Data Sources and their Data Sets

CATHGENE3D
CDD
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 glyma.Lee.gnm1 genome
glyma.Lee.gnm1.ann1.6NZV.cds_primaryTranscript.fna
CDS models for the glyma.Wm82.gnm1 genome
glyma.Wm82.gnm1.ann1.DvBy.cds_primaryTranscript.fna
CDS models for the glyma.Wm82.gnm2 genome
glyma.Wm82.gnm2.ann1.RVB6.cds_primaryTranscript.fna
CDS models for the glyma.Wm82.gnm4 genome
glyma.Wm82.gnm4.ann1.T8TQ.cds_primaryTranscript.fna
CDS models for the glyma.Zh13.gnm1 genome
glyma.Zh13.gnm1.ann1.8VV3.cds_primaryTranscript.fna
CDS models for the glyso.PI483463.gnm1 genome
glyso.PI483463.gnm1.ann1.3Q3Q.cds_primaryTranscript.fna
CDS models for the glyso.W05.gnm1 genome
glyso.W05.gnm1.ann1.T47J.cds_primaryTranscript.fna
Gene family assignments for glyma.Lee.gnm1 genes and proteins.
glyma.Lee.gnm1.ann1.6NZV.legfed_v1_0.M65K.gfa.tsv
Gene family assignments for glyma.Wm82.gnm1 genes and proteins.
glyma.Wm82.gnm1.ann1.DvBy.legfed_v1_0.M65K.gfa.tsv
Gene family assignments for glyma.Wm82.gnm2 genes and proteins.
glyma.Wm82.gnm2.ann1.RVB6.legfed_v1_0.M65K.gfa.tsv
Gene family assignments for glyma.Wm82.gnm4 genes and proteins.
glyma.Wm82.gnm4.ann1.T8TQ.legfed_v1_0.M65K.gfa.tsv
Gene family assignments for glyma.Zh13.gnm1 genes and proteins.
glyma.Zh13.gnm1.ann1.8VV3.legfed_v1_0.M65K.gfa.tsv
Gene family assignments for glyso.PI483463.gnm1 genes and proteins.
glyso.PI483463.gnm1.ann1.3Q3Q.legfed_v1_0.M65K.gfa.tsv
Gene family assignments for glyso.W05.gnm1 genes and proteins.
glyso.W05.gnm1.ann1.T47J.legfed_v1_0.M65K.gfa.tsv
Gene model annotation for the glyma.Lee.gnm1 genome
glyma.Lee.gnm1.ann1.6NZV.gene_models_main.gff3
Gene model annotation for the glyma.Wm82.gnm1 genome
glyma.Wm82.gnm1.ann1.DvBy.gene_models_main.gff3
Gene model annotation for the glyma.Wm82.gnm2 genome
glyma.Wm82.gnm2.ann1.RVB6.gene_models_main.gff3
Gene model annotation for the glyma.Wm82.gnm4 genome
glyma.Wm82.gnm4.ann1.T8TQ.gene_models_main.gff3
Gene model annotation for the glyma.Zh13.gnm1 genome
glyma.Zh13.gnm1.ann1.8VV3.gene_models_main.gff3
Gene model annotation for the glyso.PI483463.gnm1 genome
glyso.PI483463.gnm1.ann1.3Q3Q.gene_models_main.gff3
Gene model annotation for the glyso.W05.gnm1 genome
glyso.W05.gnm1.ann1.T47J.gene_models_main.gff3
Genetic marker positions on the glyma.Wm82.gnm2 genome assembly
glyma.Wm82.gnm2.mrk.XJP2.gff3
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20170707-1.gwas.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20170707-1.phen.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20170711-1.gwas.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20170711-1.phen.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20170714-1.gwas.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20170714-1.phen.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20170803-1.gwas.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20170803-1.phen.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20170808-1.gwas.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20170808-1.phen.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20170814-1.gwas.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20170814-1.phen.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20170908-1.gwas.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20170908-1.phen.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20170915-1.gwas.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20170915-1.phen.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20171006-1.gwas.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20171006-1.phen.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20171018-1.gwas.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20171018-1.phen.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20171027-1.gwas.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20171027-1.phen.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.LBC20180516-2.gwas.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.LBC20180516-2.phen.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.LBC20180516-3.gwas.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.LBC20180516-3.phen.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.LBC20180521-1.gwas.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.LBC20180521-1.phen.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.LBC20180521-5.gwas.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.LBC20180521-5.phen.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.LBC20180601-3.gwas.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.LBC20180601-3.phen.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.LBC20180625-2.gwas.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.LBC20180625-2.phen.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.LBC20180625-3.gwas.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.LBC20180625-3.phen.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.SST20180209-1.gwas.tsv
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.SST20180209-1.phen.tsv
Glycine max gene, protein and mRNA ontology annotations.
