release-updates
Data CategoryDataOrganismSourcePubMedLink

Genome Assembly

 Genome Assembly Bos taurus ARS-UCD1.2 Rosen et al. - PubMed 32191811 NCBI FTP
Genome Assembly Bubalus bubalis NDDB_SH_1 Mintoo et al. - PubMed 30962899 NCBI FTP
Genome Assembly Canis lupus familiaris UU_Cfam_GSD_1.0 Wang et al. - PubMed 33568770 NCBI FTP
Genome Assembly Capra hircus ARS1 Bickhart et al. - PubMed 28263316 NCBI FTP
Genome Assembly Equus caballus EquCab3.0 Kalbfleisch et al. - PubMed 30456315 NCBI FTP
Genome Assembly Felis catus F.catus_Fca126_mat1.0 Bredemeyer et al. - PubMed 33305796 NCBI FTP
Genome Assembly Gallus gallus GRCg6a Warren et al. - PubMed 27852011 NCBI FTP
Genome Assembly Ovis aries ARS-UI_Ramb_v2.0 Davenport et al. - PubMed 35134925 NCBI FTP
Genome Assembly Sus scrofa Sscrofa11.1 Warr et al. - PubMed 32543654 NCBI FTP

Genes

 NCBI Genes (RefSeq) Bos taurus NCBI Bos taurus Annotation Release 106; 11 May 2018 Li et al. - PubMed 33270901 NCBI FTP
Bubalus bubalis NCBI Bubalus bubalis Annotation Release 103; 17 Nov 2021 NCBI FTP
Canis lupus familiaris NCBI Canis lupus familiaris Annotation Release 106; 8 Jan 2021 NCBI FTP
Capra hircus NCBI Capra hircus Annotation Release 102; 8 Sep 2016 NCBI FTP
Equus caballus NCBI Equus caballus Annotation Release 103; 26 Jan 2018 NCBI FTP
Felis catus NCBI Felis catus Annotation Release 105; 10 Nov 2021 NCBI FTP
Gallus gallus NCBI Gallus gallus Annotation Release 104; 17 May 2018 NCBI FTP
Homo sapiens NCBI Homo sapiens Annotation Release 110; 6 Apr 2022 NCBI FTP
Mus musculus NCBI Mus musculus Annotation Release 109; 22 Sep 2020 NCBI FTP
Ovis aries NCBI Ovis aries Annotation Release 104; 3 Jul 2021 NCBI FTP
Rattus norvegicus NCBI Rattus norvegicus Annotation Release 108; 21 Jan 2021 NCBI FTP
Sus scrofa NCBI Sus scrofa Annotation Release 106; 13 May 2017 NCBI FTP
Ensembl Genes Bos taurus Ensembl Release 107; July 2022 Cunningham et al. - PubMed 34791404 Ensembl FTP
Canis lupus familiaris Ensembl FTP
Capra hircus Ensembl FTP
Equus caballus Ensembl FTP
Gallus gallus Ensembl FTP
Homo sapiens Ensembl FTP
Mus musculus Ensembl FTP
Rattus norvegicus
Sus scrofa Ensembl FTP
Felis catus Ensembl Rapid Release Ensembl FTP

Homology

 Orthologues and Paralogues from Ensembl Compara Bos taurus
Canis lupus familiaris
Capra hircus
Equus caballus
Felis catus
Gallus gallus
Homo sapiens
Mus musculus
Rattus norvegicus
Sus scrofa		 Ensembl Release 107; July 2022 Cunningham et al. - PubMed 34791404 Ensembl Biomart
Orthologue Clusters from OrthoDB All Species OrthoDB v11; October 2022 Kuznetsov et al. - PubMed 36350662 OrthoDB Download

Proteins

 Protein annotation Bos taurus
Bubalus bubalis
Canis lupus familiaris
Capra hircus
Equus caballus
Felis catus
Gallus gallus
Homo sapiens
Mus musculus
Ovis aries
Rattus norvegicus
Sus scrofa		 UniProt release 2022_01 UniProt Consortium - PubMed 33237286 UniProt FTP
Protein domains All Species InterPro - Version 88.0 Blum et al. - PubMed 33156333 InterPro FTP

