Data Sources and their Data Sets

CATHGENE3D
CDD
Cowpea Crop Ontology
A controlled vocabulary to describe crop traits in cowpea.
Cowpea Crop Ontology
GO
The Gene Ontology (GO) knowledgebase is the world's largest source of information on the functions of genes. This knowledge is both human-readable and machine-readable, and is a foundation for computational analysis of large-scale molecular biology and genetics experiments in biomedical research.
GO
HAMAP
InterMine post-processor
Gene-flanking regions created by the core InterMine post-processor
InterMine gene-flanking regions
Intergenic regions created by the InterMine core post-processor
InterMine intergenic regions
InterPro
InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites.
InterPro data set
Mapping of GO terms to InterPro entries.
InterPro domain GO annotations
LIS Datastore
Black-eyed pea (IT97K-499-35) gene expression atlas from Yao, et al. (2016).
vigun.IT97K-499-35.gnm1.ann1.expr.BWH5.samples.tsv
Black-eyed pea (IT97K-499-35) gene expression atlas from Yao, et al. (2016).
vigun.IT97K-499-35.gnm1.ann1.expr.BWH5.source.tsv
Black-eyed pea (IT97K-499-35) gene expression atlas from Yao, et al. (2016).
vigun.IT97K-499-35.gnm1.ann1.expr.BWH5.values.tsv
CDS ann2 models for the vigun.IT97K-499-35.gnm1 genome
vigun.IT97K-499-35.gnm1.ann2.FD7K.cds_primaryTranscript.fna
CDS models for the vigan.Gyeongwon.gnm3 genome
vigan.Gyeongwon.gnm3.ann1.3Nz5.cds_primaryTranscript.fna
CDS models for the vigan.Shumari.gnm1 genome
vigan.Shumari.gnm1.ann1.8BRS.cds_primaryTranscript.fna
CDS models for the vigra.VC1973A.gnm6 genome
vigra.VC1973A.gnm6.ann1.M1Qs.cds.fna
CDS models for the vigun.CB5-2.gnm1 genome
vigun.CB5-2.gnm1.ann1.0GKC.cds_primaryTranscript.fna
CDS models for the vigun.IT97K-499-35.gnm1 genome
vigun.IT97K-499-35.gnm1.ann1.zb5D.cds_primaryTranscript.fna
CDS models for the vigun.Sanzi.gnm1 genome
vigun.Sanzi.gnm1.ann1.HFH8.cds_primaryTranscript.fna
CDS models for the vigun.Suvita2.gnm1 genome
vigun.Suvita2.gnm1.ann1.1PF6.cds_primaryTranscript.fna
CDS models for the vigun.TZ30.gnm1 genome
vigun.TZ30.gnm1.ann2.59NL.cds_primaryTranscript.fna
CDS models for the vigun.UCR779.gnm1 genome
vigun.UCR779.gnm1.ann1.VF6G.cds_primaryTranscript.fna
CDS models for the vigun.ZN016.gnm1 genome
vigun.ZN016.gnm1.ann2.C7YV.cds_primaryTranscript.fna
Cowpea 1M selected SNPs positions on the vigun.IT97K-499-35.gnm1 genome assembly
vigun.IT97K-499-35.gnm1.mrk.52FC.Cowpea1MSelectedSNPs.gff3
Gene family assignments for Vigna angularis Gyeongwon genes and proteins.
vigan.Gyeongwon.gnm3.ann1.3Nz5.legfed_v1_0.M65K.gfa.tsv
Gene family assignments for Vigna angularis Shumari genes and proteins.
vigan.Shumari.gnm1.ann1.8BRS.legfed_v1_0.M65K.gfa.tsv
Gene family assignments for Vigna radiata VC1973A genes and proteins.
vigra.VC1973A.gnm6.ann1.M1Qs.legfed_v1_0.M65K.gfa.tsv
Gene family assignments for Vigna unguiculata CB5-2 genes and proteins.
vigun.CB5-2.gnm1.ann1.0GKC.legfed_v1_0.M65K.gfa.tsv
Gene family assignments for Vigna unguiculata IT97K-499-35 genes and proteins.
vigun.IT97K-499-35.gnm1.ann2.FD7K.legfed_v1_0.M65K.gfa.tsv
Gene family assignments for Vigna unguiculata Sanzi genes and proteins.
