Data Sources and their Data Sets

GO
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.
InterMine post-processor
InterMine gene-flanking regions
Gene-flanking regions created by the core InterMine post-processor
InterMine intergenic regions
Intergenic regions created by the InterMine core post-processor
InterPro
InterPro domain GO annotations
Mapping of GO terms to InterPro entries.
LIS Datastore
/data/v2/LEGUMES/Fabaceae/genefamilies/legume.genefam.fam1.M65K/legume.genefam.fam1.M65K.trees_ML_rooted
LIS gene family phylogenetic tree files
A17_HM341.gnm4.2GZ9
Medicago truncatula A17_HM341.gnm4 genome assembly
A17_HM341.gnm4.ann2.G3ZY
Genome annotations (version Mt4.0v2)
Amiga.gnm1.F4NR
Genome assembly for Lupinus albus.
Amiga.gnm1.ann1.3GKS
Genome annotation for Lupinus albus.
CDCFrontier.gnm1.GkHc
Cicer arietinum CDCFrontier.gnm1 genome assembly
CDCFrontier.gnm1.ann1.nRhs
Gene annotations, on genome assembly
CIAT22838.gnm1.XF73
Aeschynomene evenia CIAT22838.gnm1 genome assembly
CIAT22838.gnm1.ann1.ZM3R
aesev.CIAT22838.gnm1.ann1 genome annotation
Cameor.gnm1.P4FG
Pea (Pisum sativum L.), domesticated in the Middle-East ca. 10000 years ago, is a major protein crop worldwide.
Cameor.gnm1.ann1.7SZR
Pea (Pisum sativum L.), domesticated in the Middle-East ca. 10000 years ago, is a major protein crop worldwide.
G19833.gnm2.ann1.PB8d
Genome annotations for the Phaseolus vulgaris G19833 v2 genome assembly.
G27455.gnm1.7NXX
Phaseolus lunatus G27455.gnm1 genome assembly
G27455.gnm1.ann1.JD7C
phalu.G27455.gnm1.ann1 genome annotation
G27455.gnm1.ann1.JD7C
phalu.G27455.gnm1.ann1 genome annotation
Gyeongwon.gnm3.JyYC
Genome assembly (scaffolds, pseudomolecules, and information about scaffold placement in pseudomolecules)
Gyeongwon.gnm3.ann1.3Nz5
Gene annotations, on genome assembly
ICC4958.gnm2.ann1.LCVX
Gene annotations from genome assembly
ICC4958.gnm2.bg5m
Cicer arietinum ICC4958.gnm2 genome assembly
ICPL87119.gnm1.SBGP
Cajanus cajan ICPL87119.gnm1 genome assembly
ICPL87119.gnm1.ann1.Y27M
Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers
IT97K-499-35.gnm1.QnBW
Cowpea, Vigna unguiculata L. Walp, is a diploid warm-season legume, also known as black-eyed pea among other common names. Cowpea is relevant as a grain legume in the USA and Europe, and as a fresh vegetable in China and elsewhere, and is of major importance as food and fodder in sub-Saharan Africa. This release of the annotated genome (v1.0) of elite African variety IT97K-499-35 was derived from Pacific Biosciences long reads, two Bionano Genomics optical maps and ten genetic linkage maps. This work was conducted mainly under the NSF BREAD project "Advancing the Cowpea Genome for Food Security" with partial support from the Feed the Future Innovation Lab for Climate Resilient Cowpea.
