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 | *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 |