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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

C. hircus

O. aries

NCBI Genes (RefSeq) NCBI Annotation Release 105

Pruitt et al - PubMed 24259432

NCBI FTP
B. taurus Official Gene Set v2.0 Bovine Genome Database

Bovine Genome Sequencing and Analysis Consortium - PubMed 19390049

Reese et al - PubMed 21092105

BGD Download

B. taurus

O. aries

Ensembl Genes Ensembl Release 89 Cunningham et al - PubMed 25352552 Ensembl Download

Homology

B. taurus

C. familiaris

C. hircus

E. caballus

H. sapiens

M. musculus

O. aries

R. norvegicus

S. scrofa

Orthologue and paralogue relationships OrthoDB - Version 9.1 Zdobnov et al - PubMed 27899580 OrthoDB Download

B. taurus

C. familiaris

E. caballus

H. sapiens

M. musculus

O. aries

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

C. familiaris

H. sapiens

M. musculus

O. aries

R. norvegicus

S. scrofa

Orthologue and paralogue relationships HomoloGene build 68 NCBI Resource Coordinators - PubMed 25398906 NCBI FTP

Proteins

B. taurus

C. hircus

H. sapiens

M. musculus

O. aries

R. norvegicus

Protein annotation UniProt - Release 2017_08 UniProt Consortium - PubMed 25348405 UniProt FTP

B. taurus

C. hircus

H. sapiens

M. musculus

O. aries

R. norvegicus

Protein domains InterPro Version 64.0 Mitchell et al - PubMed 25428371 InterPro FTP

Interactions

B. taurus

H. sapiens

M. musculus

R. norvegicus

Interactions BioGRID - Version 3.4.151 Chatr-Aryamontri et al - PubMed 25428363 BioGRID Download

B. taurus

C. hircus

H. sapiens

M. musculus

O. aries

R. norvegicus

Interactions IntAct 2017-06-03 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: 12/22/2016 MA
BRENDA Tissue Ontology Release Date: 08/04/2016

Gremse et al - PubMed 21030441

BTO
Clinical Measurement Ontology Release Date: 04/21/2017

Shimoyama et al - PubMed 22654893

CMO
Livestock Breed Ontology Release Date: 04/12/2017 LBO
Livestock Product Trait Ontology Release Date: 03/02/2017 PTO
Vertebrate Trait Ontology Release Date: 03/06/2017 VT
Evidence Ontology Release Date: 05/05/2017

Chibucos et al - PubMed 25052702

ECO
PSI MI Ontology Release Date: 03/24/2017 MI
Gene Ontology Release Date: 05/17/2017

Gene Ontology Consortium - PubMed 27899567

GO
Sequence Ontology Release Date: 05/17/2017

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: 06/06/2017)

Huntley et al - PubMed 25378336

Gene Ontology Consortium - PubMed 25428369

GO Consortium Annotation Download

Pathways

B. taurus

C. hircus

H. sapiens

M. musculus

O. aries

R. norvegicus

Pathway information inferred through orthologues from curated human pathways Reactome - version 60, Apr 2017 Croft et al - PubMed 24243840 Reactome Download

H. sapiens

M. musculus

Pathway information BioCyc - Version 19.5 Caspi et al - PubMed 26527732 BioCyc

B. taurus

C. familiaris

E. caballus

H. sapiens

M. musculus

R. norvegicus

S. scrofa

Pathway information KEGG Kanehisa M et al - PubMed 10592173 KEGG

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 33 (Aug 2017) Hu et al - PubMed 17135205 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
B. taurus HapMap data for Bos taurus HapMap The International HapMap Consortium - Nature HapMap website

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 Kodama et al - PubMed 22009675 NCBI SRA Project Page

Assembly

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_v3.1

Jiang et al - PubMed 24904168

NCBI FTP