vigun.Sanzi.gnm1.ann1.HFH8.legfed_v1_0.M65K.gfa.tsv
Gene family assignments for Vigna unguiculata Suvita2 genes and proteins.
vigun.Suvita2.gnm1.ann1.1PF6.legfed_v1_0.M65K.gfa.tsv
Gene family assignments for Vigna unguiculata TZ30 genes and proteins.
vigun.TZ30.gnm1.ann2.59NL.legfed_v1_0.M65K.gfa.tsv
Gene family assignments for Vigna unguiculata UCR779 genes and proteins.
vigun.UCR779.gnm1.ann1.VF6G.legfed_v1_0.M65K.gfa.tsv
Gene family assignments for Vigna unguiculata Xiabao_II genes and proteins.
vigun.Xiabao_II.gnm1.ann1.4JFL.legfed_v1_0.M65K.gfa.tsv
Gene family assignments for Vigna unguiculata ZN016 genes and proteins.
vigun.ZN016.gnm1.ann2.C7YV.legfed_v1_0.M65K.gfa.tsv
Gene model annotation for the vigan.Gyeongwon.gnm3 genome
vigan.Gyeongwon.gnm3.ann1.3Nz5.gene_models_main.gff3
Gene model annotation for the vigan.Shumari.gnm1 genome
vigan.Shumari.gnm1.ann1.8BRS.gene_models_main.gff3
Gene model annotation for the vigra.VC1973A.gnm6 genome
vigra.VC1973A.gnm6.ann1.M1Qs.gene_models_main.gff3
Gene model annotation for the vigun.CB5-2.gnm1 genome
vigun.CB5-2.gnm1.ann1.0GKC.gene_models_main.gff3
Gene model annotation for the vigun.IT97K-499-35.gnm1 genome
vigun.IT97K-499-35.gnm1.ann1.zb5D.gene_models_main.gff3
Gene model annotation for the vigun.IT97K-499-35.gnm1 genome
vigun.IT97K-499-35.gnm1.ann2.FD7K.gene_models_main.gff3
Gene model annotation for the vigun.Sanzi.gnm1 genome
vigun.Sanzi.gnm1.ann1.HFH8.gene_models_main.gff3
Gene model annotation for the vigun.Suvita2.gnm1 genome
vigun.Suvita2.gnm1.ann1.1PF6.gene_models_main.gff3
Gene model annotation for the vigun.TZ30.gnm1 genome
vigun.TZ30.gnm1.ann2.59NL.gene_models_main.gff3
Gene model annotation for the vigun.UCR779.gnm1 genome
vigun.UCR779.gnm1.ann1.VF6G.gene_models_main.gff3
Gene model annotation for the vigun.Xiabao_II.gnm1 genome
vigun.Xiabao_II.gnm1.ann1.4JFL.gene_models_main.gff3
Gene model annotation for the vigun.ZN016.gnm1 genome
vigun.ZN016.gnm1.ann2.C7YV.gene_models_main.gff3
LIS datastore genomic FASTA file for Vigna angularis Gyeongwon
vigan.Gyeongwon.gnm3.JyYC.genome_main.fna
LIS datastore genomic FASTA file for Vigna angularis Shumari
vigan.Shumari.gnm1.V0CS.genome_main.fna
LIS datastore genomic FASTA file for Vigna radiata VC1973A
vigra.VC1973A.gnm6.3nL8.genome_main.fna
LIS datastore genomic FASTA file for Vigna unguiculata CB5-2
vigun.CB5-2.gnm1.WDTB.genome_main.fna
LIS datastore genomic FASTA file for Vigna unguiculata IT97K-499-35
vigun.IT97K-499-35.gnm1.QnBW.genome_main.fna
LIS datastore genomic FASTA file for Vigna unguiculata Sanzi
vigun.Sanzi.gnm1.YNCM.genome_main.fna
LIS datastore genomic FASTA file for Vigna unguiculata Suvita2
vigun.Suvita2.gnm1.5QLL.genome_main.fna
LIS datastore genomic FASTA file for Vigna unguiculata TZ30
vigun.TZ30.gnm1.TX9W.genome_main.fna
LIS datastore genomic FASTA file for Vigna unguiculata UCR779
vigun.UCR779.gnm1.M7KZ.genome_main.fna
LIS datastore genomic FASTA file for Vigna unguiculata Xiabao_II
vigun.Xiabao_II.gnm1.WDBP.genome_main.fna
LIS datastore genomic FASTA file for Vigna unguiculata ZN016
vigun.ZN016.gnm1.997F.genome_main.fna
LIS gene families
legume.genefam.fam1.M65K.info_annot_ahrd.tsv
Plant reactome pathways for Vigna angularis Gyeongwon genes via gene family membership with Vigna radiata.
