download
Gallus gallus Ensembl Release 95 Ensembl Download
Homo sapiens Ensembl Release 95 Ensembl Download
Mus musculus Ensembl Release 95 Ensembl Download
Ovis aries Ensembl Release 95 Ensembl Download
Rattus norvegicus Ensembl Release 95 Ensembl Download
Sus scrofa Ensembl Release 95 Ensembl Download
Homology B. taurus
C. familiaris
E. caballus
F. catus
G. gallus
H. sapiens
M. musculus
R. norvegicus
S. scrofa		 Orthologue and paralogue relationships Treefam - release 9.0 Schreiber et al - PubMed 24194607 Treefam Download
B. taurus
C. familiaris
C. hircus
E. caballus
F. catus
G. gallus
H. sapiens
M. musculus
O. aries
R. norvegicus
S. scrofa		 Ensembl Compara Vilella et al - PubMed 19029536 Ensembl Biomart
B. taurus
B. bubalis
C. familiaris
C. hircus
E. caballus
F. catus
G. gallus
H. sapiens
M. musculus
O. aries
R. norvegicus
S. scrofa		 OrthoDB release 10 Kriventseva et al - PubMed 30395283 OrthoDB Download
Proteins B. taurus
B. bubalis
C. familiaris
C. hircus
E. caballus
F. catus
G. gallus
H. sapiens
M. musculus
O. aries
R. norvegicus
S. scrofa		 Protein annotation UniProt - Release 2019_02 UniProt Consortium - PubMed 30395287 Uniprot Download
B. taurus
B. bubalis
C. familiaris
C. hircus
E. caballus
F. catus
G. gallus
H. sapiens
M. musculus
O. aries
R. norvegicus
S. scrofa		 Protein domains InterPro Version 72.0 Mitchell et al - PubMed 30398656 InterPro Download
Interactions B. taurus
C. familiaris
C. hircus
E. caballus
G. gallus
H. sapiens
M. musculus
O. aries
R. norvegicus
S. scrofa
 Interactions BioGRID - Version 3.5.170 Oughtred et al - PubMed 30476227 BioGRID Download
B. taurus
C. hircus
E. caballus
H. sapiens
M. musculus
O. aries
R. norvegicus
S. scrofa		 Interactions IntAct 2019-03-22 release Hermjakob H et al - PubMed 14681455 IntAct Download
Ontologies Uber Anatomy Ontology (UBERON) Release Date: 04/15/2017 Mungall et al - PubMed 22293552 UBERON
Mouse Adult Gross Anatomy Ontology Release Date: 11/14/2014 MA
BRENDA Tissue Ontology Release Date: 05/03/2016 Gremse et al - PubMed 21030441 BTO
Clinical Measurement Ontology Release Date: 01/05/2019 Shimoyama et al - PubMed 22654893 CMO
Livestock Breed Ontology Release Date: 01/14/2019 LBO
Livestock Product Trait Ontology Release Date: 09/28/2018 PTO
Vertebrate Trait Ontology Release Date: 12/07/2018 VT
Evidence Ontology Release Date: 03/09/2018 Chibucos et al - PubMed 25052702 ECO
PSI MI Ontology Release Date: 03/06/2019 MI
Gene Ontology Release Date: 03/19/2019 Gene Ontology Consortium - PubMed 27899567 GO
Sequence Ontology Release Date: 03/01/2019 Eilbeck et al - PubMed 15892872 SO
Pathways and Metabolic Reactions B. taurus
C. familiaris
C. hircus
E. caballus
F. catus
G. gallus
H. sapiens
M. musculus
O. aries
R. norvegicus
S. scrofa		 Pathway information KEGG Kanehisa M et al - PubMed 27899662 KEGG Download
B. taurus
B. bubalis
C. familiaris
C. hircus
E. caballus
F. catus
G. gallus
H. sapiens
M. musculus
O. aries
R. norvegicus
S. scrofa		 Pathway information inferred through orthologues from curated human pathways Reactome - version 68 Rigden et al - PubMed 29145629 Reactome Download
Publications B. taurus
B. bubalis
C. familiaris
C. hircus
E. caballus
F. catus
G. gallus
H. sapiens
M. musculus
O. aries
R. norvegicus
S. scrofa		 A mapping from genes to publications NCBI PubMed NCBI Resource Coordinators - PubMed 25398906 NCBI FTP
Variation B. taurus
G. gallus
O. aries
S. scrofa		 QTL data AnimalQTLdb release 36 Hu et al - PubMed 30407520 QTL Download
B. taurus
C. familiaris
C. hircus
E. caballus
F. catus
G. gallus
O. aries		 dbSNP data Ensembl95 Hunt et al - PubMed 30576484 Ensembl Download
Variant Annotations B. taurus
C. familiaris
C. hircus
E. caballus
F. catus
G. gallus
O. aries		 Variant effects predicted on RefSeq and Ensembl using Ensembl Variant Effect Predictor Ensembl95 Hunt et al - PubMed 30576484 Ensembl Download
Assembly B. taurus Chromosome Assembly ARS-UCD1.2 Rosen et al NCBI FTP
B. bubalis UOA_WB_1 Low et al - PubMed 30651564 NCBI FTP
C. familiaris CanFam3.1 Hoeppner et al - PubMed 24625832 NCBI FTP
C. hircus ARS1 Bickhart et al - PubMed 28263316 NCBI FTP
E. caballus EquCab3.0 Kalbfleisch et al - PubMed 30456315 NCBI FTP
F. catus Felis_catus_9.0 Tamazian et al - PubMed 25143822 NCBI FTP
G. gallus GRCg6a International Chicken Genome Sequencing Consortium - PubMed 15592404 NCBI FTP
O. aries Oar_v3.1 Jiang et al - PubMed 24904168 NCBI FTP
S. scrofa Sscrofa11.1 Warr et al NCBI FTP