help  | release-updates

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 CategoryDataOrganismSourcePubMedLink
Gene NCBI Genes (RefSeq) Bos taurus NCBI Bos taurus Annotation Release 106 (ARS-UCD1.2) Rosen et al. - PubMed 32191811
O'Leary et al. - PubMed 26553804
NCBI FTP
Bubalus bubalis NCBI Bubalus bubalis Annotation Release 101 (UOA_WB_1) Low et al. - PubMed 30651564
O'Leary et al. - PubMed 26553804
NCBI FTP
Canis lupus familiaris NCBI Canis lupus familiaris Annotation Release 105 (CanFam3.1) Hoeppner et al. - PubMed 24625832
O'Leary et al. - PubMed 26553804
NCBI FTP
Capra hircus NCBI Capra hircus Annotation Release 102 (ARS1) Bickhart et al. - PubMed 28263316
O'Leary et al. - PubMed 26553804
NCBI FTP
Equus caballus NCBI Equus caballus Annotation Release 103 (EquCab3.0) Kalbfleisch et al. - PubMed 30456315
O'Leary et al. - PubMed 26553804
NCBI FTP
Felis catus NCBI Felis catus Annotation Release 104 (Felis_catus_9.0) Tamazian et al. - PubMed 25143822
O'Leary et al. - PubMed 26553804
NCBI FTP
Gallus gallus NCBI Gallus gallus Annotation Release 104 (GRCg6a) International Chicken Genome Sequencing Consortium - PubMed 15592404
O'Leary et al. - PubMed 26553804
NCBI FTP
Homo sapiens NCBI Homo sapiens Annotation Release 109 (GRCh38.p12) Jain et al. - PubMed 29431738
O'Leary et al. - PubMed 26553804
NCBI FTP
Mus musculus NCBI Mus musculus Annotation Release 106 (GRCm38.p6) Church et al. - PubMed 19468303
O'Leary et al. - PubMed 26553804
NCBI FTP
Ovis aries NCBI Ovis aries Annotation Release 101 (Oar_v3.1) Jiang et al. - PubMed 24904168
O'Leary et al. - PubMed 26553804
NCBI FTP
Rattus norvegicus NCBI Rattus norvegicus Annotation Release 106 (Rnor_6.0) Gibbs et al. - PubMed 15057822
O'Leary et al. - PubMed 26553804
NCBI FTP
Sus scrofa NCBI Sus scrofa Annotation Release 106 (Sscrofa11.1) Warr et al. - PubMed 32543654
O'Leary et al. - PubMed 26553804
NCBI FTP
Ensembl Genes Bos taurus Ensembl Release 100; 29 April 2020 Howe et al. - PubMed 33137190 Ensembl Download
Canis lupus familiaris Ensembl Download
Capra hircus Ensembl Download
Equus caballus Ensembl Download
Felis catus Ensembl Download
Gallus gallus Ensembl Download
Homo sapiens Ensembl Download
Mus musculus Ensembl Download
Ovis aries Ensembl Download
Rattus norvegicus Ensembl Download
Sus scrofa Ensembl Download
Homology Orthologue and paralogue relationships B. taurus
C. familiaris
C. hircus
E. caballus
F. catus
G. gallus
H. sapiens
M. musculus
O. aries
R. norvegicus
S. scrofa
Ensembl Compara. Ensembl Release 100; 29 April 2020 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 10.1; 21 January 2020 Kriventseva et al. - PubMed 30395283 OrthoDB Download
Proteins Protein annotation B. taurus
B. bubalis
C. familiaris
C. hircus
E. caballus
F. catus
G. gallus
H. sapiens
M. musculus
O. aries
R. norvegicus
S. scrofa
UniProt release 2020_02, 22 April 2020 UniProt Consortium - PubMed 33237286 Uniprot Download
Protein domains B. taurus
B. bubalis
C. familiaris
C. hircus
E. caballus
F. catus
G. gallus
H. sapiens
M. musculus
O. aries
R. norvegicus
S. scrofa
InterPro version 79.0; 28 April 2020 Blum et al. - PubMed 33156333 InterPro Download
Interactions Interactions B. taurus
C. familiaris
C. hircus
E. caballus
G. gallus
H. sapiens
M. musculus
O. aries
R. norvegicus
S. scrofa
BioGRID release 3.5.185; 25 April 2020 Oughtred et al. - PubMed 33070389 BioGRID Download
B. taurus
C. familiaris
C. hircus
E. caballus
H. sapiens
M. musculus
O. aries
R. norvegicus
S. scrofa
IntAct v.4.2.14; 2 May 2020 Orchard et al. - PubMed 24234451 IntAct Download
Ontologies Uber Anatomy Ontology (UBERON) Release date: 22 November 2019 Mungall et al. - PubMed 22293552 UBERON
Mouse Adult Gross Anatomy Ontology Release date: 7 February 2017 Musen - PubMed 22081220 MA
BRENDA Tissue Ontology Release date: 11 May 2019 Gremse et al. - PubMed 21030441 BTO
