Data Sources and their Data Sets

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