Data Sources and their Data Sets

CATHGENE3D
CDD
Chickpea Crop Ontology
A controlled vocabulary to describe crop traits in chickpea.
Chickpea 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 cicar.CDCFrontier.gnm1 genome
cicar.CDCFrontier.gnm1.ann1.nRhs.cds.fna
LINK
CDS models for the cicar.ICC4958.gnm2 genome
cicar.ICC4958.gnm2.ann1.LCVX.cds_primaryTranscript.fna
LINK
Cicer arietinum GWAS for drought-tolerant yield traits from Li, et al. 2018
cicar.mixed.gwas.KEY4.29515606.gwas.tsv
LINK
Cicer arietinum GWAS for drought-tolerant yield traits from Li, et al. 2018
cicar.mixed.gwas.KEY4.29515606.phen.tsv
LINK
Cicer arietinum GWAS for drought-tolerant yield traits from Li, et al. 2018
cicar.mixed.gwas.KEY4.31036963.gwas.tsv
LINK
Cicer arietinum GWAS for drought-tolerant yield traits from Li, et al. 2018
cicar.mixed.gwas.KEY4.31036963.phen.tsv
LINK
Cicer arietinum ICC4958 transcription during flower development from Singh, et al. (2013).
cicar.ICC4958.gnm2.ann1.expr.4Y7B.samples.tsv
LINK
Cicer arietinum ICC4958 transcription during flower development from Singh, et al. (2013).
cicar.ICC4958.gnm2.ann1.expr.4Y7B.source.tsv
LINK
Cicer arietinum ICC4958 transcription during flower development from Singh, et al. (2013).
cicar.ICC4958.gnm2.ann1.expr.4Y7B.values.tsv
LINK
Cicer arietinum organism and strain information.
description_Cicer_arietinum.yml
LINK
Cicer arietinum organism and strain information.
strains_Cicer_arietinum.yml
LINK
Cowpea SNP positions (Li et al. 2018) on the cicar.CDCFrontier.gnm263 (kabuli 2.6.3) genome assembly
cicar.CDCFrontier.gnm263.mrk.KEY4.29515606.gff3
LINK
Cowpea SNP positions on the cicar.CDCFrontier.gnm1 genome assembly from Varshney, et al. (2019)
cicar.CDCFrontier.gnm1.mrk.KEY4.31036963.gff3
LINK
Gene family assignments for Cicer arietinum ICC4958 genes and proteins.
cicar.ICC4958.gnm2.ann1.LCVX.legfed_v1_0.M65K.gfa.tsv
LINK
Gene model annotation for the cicar.CDCFrontier.gnm1 genome
cicar.CDCFrontier.gnm1.ann1.nRhs.gene_models_main.gff3
LINK
Gene model annotation for the cicar.CDCFrontier.gnm263 (kabuli 2.6.3) genome
cicar.CDCFrontier.gnm263.ann1.KEY4.gene_models_main.gff3
LINK
Gene model annotation for the cicar.ICC4958.gnm2 genome
cicar.ICC4958.gnm2.ann1.LCVX.gene_models_main.gff3
LINK
LIS Gene family membership for Cicer arietinum CDCFrontier.
cicar.CDCFrontier.gnm1.ann1.nRhs.legfed_v1_0.M65K.gfa.tsv
LINK
LIS datastore genomic FASTA file for Cicer arietinum CDCFrontier
cicar.CDCFrontier.gnm1.GkHc.genome_main.fna
LINK
LIS datastore genomic FASTA file for Cicer arietinum CDCFrontier.gnm263 (kabuli 2.6.3)
cicar.CDCFrontier.gnm263.KEY4.genome_main.fna
LINK
LIS datastore genomic FASTA file for Cicer arietinum ICC4958
cicar.ICC4958.gnm2.bg5m.genome_main.fna
LINK
LIS gene families
legume.genefam.fam1.M65K.info_annot_ahrd.tsv
LINK
Plant Reactome pathways for Cicer arietinum CDCFrontier.
cicar.CDCFrontier.gnm1.ann1.nRhs.pathway.tsv
LINK
Plant reactome pathways for Cicer arietinum ICC4958 genes from gene family membership with Cicer arietinum CDCFrontier genes.
cicar.ICC4958.gnm2.ann1.LCVX.legfed_v1_0.M65K.pathway.tsv
LINK
Protein models for the cicar.CDCFrontier.gnm1 genome
cicar.CDCFrontier.gnm1.ann1.nRhs.protein.faa
LINK
Protein models for the cicar.ICC4958.gnm2 genome
cicar.ICC4958.gnm2.ann1.LCVX.protein_primaryTranscript.faa
LINK
Synteny between cicar.CDCFrontier.gnm1 and other species.
cicar.CDCFrontier.gnm1.ann1.x.cicar.CDCFrontier.gnm1.ann1.gff
LINK
Synteny between cicar.CDCFrontier.gnm1 and other species.
cicar.CDCFrontier.gnm1.ann1.x.cicar.ICC4958.gnm2.ann1.gff
LINK
Synteny between cicar.CDCFrontier.gnm1 and other species.
cicar.CDCFrontier.gnm1.ann1.x.lotja.MG20.gnm3.ann1.gff
LINK
Synteny between cicar.CDCFrontier.gnm1 and other species.
cicar.CDCFrontier.gnm1.ann1.x.medtr.A17_HM341.gnm4.ann2.gff
LINK
Synteny between cicar.CDCFrontier.gnm1 and other species.
cicar.CDCFrontier.gnm1.ann1.x.tripr.MilvusB.gnm2.ann1.gff
LINK
Synteny between cicar.ICC4958.gnm2 and other species.
cicar.ICC4958.gnm2.ann1.x.cicar.CDCFrontier.gnm1.ann1.gff
LINK
Synteny between cicar.ICC4958.gnm2 and other species.
cicar.ICC4958.gnm2.ann1.x.cicar.ICC4958.gnm2.ann1.gff
LINK
Synteny between cicar.ICC4958.gnm2 and other species.
cicar.ICC4958.gnm2.ann1.x.lotja.MG20.gnm3.ann1.gff
LINK
Synteny between cicar.ICC4958.gnm2 and other species.
cicar.ICC4958.gnm2.ann1.x.medtr.A17_HM341.gnm4.ann2.gff
LINK
Synteny between cicar.ICC4958.gnm2 and other species.
cicar.ICC4958.gnm2.ann1.x.tripr.MilvusB.gnm2.ann1.gff
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
USDA
Legume Federation
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