Clinical Measurement Ontology Release date: 8 March 2019 Shimoyama et al. - PubMed 22654893 CMO
Livestock Breed Ontology Release date: 26 March 2020 Musen - PubMed 22081220 LBO
Livestock Product Trait Ontology Release date: 28 September 2018 Musen - PubMed 22081220 PTO
Vertebrate Trait Ontology Release date: 3 April 2019 Musen - PubMed 22081220 VT
Evidence Ontology Release date: 1 May 2020 Chibucos et al. - PubMed 25052702 ECO
PSI MI Ontology Release date: 8 May 2020 Musen - PubMed 22081220 MI
Gene Ontology Release date: 2 May 2020 Gene Ontology Consortium - PubMed 27899567 GO
Sequence Ontology Release date: 13 May 2020 Eilbeck et al. - PubMed 15892872 SO
Gene Ontology Annotation Gene Ontology annotations B. taurus
B. bubalis
C. familiaris
C. hircus
E. caballus
F. catus
G. gallus
H. sapiens
M. musculus
O. aries
R. norvegicus
S. scrofa
UniProt release 2020_02, 22 April 2020 UniProt Consortium - PubMed 33237286 Uniprot Download
Pathways and Metabolic Reactions Pathway information B. taurus
C. familiaris
C. hircus
E. caballus
F. catus
G. gallus
H. sapiens
M. musculus
O. aries
R. norvegicus
S. scrofa
KEGG Release 94.2, 1 June 2020 Kanehisa et al. - PubMed 33125081 KEGG Download
Pathway information inferred through orthologues from curated human pathways B. taurus
B. bubalis
C. familiaris
C. hircus
E. caballus
F. catus
G. gallus
H. sapiens
M. musculus
O. aries
R. norvegicus
S. scrofa
Reactome release 3.5.185; 25 April 2020 Jassal et al. - PubMed 31691815 Reactome Download
Publications A mapping from genes to publications B. taurus
B. bubalis
C. familiaris
C. hircus
E. caballus
F. catus
G. gallus
O. aries
S. scrofa
NCBI PubMed Sayers et al. - PubMed 31602479 NCBI FTP
Variation QTL data B. taurus
G. gallus
O. aries
S. scrofa
AnimalQTLdb version 72; 11 March 2020 Hu et al. - PubMed 30407520 QTL Download
SNP data B. taurus
C. familiaris
C. hircus
E. caballus
F. catus
G. gallus
O. aries
S. scrofa
Ensembl Release 100; 29 April 2020 Howe et al. - PubMed 33137190 Ensembl Download
SNP Array Alias IDs from SNPchiMp v.3 B. taurus Affymetrix_Axiom_Bovine
GeneSeek_Genomic_Profiler_LD_v1
GeneSeek_Dairy_Ultra_LD_v2
GeneSeek_Genomic_Profiler_HD
GeneSeek_Genomic_Profiler_HD_v2
GeneSeek_Genomic_Profiler_LD_v2
GeneSeek_Genomic_Profiler_LD_v3
ICBF_International_Dairy_and_Beef_v2
ICBF_International_Dairy_and_Beef_v3
Illumina_Bovine3k_BeadChip
Illumina_BovineHD_BeadChip
Illumina_BovineLD_BeadChip
Illumina_BovineLD_v1.1_BeadChip
Illumina_BovineLD_v2_BeadChip
Illumina_BovineSNP50v1_BeadChip
Illumina_BovineSNP50v2_BeadChip
Nicolazzi et al. - PubMed: 25881165 No longer available
C. hircus IGGC_CaprineSNP50_BeadChip
E. caballus GeneSeek_EquineSNP65_BeadChip
Illumina_Infinium_EquineSNP50_BeadChip
G. gallus Affymetrix_Axiom_Chicken
O. aries AgResearch_OvineHD_BeadChip
Illumina_Infinium_Ovine_SNP50_v1_BeadChip
S. scrofa Affymetrix_Axiom_PorcineHD
GeneSeek-Neogen_Genomic_Profiler_10k_BeadChip
GeneSeek-Neogen_PorcineSNP80_BeadChip
Illumina_Infinium_PorcineSNP60_v1_BeadChip
Illumina_Infinium_PorcineSNP60_v2_BeadChip
Variant effects on Ensembl genes B. taurus
C. familiaris
C. hircus
E. caballus
F. catus
G. gallus
O. aries
S. scrofa
Ensembl Release 100; 29 April 2020 Howe et al. - PubMed 33137190 Ensembl Download
Gene Expression RNA-seq-based gene expression levels B. taurus
B. bubalis
C. familiaris
C. hircus
E. caballus
F. catus
G. gallus
O. aries
S. scrofa
NCBI SRA and BGD Sayers et al. - PubMed 31602479 NCBI FTP
FAANG Histone marks E. caballus FAANG Data Portal; 11 February 2020 Kingsley et al. - PubMed - 31861495 FAANG Download
Disease and Phenotypes Gene-disease associations H. sapiens OMIM; 7 February 2020 Amberger et al. - PubMed 30445645 OMIM Download
Assembly Chromosome Assembly B. taurus ARS-UCD1.2 Rosen et al. - PubMed 32191811 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. - PubMed 32543654 NCBI FTP