Gene Ontology

 Gene Ontology Annotations See UniProt Protein List UniProt release 2022_01 UniProt Consortium - PubMed 33237286 UniProt FTP
Gene Ontology Gene Ontology Consortium GO release 2021 Dec 15 Gene Ontology Consortium - PubMed 33290552 GOC Download

Pathways

 Pathway information from KEGG All Species KEGG Release 102.0, 1 Apr 2022 Kanehisha et al. - PubMed 33125081 KEGG Download
Pathway information from Reactome Bos taurus
Canis lupus familiaris
Gallus gallus
Homo sapiens
Mus musculus
Rattus norvegicus
Sus scrofa		 Version 81; Release 16 Jun 2022 Gillespie et al. - PubMed 34788843 Reactome Download

Diseases

 Gene-disease associations Homo sapiens OMIM; 14 Jul 2022 Amberger et al. - PubMed 30445645 OMIM Download

Interactions

 BioGRID Bos taurus
Canis lupus familiaris
Capra hircus
Equus caballus
Gallus gallus
Homo sapiens
Mus musculus
Ovis aries
Rattus norvegicus
Sus scrofa		 BioGRID version 4.4.210; 31 May 2022 Oughtred et al. - PubMed 33070389 BioGRID Download
IntAct Bos taurus
Canis lupus familiaris
Capra hircus
Equus caballus
Homo sapiens
Mus musculus
Ovis aries
Rattus norvegicus
Sus scrofa		 IntAct Release 242; February 2022 Del Toro et al. - PubMed 34761267 IntAct Download

Genomic Variation

 QTL Bos taurus
Capra hircus
Equus caballus
Gallus gallus
Ovis aries
Sus scrofa		 AnimalQTLdb Release 47; 25 Apr 2022 Hu et al. - PubMed 34850103 QTL Download
Variants Bos taurus Ensembl Variation Release 107; July 2022 Cunningham et al. - PubMed 34791404 Ensembl FTP
Capra hircus Ensembl FTP
Equus caballus Ensembl FTP
Gallus gallus Ensembl FTP
Sus scrofa Ensembl FTP
Ovis aries European Variation Archive RS Release 3; 24 Feb 2022 Cezard el al. - PubMed 34718739 EVA Download
Variant effects on Ensembl genes Bos taurus Ensembl Variation Release 107; July 2022 Cunningham et al. - PubMed 34791404 Ensembl FTP
Capra hircus Ensembl FTP
Equus caballus Ensembl FTP
Gallus gallus Ensembl FTP
Sus scrofa Ensembl FTP
SNP Array Alias IDs from SNPchiMp v.3 Bos taurus Affymetrix_Axiom_Bovine
GeneSeek_Genomic_Profiler_LD_v1
GeneSeek_Dairy_Ultra_LD_v2
GeneSeek_Genomic_Profiler_HD
GeneSeek_Genomic_Profiler_HD_v2
GeneSeek_Genomic_Profiler_LD_v2
GeneSeek_Genomic_Profiler_LD_v3
ICBF_International_Dairy_and_Beef_v2
ICBF_International_Dairy_and_Beef_v3
Illumina_Bovine3k_BeadChip
Illumina_BovineHD_BeadChip
Illumina_BovineLD_BeadChip
Illumina_BovineLD_v1.1_BeadChip
Illumina_BovineLD_v2_BeadChip
Illumina_BovineSNP50v1_BeadChip
Illumina_BovineSNP50v2_BeadChip		 Nicolazzi et al. - PubMed 25881165 No longer available
Capra hircus IGGC_CaprineSNP50_BeadChip
Equus caballus GeneSeek_EquineSNP65_BeadChip
Illumina_Infinium_EquineSNP50_BeadChip
Gallus gallus Affymetrix_Axiom_Chicken
Ovis aries AgResearch_OvineHD_BeadChip
Illumina_Infinium_Ovine_SNP50_v1_BeadChip
Sus scrofa Affymetrix_Axiom_PorcineHD
GeneSeek-Neogen_Genomic_Profiler_10k_BeadChip
GeneSeek-Neogen_PorcineSNP80_BeadChip
Illumina_Infinium_PorcineSNP60_v1_BeadChip
Illumina_Infinium_PorcineSNP60_v2_BeadChip

