Data Sources and their Data Sets

CATHGENE3D
CDD
Common Bean Crop Ontology
A controlled vocabulary to describe crop traits in common bean.
Common Bean Crop Ontology
LINK
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
LINK
HAMAP
InterMine post-processor
Gene-flanking regions created by the core InterMine post-processor
InterMine gene-flanking regions
LINK
Intergenic regions created by the InterMine core post-processor
InterMine intergenic regions
LINK
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
CDS models for the phalu.G27455.gnm1 genome
phalu.G27455.gnm1.ann1.JD7C.cds_primaryTranscript.fna
LINK
CDS models for the phavu.G19833.gnm1 genome
phavu.G19833.gnm1.ann1.pScz.cds_primaryTranscript.fna
LINK
CDS models for the phavu.G19833.gnm2 genome
phavu.G19833.gnm2.ann1.PB8d.cds_primaryTranscript.fna
LINK
CDS models for the phavu.UI111.gnm1 genome
phavu.UI111.gnm1.ann1.8L4N.cds_primaryTranscript.fna
LINK
Gene family assignments for Phaseolus lunatus G27455 genes and proteins.
phalu.G27455.gnm1.ann1.JD7C.legfed_v1_0.M65K.gfa.tsv
LINK
Gene family assignments for Phaseolus vulgaris G19833 genes and proteins.
phavu.G19833.gnm2.ann1.PB8d.legfed_v1_0.M65K.gfa.tsv
LINK
Gene family assignments for Phaseolus vulgaris UI111 genes and proteins.
phavu.UI111.gnm1.ann1.8L4N.legfed_v1_0.M65K.gfa.tsv
LINK
Gene family assignments for phavu.G19833.gnm1 genes and proteins
phavu.G19833.gnm1.ann1.pScz.legfed_v1_0.M65K.gfa.tsv
LINK
Gene model annotation for the phalu.G27455.gnm1 genome
phalu.G27455.gnm1.ann1.JD7C.gene_models_main.gff3
LINK
Gene model annotation for the phavu.G19833.gnm1 genome
phavu.G19833.gnm1.ann1.pScz.gene_models_main.gff3
LINK
Gene model annotation for the phavu.G19833.gnm2 genome
phavu.G19833.gnm2.ann1.PB8d.gene_models_main.gff3
LINK
Gene model annotation for the phavu.UI111.gnm1 genome
phavu.UI111.gnm1.ann1.8L4N.gene_models_main.gff3
LINK
LIS datastore genomic FASTA file for Phaseolus lunatus G27455
phalu.G27455.gnm1.7NXX.genome_main.fna
LINK
LIS datastore genomic FASTA file for Phaseolus vulgaris G19833
phavu.G19833.gnm1.zBnF.genome_main.fna
LINK
LIS datastore genomic FASTA file for Phaseolus vulgaris G19833
phavu.G19833.gnm2.fC0g.genome_main.fna
LINK
LIS datastore genomic FASTA file for Phaseolus vulgaris UI111
phavu.UI111.gnm1.3VTM.genome_main.fna
LINK
LIS gene families
legume.genefam.fam1.M65K.info_annot_ahrd.tsv
LINK
Phaseolus lunatus organism and strain information.
description_Phaseolus_lunatus.yml
LINK
Phaseolus lunatus organism and strain information.
strains_Phaseolus_lunatus.yml
LINK
Phaseolus vulgaris GWAS experiments.
phavu.mixed.gwas.5HCM.31428109.gwas.tsv
LINK
Phaseolus vulgaris GWAS experiments.
phavu.mixed.gwas.5HCM.31428109.phen.tsv
LINK
Phaseolus vulgaris cv. Negro jamapa gene expression atlas from O'Rourke, et al. (2014).
phavu.G19833.gnm1.ann1.expr.4ZDQ.samples.tsv
LINK
Phaseolus vulgaris cv. Negro jamapa gene expression atlas from O'Rourke, et al. (2014).
phavu.G19833.gnm1.ann1.expr.4ZDQ.source.tsv
LINK
Phaseolus vulgaris cv. Negro jamapa gene expression atlas from O'Rourke, et al. (2014).
