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
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
CDS models for the phalu.G27455.gnm1 genome
phalu.G27455.gnm1.ann1.JD7C.cds_primaryTranscript.fna
CDS models for the phavu.G19833.gnm1 genome
phavu.G19833.gnm1.ann1.pScz.cds_primaryTranscript.fna
CDS models for the phavu.G19833.gnm2 genome
phavu.G19833.gnm2.ann1.PB8d.cds_primaryTranscript.fna
CDS models for the phavu.UI111.gnm1 genome
phavu.UI111.gnm1.ann1.8L4N.cds_primaryTranscript.fna
Gene family assignments for Phaseolus lunatus G27455 genes and proteins.
phalu.G27455.gnm1.ann1.JD7C.legfed_v1_0.M65K.gfa.tsv
Gene family assignments for Phaseolus vulgaris G19833 genes and proteins.
phavu.G19833.gnm2.ann1.PB8d.legfed_v1_0.M65K.gfa.tsv
Gene family assignments for Phaseolus vulgaris UI111 genes and proteins.
phavu.UI111.gnm1.ann1.8L4N.legfed_v1_0.M65K.gfa.tsv
Gene family assignments for phavu.G19833.gnm1 genes and proteins
phavu.G19833.gnm1.ann1.pScz.legfed_v1_0.M65K.gfa.tsv
Gene model annotation for the phalu.G27455.gnm1 genome
phalu.G27455.gnm1.ann1.JD7C.gene_models_main.gff3
Gene model annotation for the phavu.G19833.gnm1 genome
phavu.G19833.gnm1.ann1.pScz.gene_models_main.gff3
Gene model annotation for the phavu.G19833.gnm2 genome
phavu.G19833.gnm2.ann1.PB8d.gene_models_main.gff3
Gene model annotation for the phavu.UI111.gnm1 genome
phavu.UI111.gnm1.ann1.8L4N.gene_models_main.gff3
LIS datastore genomic FASTA file for Phaseolus lunatus G27455
phalu.G27455.gnm1.7NXX.genome_main.fna
LIS datastore genomic FASTA file for Phaseolus vulgaris G19833
phavu.G19833.gnm1.zBnF.genome_main.fna
LIS datastore genomic FASTA file for Phaseolus vulgaris G19833
phavu.G19833.gnm2.fC0g.genome_main.fna
LIS datastore genomic FASTA file for Phaseolus vulgaris UI111
phavu.UI111.gnm1.3VTM.genome_main.fna
LIS gene families
legume.genefam.fam1.M65K.info_annot_ahrd.tsv
Phaseolus lunatus organism and strain information.
description_Phaseolus_lunatus.yml
Phaseolus lunatus organism and strain information.
strains_Phaseolus_lunatus.yml
Phaseolus vulgaris GWAS experiments.
phavu.mixed.gwas.5HCM.31428109.gwas.tsv
Phaseolus vulgaris GWAS experiments.
phavu.mixed.gwas.5HCM.31428109.phen.tsv
Phaseolus vulgaris cv. Negro jamapa gene expression atlas from O'Rourke, et al. (2014).
phavu.G19833.gnm1.ann1.expr.4ZDQ.samples.tsv
Phaseolus vulgaris cv. Negro jamapa gene expression atlas from O'Rourke, et al. (2014).
phavu.G19833.gnm1.ann1.expr.4ZDQ.source.tsv
Phaseolus vulgaris cv. Negro jamapa gene expression atlas from O'Rourke, et al. (2014).
phavu.G19833.gnm1.ann1.expr.4ZDQ.values.tsv
Phaseolus vulgaris gene, protein and mRNA ontology annotations.
phavu.G19833.gnm1.ann1.pScz.info_annot.txt
Phaseolus vulgaris gene, protein and mRNA ontology annotations.
phavu.G19833.gnm2.ann1.PB8d.info_annot.txt
Phaseolus vulgaris gene, protein and mRNA ontology annotations.
phavu.UI111.gnm1.ann1.8L4N.info_annot.txt
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.ALL.phen.tsv
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.BAT93_x_JALOEEP558_a.expt.tsv
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.BAT93_x_JALOEEP558_a.qtl.tsv
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.BAT93_x_JALOEEP558_b.expt.tsv
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.BAT93_x_JALOEEP558_b.mrk.tsv
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.BAT93_x_JALOEEP558_c.expt.tsv
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.BAT93_x_JALOEEP558_c.mrk.tsv
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.Cerinza_x_G24404_a.expt.tsv
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.Cerinza_x_G24404_a.mrk.tsv
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.Cerinza_x_G24404_a.qtl.tsv
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.DOR364_x_BAT477_a.expt.tsv
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.DOR364_x_BAT477_a.mrk.tsv
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.DOR364_x_BAT477_a.qtl.tsv
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.G2333_x_G19839_a.expt.tsv
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.G2333_x_G19839_a.qtl.tsv
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.PvConsensus_GaleanoFernandez2011_a.expt.tsv
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.PvConsensus_GaleanoFernandez2011_a.mrk.tsv
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.PvCookUCDavis2009.expt.tsv
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.PvCookUCDavis2009.mrk.tsv
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.PvMcCleanNDSU2007.expt.tsv
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.PvMcCleanNDSU2007.mrk.tsv
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.Stampede_x_RedHawk_F2_a.expt.tsv
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.Stampede_x_RedHawk_F2_a.mrk.tsv
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.Xana_x_Cornell49242_a.expt.tsv
Phaseolus vulgaris genetic maps
phavu.mixed.map.7PMp.Xana_x_Cornell49242_a.qtl.tsv
Phaseolus vulgaris organism and strain information.