IT97K-499-35.gnm1.ann2.FD7K
IT97K-499-35.gnm1.ann2 genome annotation
K30076.gnm1.ann1.J37m
araip.K30076.gnm1.ann1 annotation
K30076.gnm1.bXJ8
Arachis ipaensis K30076.gnm1 genome assembly
MG20.gnm3.QPGB
Lotus japonicus MG20.gnm3 genome assembly
MG20.gnm3.ann1.WF9B
Genome annotation
MilvusB.gnm2.ann1.DFgp
Genome assembly (seudomolecules) for Trifolium pratense, Milvus B
MilvusB.gnm2.gNmT
Genome assembly (seudomolecules) for Trifolium pratense, Milvus B
R108_HM340.gnm1.XT6J
Medicago truncatula R108_HM340.gnm1 genome assembly
R108_HM340.gnm1.ann1.85YW
Genome annotation for R108_HM340.gnm1.ann1
Tanjil.gnm1.Qq0N
Genome assembly (scaffolds, pseudomolecules, and information about scaffold placement in pseudomolecules), for Lupinus angustifolius.
Tanjil.gnm1.ann1.nnV9
Genome annotations for the Tanjil genome assembly for Lupinus angustifolius.
Tifrunner.gnm2.J5K5
Arachis hypogaea Tifrunner.gnm2 genome assembly
Tifrunner.gnm2.ann1.4K0L
Genome annotation for Arachis hypogaea cultivar Tifrunner, assembly version 2 (Tifrunner.gnm2). Gene models (gene_models_main.gff3) have been projected from Tifrunner.gnm1 into Tifrunner.gnm2 using CrossMap and chain files derived from MUMmer comparisons between the respective assemblies. The CDS, protein, and transcript files are identical to those from Tifrunner.gnm1.ann1.CCJH. Gene model mappings are incomplete: 145 models could not be automatically projected into Tifrunner.gnm2 using CrossMap. See file arahy.Tifrunner.gnm2.ann1.4K0L.info_unmapped_models.txt for the listing of unmapped genes.
V14167.gnm1.SWBf
Arachis duranensis V14167.gnm1 genome assembly
V14167.gnm1.ann1.cxSM
aradu.V14167.gnm1.ann1 annotation
VC1973A.gnm6.3nL8
Genome assembly (scaffolds and pseudomolecules) for Vigna radiata
VC1973A.gnm6.ann1.M1Qs
Genome annotations
W05.gnm1.SVL1
Genome assembly files for cultivar W05 from Xie, Chung, et al. (2019)
W05.gnm1.ann1.T47J
Genome annotations for the Glycine soja W05 genome assembly
Wm82.gnm4.4PTR
Genome assembly for Williams 82. The Williams 82 version 4 assembly (Wm82v4) builds on the widely-used assembly version 2, as well as an incremental version 3 that involved incorporation of BAC sequence to fill contig gaps in 2016. The Wm82v2 assembly was primarily Sanger-based, and new gap-filling in v3 and v4 utilized PacBio-based BAC assemblies targeted to gap regions. The Wm82v4 assembly closed 3,626 gaps and added 5,138,978 bp of sequence relative to Wm82v2, increasing the contig N50 from 233.1 kbp to 419.3 kbp.
Wm82.gnm4.ann1.T8TQ
Genome annotations for the Glycine max Williams 82 v4 genome assembly
XinJiangDaYe.gnm1.12MR
Medicago sativa XinJiangDaYe.gnm1 genome assembly
XinJiangDaYe.gnm1.ann1.RKB9
medsa.XinJiangDaYe.gnm1.ann1 genome annotation
Zh13.gnm2.LV9P
Genome assembly files for the Glycine max Zhonghuang 13 v02 genome assembly
Zh13.gnm2.ann1.FJ3G
Files in this directory are genome assembly files for cultivar Zhonghuang 13, Shen et al. (2019): Update soybean Zhonghuang 13 genome to a golden reference
jemalong_A17.gnm5.MVZ2
Medicago truncatula jemalong_A17.gnm5 genome assembly
jemalong_A17.gnm5.ann1_6.L2RX
Genome annotations (version Mt5.0-1.6)
legume.genefam.fam1.M65K
LIS gene families
Plant Ontology
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 Trait Ontology
Plant Trait Ontology
A controlled vocabulary of describe phenotypic traits in plants.
Sequence Ontology
Sequence Ontology
The Sequence Ontology is a set of terms and relationships used to describe the features and attributes of biological sequence.
USDA
Legume Federation
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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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