Gene Expression

 RNA-seq-based gene expression levels Bos taurus PRJEB14330 Kern et al. - PubMed 30227846 NCBI BioProject
PRJEB25677 Chamberlain et al. - PubMed 26596891 NCBI BioProject
PRJEB27455 Foissac et al. - PubMed 31884969 NCBI BioProject
PRJEB34570 Nolte et al. - PubMed 31824560 NCBI BioProject
PRJEB35127 Dorji et al. - PubMed 33076826 NCBI BioProject
PRJNA263600 Triant et al. - PubMed 32537769 NCBI BioProject
PRJNA294306 Triant et al. - PubMed 32537769 NCBI BioProject
PRJNA379574 Triant et al. - PubMed 32537769 NCBI BioProject
PRJNA665193 Kern et al. - PubMed 33758196 NCBI BioProject
Bubalus bubalis PRJEB25226 Young et al. - PubMed 31428126 NCBI BioProject
PRJEB4351 Low et al. - PubMed 30651564 NCBI BioProject
Canis lupus familiaris PRJNA78827 Hoeppner et al. - PubMed 24625832 NCBI BioProject
PRJNA396033 Megquier et al. - PubMed 31181663 NCBI BioProject
Capra hircus PRJEB23196 Muriuki et al. - PubMed 31749840 NCBI BioProject
PRJEB27455 Foissac et al. - PubMed 31884969 NCBI BioProject
Felis catus PRJNA312519 Visser et al. - PubMed 30171610 NCBI BioProject
Equus caballus PRJEB26787 Gao et al. - PubMed 32512843 NCBI BioProject
PRJEB35307 Kingsley et al. - PubMed 31861495 NCBI BioProject
Gallus gallus PRJEB12891 Kuo et al. - PubMed 28438136 NCBI BioProject
PRJEB14330 Kern et al. - PubMed 30227846 NCBI BioProject
PRJEB27455 Foissac et al. - PubMed 31884969 NCBI BioProject
PRJNA204941 McCarthy et al. - PubMed 31210271 NCBI BioProject
PRJNA665193 Kern et al. - PubMed 33758196 NCBI BioProject
Ovis aries PRJEB19199 Clark et al. - PubMed 28915238 NCBI BioProject
PRJEB6169 Clark et al. - PubMed 28915238 NCBI BioProject
PRJNA414087 Davenport et al. - PubMed 35134925 NCBI BioProject
Sus scrofa PRJEB14330 Kern et al. - PubMed 30227846 NCBI BioProject
PRJEB19268 Derks et al. - PubMed 30231021 NCBI BioProject
PRJEB19386 Warr et al. - PubMed 32543654 NCBI BioProject
PRJEB27455 Foissac et al. - PubMed 31884969 NCBI BioProject
PRJEB37735 Pan et al. - PubMed 34615879 NCBI BioProject
PRJNA311523 Li et al. - PubMed 27646534 NCBI BioProject
PRJNA665193 Kern et al. - PubMed 33758196 NCBI BioProject

