BovineMine: Data Categories

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
Proteins	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
Interactions	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

Questions? Comments? Concerns? Click Here!

The Bovine Genome Database is supported by the European Union's Seventh Framework Programme for research, technological development and demonstration under grant agreement no. 613689, and has been supported by grants 2007-35616-17882 and 2010-65205-20407 from the USDA National Institute of Food and Agriculture. BGD is hosted at the University of Missouri.

If you have comments or if you wish to report a problem, please contact the Bovine Genome Database Administrator.

Your name:
Your email address:
Subject:
Message:	---- Current page: ---- /bovinemine/dataCategories.do

BovineMine

Data

Genes

Homology

Proteins

Interactions

Ontologies

Gene Ontology Annotation

Pathways

Publications

Variation

Variant Annotations

Gene expression

Assembly