phavu.G19833.gnm1.ann1.expr.4ZDQ.values.tsv
LINK
Phaseolus vulgaris gene, protein and mRNA ontology annotations.
phavu.G19833.gnm1.ann1.pScz.info_annot.txt
LINK
Phaseolus vulgaris gene, protein and mRNA ontology annotations.
phavu.G19833.gnm2.ann1.PB8d.info_annot.txt
LINK
Phaseolus vulgaris gene, protein and mRNA ontology annotations.
phavu.UI111.gnm1.ann1.8L4N.info_annot.txt
LINK
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.ALL.phen.tsv
LINK
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.BAT93_x_JALOEEP558_a.expt.tsv
LINK
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.BAT93_x_JALOEEP558_a.qtl.tsv
LINK
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.BAT93_x_JALOEEP558_b.expt.tsv
LINK
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.BAT93_x_JALOEEP558_b.mrk.tsv
LINK
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.BAT93_x_JALOEEP558_c.expt.tsv
LINK
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.BAT93_x_JALOEEP558_c.mrk.tsv
LINK
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.Cerinza_x_G24404_a.expt.tsv
LINK
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.Cerinza_x_G24404_a.mrk.tsv
LINK
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.Cerinza_x_G24404_a.qtl.tsv
LINK
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.DOR364_x_BAT477_a.expt.tsv
LINK
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.DOR364_x_BAT477_a.mrk.tsv
LINK
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.DOR364_x_BAT477_a.qtl.tsv
LINK
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.G2333_x_G19839_a.expt.tsv
LINK
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.G2333_x_G19839_a.qtl.tsv
LINK
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.PvConsensus_GaleanoFernandez2011_a.expt.tsv
LINK
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.PvConsensus_GaleanoFernandez2011_a.mrk.tsv
LINK
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.PvCookUCDavis2009.expt.tsv
LINK
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.PvCookUCDavis2009.mrk.tsv
LINK
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.PvMcCleanNDSU2007.expt.tsv
LINK
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.PvMcCleanNDSU2007.mrk.tsv
LINK
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.Stampede_x_RedHawk_F2_a.expt.tsv
LINK
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.Stampede_x_RedHawk_F2_a.mrk.tsv
LINK
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.Xana_x_Cornell49242_a.expt.tsv
LINK
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.Xana_x_Cornell49242_a.qtl.tsv
LINK
Phaseolus vulgaris organism and strain information.
description_Phaseolus_vulgaris.yml
LINK
Phaseolus vulgaris organism and strain information.
strains_Phaseolus_vulgaris.yml
LINK
Plant Reactome assignments for Phaseolus lunatus G27455 genes, via gene familie membership with Phaseolus vulgaris genes.
phalu.G27455.gnm1.ann1.JD7C.legfed_v1_0.M65K.pathway.tsv
LINK
Plant Reactome pathway assignments for phavu.UI111.gnm1 genes via gene family membership with phavu.G19833 genes.
phavu.UI111.gnm1.ann1.8L4N.legfed_v1_0.M65K.pathway.tsv
LINK
Plant Reactome pathways for phavu.G19833.gnm1
phavu.G19833.gnm1.ann1.pScz.pathway.tsv
LINK
Plant Reactome pathways for phavu.G19833.gnm2
phavu.G19833.gnm2.ann1.PB8d.pathway.tsv
LINK
Protein models for the phalu.G27455.gnm1 genome
phalu.G27455.gnm1.ann1.JD7C.protein_primaryTranscript.faa
LINK
Protein models for the phavu.G19833.gnm1 genome
phavu.G19833.gnm1.ann1.pScz.protein_primaryTranscript.faa
LINK
Protein models for the phavu.G19833.gnm2 genome
phavu.G19833.gnm2.ann1.PB8d.protein_primaryTranscript.faa
LINK
Protein models for the phavu.UI111.gnm1 genome
phavu.UI111.gnm1.ann1.8L4N.protein_primaryTranscript.faa
LINK
Synteny between phavu.G19833.gnm1 and other species.
phavu.G19833.gnm1.ann1.x.aradu.V14167.gnm1.ann1.gff
LINK
Synteny between phavu.G19833.gnm1 and other species.