FAANG Sequence Annotation

 Chromatin accessibility Bos taurus PRJNA665194 Kern et al. - PubMed 33758196 UC-Davis Server
Capra hircus PRJEB27111 Foissac et al. - PubMed 31884969 FR-AgENCODE
Gallus gallus PRJNA665194 Kern et al. - PubMed 33758196 UC-Davis Server
PRJNA665196 Kern et al. - PubMed 33758196 UC-Davis Server
Sus scrofa PRJEB27111 Foissac et al. - PubMed 31884969 FR-AgENCODE
PRJNA665194 Kern et al. - PubMed 33758196 UC-Davis Server
Chromatin architecture Capra hircus PRJEB27364 Foissac et al. - PubMed 31884969 FR-AgENCODE
Sus scrofa Foissac et al. - PubMed 31884969 FR-AgENCODE
Chromatin state Bos taurus PRJNA665212 Kern et al. - PubMed 33758196 UC-Davis Server
Gallus gallus Kern et al. - PubMed 33758196 UC-Davis Server
Sus scrofa Kern et al. - PubMed 33758196 UC-Davis Server
Pan et al. - PubMed 34615879 UC-Davis Server
CTCF binding Bos taurus PRJNA665197 Kern et al. - PubMed 33758196 UC-Davis Server
Gallus gallus Kern et al. - PubMed 33758196 UC-Davis Server
Sus scrofa Kern et al. - PubMed 33758196 UC-Davis Server
Histone modification Bos taurus PRJNA665199 Kern et al. - PubMed 33758196 UC-Davis Server
PRJNA665209 Kern et al. - PubMed 33758196 UC-Davis Server
PRJNA665214 Kern et al. - PubMed 33758196 UC-Davis Server
PRJNA665216 Kern et al. - PubMed 33758196 UC-Davis Server
Equus caballus PRJEB35307 Kingsley et al. - PubMed 31861495 FAANG Data Portal
PRJEB42315 Kingsley et al. - PubMed 33841506 FAANG Data Portal
Gallus gallus PRJNA665199 Kern et al. - PubMed 33758196 UC-Davis Server
PRJNA665209 Kern et al. - PubMed 33758196 UC-Davis Server
PRJNA665214 Kern et al. - PubMed 33758196 UC-Davis Server
PRJNA665216 Kern et al. - PubMed 33758196 UC-Davis Server
Sus scrofa PRJEB37735 Pan et al. - PubMed 34615879 UC-Davis Server
PRJNA665199 Kern et al. - PubMed 33758196 UC-Davis Server
PRJNA665209 Kern et al. - PubMed 33758196 UC-Davis Server
PRJNA665214 Kern et al. - PubMed 33758196 UC-Davis Server
PRJNA665216 Kern et al. - PubMed 33758196 UC-Davis Server

Publications

 A mapping from genes to publications Bos taurus
Bubalus bubalis
Canis lupus familiaris
Capra hircus
Equus caballus
Felis catus
Gallus gallus
Ovis aries
Sus scrofa		 NCBI PubMed Sayers et al. - PubMed 33095870 NCBI FTP

Ontologies

 Animal Trait Ontology for Livestock Release date: 13 Sep 2018 Meunier-Salaün et al. - HAL hal-02626650 ATOL
BRENDA Tissue Ontology Release date: 26 Oct 2021 Chang et al. - PubMed 33211880 BTO
Cell Ontology Release date: 16 Aug 2022 Diehl et al. - PubMed 27377652 CL
Clinical Measurement Ontology Release date: 13 Aug 2022 Smith et al. - PubMed 24103152 CMO
Environmental Ontology for Livestock Release date: 2016 Meunier-Salaün et al. - HAL hal-02626650 EOL
Evidence Ontology Release date: 5 Aug 2022 Nadendla et al. - PubMed 34986598 ECO
Experimental Factor Ontology Release date: 15 Aug 2022 Malone et al. - PubMed 20200009 EFO
Gene Ontology Release date: 1 Jul 2022 Gene Ontology Consortium - PubMed 27899567 GO
Human Developmental Stage Ontology Release date: 10 Mar 2020 GitHub HSAPDV
Human Phenotype Ontology Release date: 11 Jun 2022 Köhler et al. - PubMed 33264411 HP
Livestock Breed Ontology Release date: 19 Aug 2022 Hu et al. - PubMed 23180796 LBO
Livestock Product Trait Ontology Release date: 16 Dec 2021 Hu et al. - PubMed 30407520 LPT
MONDO Diesease Ontology Release date: 6 Sep 2022 Shefchek et al. - PubMed 31701156 MONDO
Mouse Adult Gross Anatomy Ontology Release date: 7 Feb 2017 Hayamizu et al. - PubMed 26208972 MA
Ontology for Biomedical Investigations Release date: 11 Jul 2022 Bandrowski et al. - PubMed 27128319 OBI
Orphanet Rare Disease Ontology Release date: 1 Jul 2022 Rath et al. - PubMed 22422702 ORDO
Phenotype and Trait Ontology Release date: 31 Aug 2022 Shimoyama et al. - PubMed 22654893 PATO
PSI MI Ontology Release date: 15 Apr 2021 Orchard et al. - PubMed 20013380 PSI-MI
Sequence Ontology Release date: 22 Nov 2021 Eilbeck et al. - PubMed: 15892872 SO
Uber Anatomy Ontology (UBERON) Release date: 19 Aug 2022 Haendel et al. - PubMed 25009735 UBERON
Vertebrate Trait Ontology Release date: 19 Jul 2022 Park et al. - PubMed 23937709 VT