glyma.Lee.gnm1.ann1.6NZV.info_annot.txt
Glycine max gene, protein and mRNA ontology annotations.
glyma.Wm82.gnm1.ann1.DvBy.info_annot.txt
Glycine max gene, protein and mRNA ontology annotations.
glyma.Wm82.gnm2.ann1.RVB6.info_annot.txt
Glycine max gene, protein and mRNA ontology annotations.
glyma.Wm82.gnm4.ann1.T8TQ.info_annot.txt
Glycine max genetic map imported from SoyBase.
glyma.mixed.map.9M0V.GmComposite2003.expt.tsv
Glycine max genetic map imported from SoyBase.
glyma.mixed.map.9M0V.GmComposite2003.mrk.tsv
Glycine max genetic map imported from SoyBase.
glyma.mixed.map.9M0V.GmComposite2003.phen.tsv
Glycine max genetic map imported from SoyBase.
glyma.mixed.map.9M0V.GmComposite2003.qtl.tsv
Glycine max organism and strain information.
description_Glycine_max.yml
Glycine max organism and strain information.
strains_Glycine_max.yml
Glycine soja gene, protein and mRNA ontology annotations.
glyso.PI483463.gnm1.ann1.3Q3Q.info_annot.txt
Glycine soja organism and strain information.
description_Glycine_soja.yml
Glycine soja organism and strain information.
strains_Glycine_soja.yml
LIS datastore genomic FASTA file for Glycine max Lee
glyma.Lee.gnm1.BXNC.genome_main.fna
LIS datastore genomic FASTA file for Glycine max Wm82.gnm1
glyma.Wm82.gnm1.FCtY.genome_main.fna
LIS datastore genomic FASTA file for Glycine max Wm82.gnm2
glyma.Wm82.gnm2.DTC4.genome_main.fna
LIS datastore genomic FASTA file for Glycine max Wm82.gnm4
glyma.Wm82.gnm4.4PTR.genome_main.fna
LIS datastore genomic FASTA file for Glycine max Zh13
glyma.Zh13.gnm1.N6C8.genome_main.fna
LIS datastore genomic FASTA file for Glycine soja PI483463
glyso.PI483463.gnm1.YJWS.genome_main.fna
LIS datastore genomic FASTA file for Glycine soja W05
glyso.W05.gnm1.SVL1.genome_main.fna
LIS gene families
legume.genefam.fam1.M65K.info_annot_ahrd.tsv
Plant Reactome pathway assignments for glyma.Lee.gnm1 genes.
glyma.Lee.gnm1.ann1.6NZV.legfed_v1_0.M65K.pathway.tsv
Plant Reactome pathway assignments for glyma.Wm82.gnm1 genes.
glyma.Wm82.gnm1.ann1.DvBy.legfed_v1_0.M65K.pathway.tsv
Plant Reactome pathway assignments for glyma.Wm82.gnm2 genes.
glyma.Wm82.gnm2.ann1.RVB6.pathway.tsv
Plant Reactome pathway assignments for glyma.Wm82.gnm4 genes.
glyma.Wm82.gnm4.ann1.T8TQ.legfed_v1_0.M65K.pathway.tsv
Plant Reactome pathway assignments for glyma.Zh13.gnm1 genes.
glyma.Zh13.gnm1.ann1.8VV3.legfed_v1_0.M65K.pathway.tsv
Plant Reactome pathway assignments for glyso.PI483463.gnm1 genes.
glyso.PI483463.gnm1.ann1.3Q3Q.legfed_v1_0.M65K.pathway.tsv
Plant Reactome pathway assignments for glyso.W05.gnm1 genes.