vigan.Gyeongwon.gnm3.ann1.3Nz5.legfed_v1_0.M65K.pathway.tsv
Plant reactome pathways for Vigna angularis Shumari genes via gene family membership with Vigna radiata.
vigan.Shumari.gnm1.ann1.8BRS.legfed_v1_0.M65K.pathway.tsv
Plant reactome pathways for Vigna radiata VC1973A genes.
vigra.VC1973A.gnm6.ann1.M1Qs.pathway.tsv
Plant reactome pathways for Vigna unguiculata CB5-2 genes via gene family membership with Vigna radiata.
vigun.CB5-2.gnm1.ann1.0GKC.legfed_v1_0.M65K.pathway.tsv
Plant reactome pathways for Vigna unguiculata IT97K-499-35 genes via gene family membership with Vigna radiata.
vigun.IT97K-499-35.gnm1.ann2.FD7K.legfed_v1_0.M65K.pathway.tsv
Plant reactome pathways for Vigna unguiculata Sanzi genes via gene family membership with Vigna radiata.
vigun.Sanzi.gnm1.ann1.HFH8.legfed_v1_0.M65K.pathway.tsv
Plant reactome pathways for Vigna unguiculata Suvita2 genes via gene family membership with Vigna radiata.
vigun.Suvita2.gnm1.ann1.1PF6.legfed_v1_0.M65K.pathway.tsv
Plant reactome pathways for Vigna unguiculata TZ30 genes via gene family membership with Vigna radiata.
vigun.TZ30.gnm1.ann2.59NL.legfed_v1_0.M65K.pathway.tsv
Plant reactome pathways for Vigna unguiculata UCR779 genes via gene family membership with Vigna radiata.
vigun.UCR779.gnm1.ann1.VF6G.legfed_v1_0.M65K.pathway.tsv
Plant reactome pathways for Vigna unguiculata Xiabao_II genes via gene family membership with Vigna radiata.
vigun.Xiabao_II.gnm1.ann1.4JFL.legfed_v1_0.M65K.pathway.tsv
Plant reactome pathways for Vigna unguiculata ZN016 genes via gene family membership with Vigna radiata.
vigun.ZN016.gnm1.ann2.C7YV.legfed_v1_0.M65K.pathway.tsv
Protein models for the vigan.Gyeongwon.gnm3 genome
vigan.Gyeongwon.gnm3.ann1.3Nz5.protein_primaryTranscript.faa
Protein models for the vigan.Shumari.gnm1 genome
vigan.Shumari.gnm1.ann1.8BRS.protein_primaryTranscript.faa
Protein models for the vigra.VC1973A.gnm6 genome
vigra.VC1973A.gnm6.ann1.M1Qs.protein.faa
Protein models for the vigun.CB5-2.gnm1 genome
vigun.CB5-2.gnm1.ann1.0GKC.protein_primaryTranscript.faa
Protein models for the vigun.IT97K-499-35.gnm1 genome
vigun.IT97K-499-35.gnm1.ann1.zb5D.protein_primaryTranscript.faa
Protein models for the vigun.IT97K-499-35.gnm1 genome
vigun.IT97K-499-35.gnm1.ann1.zb5D.transcript_primaryTranscript.fna
Protein models for the vigun.IT97K-499-35.gnm1 genome
vigun.IT97K-499-35.gnm1.ann2.FD7K.protein_primaryTranscript.faa
Protein models for the vigun.Sanzi.gnm1 genome
vigun.Sanzi.gnm1.ann1.HFH8.protein_primaryTranscript.faa
Protein models for the vigun.Suvita2.gnm1 genome
vigun.Suvita2.gnm1.ann1.1PF6.protein_primaryTranscript.faa
Protein models for the vigun.TZ30.gnm1 genome
vigun.TZ30.gnm1.ann2.59NL.protein_primaryTranscript.faa
Protein models for the vigun.UCR779.gnm1 genome
vigun.UCR779.gnm1.ann1.VF6G.protein_primaryTranscript.faa
Protein models for the vigun.Xiabao_II.gnm1 genome
vigun.Xiabao_II.gnm1.ann1.4JFL.protein.faa
Protein models for the vigun.ZN016.gnm1 genome
vigun.ZN016.gnm1.ann2.C7YV.protein_primaryTranscript.faa
Synteny between Vigna angularis Gyeongwon.gnm3 and other species and strains.
