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 |
| Homo sapiens | NCBI Genes (RefSeq) | NCBI Homo sapiens Annotation Release 109 (GRCh38.p12) | O'Leary et al - PubMed 26553804 |
NCBI FTP | |
| Mus musculus | NCBI Genes (RefSeq) | NCBI Mus musculus Annotation Release 106 (GRCm38.p6) | O'Leary et al - PubMed 26553804 |
NCBI FTP | |
| Rattus norvegicus | NCBI Genes (RefSeq) | NCBI Rattus norvegicus Annotation Release 106 (Rnor_6.0) | O'Leary et al - PubMed 26553804 |
NCBI FTP | |
| Sus scrofa | NCBI Genes (RefSeq) | NCBI Sus scrofa Annotation Release 106 (Sscrofa11.1) | 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 |
Ensembl Genes | Ensembl Release 95 Ensembl Release 93 |
Cunningham et al - PubMed 30407521 | ||
|
C. hircus |
Ensembl Genes | Ensembl Release 95 | Cunningham et al - PubMed 30407521 | Ensembl Download | |
|
O. aries |
Ensembl Genes | Ensembl Release 95 | Cunningham et al - PubMed 30407521 | Ensembl Download | |
|
Homo sapiens |
Ensembl Genes | Ensembl Release 95 | Cunningham et al - PubMed 30407521 | Ensembl Download | |
|
Mus musculus |
Ensembl Genes | Ensembl Release 95 | Cunningham et al - PubMed 30407521 | Ensembl Download | |
|
Rattus norvegicus |
Ensembl Genes | Ensembl Release 95 | Cunningham et al - PubMed 30407521 | Ensembl Download | |
|
Sus scrofa |
Ensembl Genes | Ensembl Release 95 | 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 | Cunningham et al - PubMed 30407521 | *SNP arrays and SNP IDs* |
|
| B. taurus | SNP Alias Identifiers | SNPchiMp v.3 | Nicolazzi et al - PubMed 25881165 | SNPchiMp | |
Variant Annotations |
B. taurus | Variant effects predicted on RefSeq and Ensembl using Ensembl Variant Effect Predictor | Ensembl VEP (Release 88) | Cunningham et al - PubMed 30407521 | 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 |
Elsik CG, Unni DR, Diesh CM, Tayal A, Emery ML, Nguyen HN, Hagen DE. Bovine Genome Database: new tools for gleaning function from the Bos taurus genome. Nucleic Acids Res. 2016 Jan 4;44(D1):D834-9. doi: 10.1093/nar/gkv1077. Epub 2015 Oct 19. PubMed PMID: 26481361.
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