phavu.G19833.gnm1.ann1.x.araip.K30076.gnm1.ann1.gff
LINK
Synteny between phavu.G19833.gnm1 and other species.
phavu.G19833.gnm1.ann1.x.cajca.ICPL87119.gnm1.ann1.gff
LINK
Synteny between phavu.G19833.gnm1 and other species.
phavu.G19833.gnm1.ann1.x.glyma.Wm82.gnm2.ann1.gff
LINK
Synteny between phavu.G19833.gnm1 and other species.
phavu.G19833.gnm1.ann1.x.lotja.MG20.gnm3.ann1.gff
LINK
Synteny between phavu.G19833.gnm1 and other species.
phavu.G19833.gnm1.ann1.x.lupan.Tanjil.gnm1.ann1.gff
LINK
Synteny between phavu.G19833.gnm1 and other species.
phavu.G19833.gnm1.ann1.x.medtr.A17_HM341.gnm4.ann2.gff
LINK
Synteny between phavu.G19833.gnm1 and other species.
phavu.G19833.gnm1.ann1.x.phavu.G19833.gnm1.ann1.gff
LINK
Synteny between phavu.G19833.gnm1 and other species.
phavu.G19833.gnm1.ann1.x.phavu.G19833.gnm2.ann1.gff
LINK
Synteny between phavu.G19833.gnm1 and other species.
phavu.G19833.gnm1.ann1.x.vigan.Gyeongwon.gnm3.ann1.gff
LINK
Synteny between phavu.G19833.gnm1 and other species.
phavu.G19833.gnm1.ann1.x.vigra.VC1973A.gnm6.ann1.gff
LINK
Synteny between phavu.G19833.gnm2 and other species.
phavu.G19833.v2.x.aradu.V14167.v1.gff
LINK
Synteny between phavu.G19833.gnm2 and other species.
phavu.G19833.v2.x.araip.K30076.v1.gff
LINK
Synteny between phavu.G19833.gnm2 and other species.
phavu.G19833.v2.x.cajca.ICPL87119.v1.gff
LINK
Synteny between phavu.G19833.gnm2 and other species.
phavu.G19833.v2.x.glyma.Wm82.a2.gff
LINK
Synteny between phavu.G19833.gnm2 and other species.
phavu.G19833.v2.x.lotja.MG20.v3.gff
LINK
Synteny between phavu.G19833.gnm2 and other species.
phavu.G19833.v2.x.medtr.A17_HM341.v4.gff
LINK
Synteny between phavu.G19833.gnm2 and other species.
phavu.G19833.v2.x.phavu.G19833.v1.gff
LINK
Synteny between phavu.G19833.gnm2 and other species.
phavu.G19833.v2.x.vigan.Gyeongwon.v3.gff
LINK
Synteny between phavu.G19833.gnm2 and other species.
phavu.G19833.v2.x.vigra.VC1973A.v6.gff
LINK
mRNA models for the phalu.G27455.gnm1 genome
phalu.G27455.gnm1.ann1.JD7C.transcript_primaryTranscript.fna
LINK
mRNA models for the phavu.G19833.gnm1 genome
phavu.G19833.gnm1.ann1.pScz.transcript_primaryTranscript.fna
LINK
mRNA models for the phavu.G19833.gnm2 genome
phavu.G19833.gnm2.ann1.PB8d.transcript_primaryTranscript.fna
LINK
mRNA models for the phavu.UI111.gnm1 genome
phavu.UI111.gnm1.ann1.8L4N.transcript_primaryTranscript.fna
LINK
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
LINK
Plant Trait Ontology
A controlled vocabulary of describe phenotypic traits in plants.
Plant Trait Ontology
LINK
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
LINK
TIGRFAMs
null
Illumina GoldenGate SNP positions on the phavu.G19833.gnm1 genome assembly
phavu.G19833.gnm1.mrk.7KYW.PvCookUCDavis2009.gff3
LINK
USDA
Legume Federation
InterMine logo
The Legume Information System (LIS) is a research project of the USDA-ARS:Corn Insects and Crop Genetics Research in Ames, IA.
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