vigan.Gyeongwon.v3.x.cajca.ICPL87119.v1.gff
Synteny between Vigna angularis Gyeongwon.gnm3 and other species and strains.
vigan.Gyeongwon.v3.x.glyma.Wm82.a2.gff
Synteny between Vigna angularis Gyeongwon.gnm3 and other species and strains.
vigan.Gyeongwon.v3.x.phavu.G19833.v1.gff
Synteny between Vigna angularis Gyeongwon.gnm3 and other species and strains.
vigan.Gyeongwon.v3.x.phavu.G19833.v2.gff
Synteny between Vigna angularis Gyeongwon.gnm3 and other species and strains.
vigan.Gyeongwon.v3.x.vigan.Gyeongwon.v3.gff
Synteny between Vigna angularis Gyeongwon.gnm3 and other species and strains.
vigan.Gyeongwon.v3.x.vigra.VC1973A.v6.gff
Synteny between cowpea IT97K-499-35.gnm1 and other species and strains.
vigun.IT97K-499-35.gnm1.x.glyma.Wm82.gnm2.gff
Synteny between cowpea IT97K-499-35.gnm1 and other species and strains.
vigun.IT97K-499-35.gnm1.x.phavu.G19833.gnm1.gff
Synteny between cowpea IT97K-499-35.gnm1 and other species and strains.
vigun.IT97K-499-35.gnm1.x.vigan.Gyeongwon.gnm3.gff
Synteny between cowpea IT97K-499-35.gnm1 and other species and strains.
vigun.IT97K-499-35.gnm1.x.vigra.VC1973A.gnm6.gff
Synteny between cowpea IT97K-499-35.gnm1 and other species and strains.
vigun.IT97K-499-35.gnm1.x.vigun.IT97K-499-35.gnm1.gff
Vigna angularis organism and strain information.
description_Vigna_angularis.yml
Vigna angularis organism and strain information.
strains_Vigna_angularis.yml
Vigna radiata organism and strain information.
description_Vigna_radiata.yml
Vigna radiata organism and strain information.
strains_Vigna_radiata.yml
Vigna unguiculata GWAS for seed size and weight from Lo, et al. 2019
vigun.mixed.gwas.02X4.31367839.gwas.tsv
Vigna unguiculata GWAS for seed size and weight from Lo, et al. 2019
vigun.mixed.gwas.02X4.31367839.phen.tsv
Vigna unguiculata genetic maps
vigun.mixed.map.SM2W.MAGIC-2017.expt.tsv
Vigna unguiculata genetic maps
vigun.mixed.map.SM2W.MAGIC-2017.mrk.tsv
Vigna unguiculata genetic maps
vigun.mixed.map.SM2W.MAGIC-2017.phen.tsv
Vigna unguiculata genetic maps
vigun.mixed.map.SM2W.MAGIC-2017.qtl.tsv
Vigna unguiculata genetic maps
vigun.mixed.map.SM2W.iSelect-consensus-2016.expt.tsv
Vigna unguiculata genetic maps
vigun.mixed.map.SM2W.iSelect-consensus-2016.mrk.tsv
Vigna unguiculata organism and strain information.
description_Vigna_unguiculata.yml
Vigna unguiculata organism and strain information.
strains_Vigna_unguiculata.yml
mRNA models for the vigan.Shumari.gnm1 genome
vigan.Shumari.gnm1.ann1.8BRS.transcript.fna
PANTHER
PFAM
PIRSF
PRINTS
PROFILE
PROSITE
Plant Ontology
The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies.
Plant Ontology
Plant Trait Ontology
A controlled vocabulary of describe phenotypic traits in plants.
Plant Trait Ontology
SFLD
SMART
SSF
Sequence Ontology
The Sequence Ontology is a set of terms and relationships used to describe the features and attributes of biological sequence.
Sequence Ontology
TIGRFAMs
USDA
Legume Federation
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