glyso.W05.gnm1.ann1.T47J.legfed_v1_0.M65K.pathway.tsv
Protein models for the glyma.Lee.gnm1 genome
glyma.Lee.gnm1.ann1.6NZV.protein_primaryTranscript.faa
Protein models for the glyma.Wm82.gnm1 genome
glyma.Wm82.gnm1.ann1.DvBy.protein_primaryTranscript.faa
Protein models for the glyma.Wm82.gnm2 genome
glyma.Wm82.gnm2.ann1.RVB6.protein_primaryTranscript.faa
Protein models for the glyma.Wm82.gnm4 genome
glyma.Wm82.gnm4.ann1.T8TQ.protein_primaryTranscript.faa
Protein models for the glyma.Zh13.gnm1 genome
glyma.Zh13.gnm1.ann1.8VV3.protein_primaryTranscript.faa
Protein models for the glyso.PI483463.gnm1 genome
glyso.PI483463.gnm1.ann1.3Q3Q.protein_primaryTranscript.faa
Protein models for the glyso.W05.gnm1 genome
glyso.W05.gnm1.ann1.T47J.protein_primaryTranscript.faa
Soybean gene expression atlas from the Libault Lab.
glyma.Wm82.gnm2.ann1.expr.G7ZY.samples.tsv
Soybean gene expression atlas from the Libault Lab.
glyma.Wm82.gnm2.ann1.expr.G7ZY.source.tsv
Soybean gene expression atlas from the Libault Lab.
glyma.Wm82.gnm2.ann1.expr.G7ZY.values.tsv
Synteny between soybean Wm82.gnm2 and other species.
glyma.Wm82.gnm2.ann1.x.aradu.V14167.gnm1.ann1.gff
Synteny between soybean Wm82.gnm2 and other species.
glyma.Wm82.gnm2.ann1.x.araip.K30076.gnm1.ann1.gff
Synteny between soybean Wm82.gnm2 and other species.
glyma.Wm82.gnm2.ann1.x.cajca.ICPL87119.gnm1.ann1.gff
Synteny between soybean Wm82.gnm2 and other species.
glyma.Wm82.gnm2.ann1.x.lotja.MG20.gnm3.ann1.gff
Synteny between soybean Wm82.gnm2 and other species.
glyma.Wm82.gnm2.ann1.x.lupan.Tanjil.gnm1.ann1.gff
Synteny between soybean Wm82.gnm2 and other species.
glyma.Wm82.gnm2.ann1.x.medtr.A17_HM341.gnm4.ann2.gff
Synteny between soybean Wm82.gnm2 and other species.
glyma.Wm82.gnm2.ann1.x.phavu.G19833.gnm1.ann1.gff
Synteny between soybean Wm82.gnm2 and other species.
glyma.Wm82.gnm2.ann1.x.phavu.G19833.gnm2.ann1.gff
Synteny between soybean Wm82.gnm2 and other species.
glyma.Wm82.gnm2.ann1.x.vigan.Gyeongwon.gnm3.ann1.gff
Synteny between soybean Wm82.gnm2 and other species.
glyma.Wm82.gnm2.ann1.x.vigra.VC1973A.gnm6.ann1.gff
mRNA models for the glyma.Lee.gnm1 genome
glyma.Lee.gnm1.ann1.6NZV.transcript_primaryTranscript.fna
mRNA models for the glyma.Wm82.gnm1 genome
glyma.Wm82.gnm1.ann1.DvBy.transcript_primaryTranscript.fna
mRNA models for the glyma.Wm82.gnm2 genome
glyma.Wm82.gnm2.ann1.RVB6.transcript_primaryTranscript.fna
mRNA models for the glyma.Wm82.gnm4 genome
glyma.Wm82.gnm4.ann1.T8TQ.transcript_primaryTranscript.fna
mRNA models for the glyso.PI483463.gnm1 genome
glyso.PI483463.gnm1.ann1.3Q3Q.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
Soybean Crop Ontology
A controlled vocabulary to describe crop traits in soybean.
Soybean Crop Ontology
Soybean Growth and Trait Ontology V3.0 revision 1.0
Currently, there are 4 divisions to SOY terms, soybean structural terms (Soybean Structure Ontology), developmental stages (Soybean Developmental Ontology), whole plant development terms (Soybean Whole Plant Growth Stages) and trait terms (Soybean Trait Ontology).
Soybean Growth and Trait Ontology V3.0 revision 1.0
TIGRFAMs
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