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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 Category Organism Data Source PubMed Note

Genes

B. taurus NCBI Genes (RefSeq) NCBI Bos taurus Annotation Release 106 (ARS-UCD1.2)

O'Leary et al - PubMed 26553804

NCBI FTP
B. taurus NCBI Genes (RefSeq) NCBI Bos taurus Annotation Release 105 (UMD3.1.1)

O'Leary et al - PubMed 26553804

NCBI FTP
C. hircus NCBI Genes (RefSeq) NCBI Capra hircus Annotation Release 102 (ARS1)

O'Leary et al - PubMed 26553804

NCBI FTP
O. aries NCBI Genes (RefSeq) NCBI Ovis aries Annotation Release 102 (Oar_v4.0)

O'Leary et al - PubMed 26553804

NCBI FTP
O. aries NCBI Genes (RefSeq) NCBI Ovis aries Annotation Release 101 (Oar_v3.1)

O'Leary et al - PubMed 26553804

NCBI FTP
B. taurus Official Gene Set v2.0 (UMD3.1.1) Bovine Genome Database

Bovine Genome Sequencing and Analysis Consortium - PubMed 19390049

Reese et al - PubMed 21092105

BGD Download

B. taurus

C. hircus

O. aries

Ensembl Genes Ensembl Release 93 Cunningham et al - PubMed 30407521 Ensembl Download

Homology

B. taurus

C. familiaris

E. caballus

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

E. caballus

H. sapiens

M. musculus

O. aries

R. norvegicus

S. scrofa

Orthologue and paralogue relationships Ensembl Compara Vilella et al - PubMed 19029536 Ensembl BioMart

B. taurus

H. sapiens

M. musculus

O. aries

S. scrofa

Orthologue and paralogue relationships ORIS (Orthology Inference Using Synteny) Conant et al

Proteins

B. taurus

C. hircus

H. sapiens

M. musculus

O. aries

R. norvegicus

Protein annotation UniProt - Release 2018_09 UniProt Consortium - PubMed 30395287 UniProt FTP

B. taurus

C. hircus

H. sapiens

M. musculus

O. aries

R. norvegicus

Protein domains InterPro Version 69.0 Mitchell et al - PubMed 30398656 InterPro FTP

Interactions

B. taurus

H. sapiens

M. musculus

O. aries

R. norvegicus

Interactions BioGRID - Version 3.4.164 Oughtred et al - PubMed 30476227 BioGRID Download

B. taurus

C. hircus

H. sapiens

M. musculus

O. aries

R. norvegicus

Interactions IntAct 2018-09-07 release Hermjakob H et al - PubMed 14681455 IntAct FTP

Ontologies

Uber Anatomy Ontology (UBERON) Release Date: 04/25/2017

Mungall et al - PubMed 22293552

UBERON
Mouse Adult Gross Anatomy Ontology Release Date: 10/11/2018 MA
BRENDA Tissue Ontology Release Date: 10/11/2018

Gremse et al - PubMed 21030441

BTO
Clinical Measurement Ontology Release Date: 10/11/2018

Shimoyama et al - PubMed 22654893

CMO
Livestock Breed Ontology Release Date: 10/11/2018 LBO
Livestock Product Trait Ontology Release Date: 10/11/2018 PTO
Vertebrate Trait Ontology Release Date: 10/11/2018 VT
Evidence Ontology Release Date: 10/11/2018

Chibucos et al - PubMed 25052702

ECO
PSI MI Ontology Release Date: 10/11/2018 MI
Gene Ontology Release Date: 10/11/2018

Gene Ontology Consortium - PubMed 27899567

GO
Sequence Ontology Release Date: 10/11/2018

Eilbeck et al - PubMed 15892872

SO

Gene Ontology Annotation

B. taurus

C. hircus

H. sapiens

M. musculus

O. aries

R. norvegicus

Gene Ontology Annotation GOA at UniProt (GOC Validation Date: 2018-07-24)

Huntley et al - PubMed 25378336

Gene Ontology Consortium - PubMed 25428369

GO Consortium Annotation Download

Pathways and Metabolic Reactions

B. taurus

C. familiaris

E. caballus

H. sapiens

M. musculus

R. norvegicus

S. scrofa

Pathway information KEGG Kanehisa M et al - PubMed 27899662 KEGG

B. taurus

C. hircus

H. sapiens

M. musculus

O. aries

R. norvegicus

Pathway information inferred through orthologues from curated human pathways Reactome - version 65 Rigden et al - PubMed 29145629 Reactome Download

H. sapiens

M. musculus

Pathway information GplusE Metabolic Reactions Conant et al

Publications

B. taurus A mapping from genes to publications NCBI PubMed NCBI Resource Coordinators - PubMed 25398906 NCBI FTP

Variation

B. taurus QTL data for Bos taurus AnimalQTLdb release 36 Hu et al - PubMed 30407520 CattleQTLdb Download
B. taurus dbSNP data for Bos taurus dbSNP v146 Sherry et al - PubMed 11125122

NCBI FTP

*SNP arrays and SNP NCBI IDs*

B. taurus SNP Alias Identifiers SNPchiMp v.3 Nicolazzi et al - PubMed 25881165 SNPchiMp
B. taurus dbVar data for Bos taurus dbVar (May, 2017) Lappalainen et al - PubMed 23193291 NCBI FTP

Variant Annotations

B. taurus Variant effects predicted on RefSeq and Ensembl using Ensembl Variant Effect Predictor Ensembl VEP (Release 88) McLaren et al - PubMed 20562413 Ensembl VEP

Gene expression

B. taurus

RNA-seq gene expression data from L1 Dominette 01449 and her relatives NCBI SRA and BGD Kodama et al - PubMed 22009675 NCBI SRA Project Page

Assembly

B. taurus Chromosome Assembly ARS-UCD1.2 Rosen et al NCBI FTP
B. taurus Chromosome Assembly UMD3.1.1 Zimin et al - PubMed 19393038 NCBI FTP
C. hircus Chromosome Assembly ARS1

Bickhart et al - PubMed 28263316

NCBI FTP
O. aries Chromosome Assembly Oar_v4.0

International Sheep Genomics Consortium - PubMed 24904168

NCBI FTP
O. aries Chromosome Assembly Oar_v3.1

Jiang et al - PubMed 24904168

NCBI FTP