description_Phaseolus_vulgaris.yml
Phaseolus vulgaris organism and strain information.
strains_Phaseolus_vulgaris.yml
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
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
Plant Reactome pathways for phavu.G19833.gnm1
phavu.G19833.gnm1.ann1.pScz.pathway.tsv
Plant Reactome pathways for phavu.G19833.gnm2
phavu.G19833.gnm2.ann1.PB8d.pathway.tsv
Protein models for the phalu.G27455.gnm1 genome
phalu.G27455.gnm1.ann1.JD7C.protein_primaryTranscript.faa
Protein models for the phavu.G19833.gnm1 genome
phavu.G19833.gnm1.ann1.pScz.protein_primaryTranscript.faa
Protein models for the phavu.G19833.gnm2 genome
phavu.G19833.gnm2.ann1.PB8d.protein_primaryTranscript.faa
Protein models for the phavu.UI111.gnm1 genome
phavu.UI111.gnm1.ann1.8L4N.protein_primaryTranscript.faa
Synteny between phavu.G19833.gnm1 and other species.
phavu.G19833.gnm1.ann1.x.aradu.V14167.gnm1.ann1.gff
Synteny between phavu.G19833.gnm1 and other species.
phavu.G19833.gnm1.ann1.x.araip.K30076.gnm1.ann1.gff
Synteny between phavu.G19833.gnm1 and other species.
phavu.G19833.gnm1.ann1.x.cajca.ICPL87119.gnm1.ann1.gff
Synteny between phavu.G19833.gnm1 and other species.
phavu.G19833.gnm1.ann1.x.glyma.Wm82.gnm2.ann1.gff
Synteny between phavu.G19833.gnm1 and other species.
phavu.G19833.gnm1.ann1.x.lotja.MG20.gnm3.ann1.gff
Synteny between phavu.G19833.gnm1 and other species.
phavu.G19833.gnm1.ann1.x.lupan.Tanjil.gnm1.ann1.gff
Synteny between phavu.G19833.gnm1 and other species.
phavu.G19833.gnm1.ann1.x.medtr.A17_HM341.gnm4.ann2.gff
Synteny between phavu.G19833.gnm1 and other species.
phavu.G19833.gnm1.ann1.x.phavu.G19833.gnm1.ann1.gff
Synteny between phavu.G19833.gnm1 and other species.
phavu.G19833.gnm1.ann1.x.phavu.G19833.gnm2.ann1.gff
Synteny between phavu.G19833.gnm1 and other species.
phavu.G19833.gnm1.ann1.x.vigan.Gyeongwon.gnm3.ann1.gff
Synteny between phavu.G19833.gnm1 and other species.
phavu.G19833.gnm1.ann1.x.vigra.VC1973A.gnm6.ann1.gff
Synteny between phavu.G19833.gnm2 and other species.
phavu.G19833.v2.x.aradu.V14167.v1.gff
Synteny between phavu.G19833.gnm2 and other species.
phavu.G19833.v2.x.araip.K30076.v1.gff
Synteny between phavu.G19833.gnm2 and other species.
phavu.G19833.v2.x.cajca.ICPL87119.v1.gff
Synteny between phavu.G19833.gnm2 and other species.
phavu.G19833.v2.x.glyma.Wm82.a2.gff
Synteny between phavu.G19833.gnm2 and other species.
phavu.G19833.v2.x.lotja.MG20.v3.gff
Synteny between phavu.G19833.gnm2 and other species.
phavu.G19833.v2.x.medtr.A17_HM341.v4.gff
Synteny between phavu.G19833.gnm2 and other species.
phavu.G19833.v2.x.phavu.G19833.v1.gff
Synteny between phavu.G19833.gnm2 and other species.
phavu.G19833.v2.x.vigan.Gyeongwon.v3.gff
Synteny between phavu.G19833.gnm2 and other species.
phavu.G19833.v2.x.vigra.VC1973A.v6.gff
mRNA models for the phalu.G27455.gnm1 genome
phalu.G27455.gnm1.ann1.JD7C.transcript_primaryTranscript.fna
mRNA models for the phavu.G19833.gnm1 genome
phavu.G19833.gnm1.ann1.pScz.transcript_primaryTranscript.fna
mRNA models for the phavu.G19833.gnm2 genome
phavu.G19833.gnm2.ann1.PB8d.transcript_primaryTranscript.fna
mRNA models for the phavu.UI111.gnm1 genome
phavu.UI111.gnm1.ann1.8L4N.transcript_primaryTranscript.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
null
Illumina GoldenGate SNP positions on the phavu.G19833.gnm1 genome assembly
phavu.G19833.gnm1.mrk.7KYW.PvCookUCDavis2009.gff3
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.
BeanMine | ChickpeaMine | CowpeaMine | LupinMine | PeanutMine | SoyMine | MedicMine | LegumeMine
InterMine © 2002 - 2020 Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, United Kingdom