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
Arachis duranensis organism and strain information.
description_Arachis_duranensis.yml
Arachis duranensis organism and strain information.
strains_Arachis_duranensis.yml
Arachis hypogaea organism and strain information.
description_Arachis_hypogaea.yml
Arachis hypogaea organism and strain information.
strains_Arachis_hypogaea.yml
Arachis ipaensis organism and strain information.
description_Arachis_ipaensis.yml
Arachis ipaensis organism and strain information.
strains_Arachis_ipaensis.yml
CDS models for the aradu.V14167.gnm1 genome
aradu.V14167.gnm1.ann1.cxSM.cds.fna
CDS models for the arahy.Tifrunner.gnm1 genome
arahy.Tifrunner.gnm1.ann1.CCJH.cds_primaryTranscript.fna
CDS models for the arahy.Tifrunner.gnm2 genome
arahy.Tifrunner.gnm2.ann1.4K0L.cds_primaryTranscript.fna
CDS models for the araip.K30076.gnm1 genome
araip.K30076.gnm1.ann1.J37m.cds.fna
Gene family assignments for Arachis duranensis V14167 genes and proteins.
aradu.V14167.gnm1.ann1.cxSM.legfed_v1_0.M65K.gfa.tsv
Gene family assignments for Arachis hypogaea Tifrunner gnm1 genes and proteins.
arahy.Tifrunner.gnm1.ann1.CCJH.legfed_v1_0.M65K.gfa.tsv
Gene family assignments for Arachis hypogaea Tifrunner gnm2 genes and proteins.
arahy.Tifrunner.gnm2.ann1.4K0L.legfed_v1_0.M65K.gfa.tsv
Gene family assignments for Arachis ipaensis K30076 genes and proteins.
araip.K30076.gnm1.ann1.J37m.legfed_v1_0.M65K.gfa.tsv
Gene model annotation for the aradu.V14167.gnm1 genome
aradu.V14167.gnm1.ann1.cxSM.gene_models_main.gff3
Gene model annotation for the arahy.Tifrunner.gnm1 genome
arahy.Tifrunner.gnm1.ann1.CCJH.gene_models_main.gff3
Gene model annotation for the arahy.Tifrunner.gnm2 genome
arahy.Tifrunner.gnm2.ann1.4K0L.gene_models_main.gff3
Gene model annotation for the araip.K30076.gnm1 genome
araip.K30076.gnm1.ann1.J37m.gene_models_main.gff3
LIS datastore genomic FASTA file for Arachis duranensis V14167
aradu.V14167.gnm1.SWBf.genome_main.fna
LIS datastore genomic FASTA file for Arachis hypogaea Tifrunner
arahy.Tifrunner.gnm1.KYV3.genome_main.fna
LIS datastore genomic FASTA file for Arachis hypogaea Tifrunner
arahy.Tifrunner.gnm2.J5K5.genome_main.fna
LIS datastore genomic FASTA file for Arachis ipaensis K30076
araip.K30076.gnm1.bXJ8.genome_main.fna
LIS gene families
legume.genefam.fam1.M65K.info_annot_ahrd.tsv
MRNA models for the araip.K30076.gnm1 genome
araip.K30076.gnm1.ann1.J37m.transcript.fna
Plant Reactome pathways for aradu.V14167.gnm1
aradu.V14167.gnm1.ann1.cxSM.pathway.tsv
Plant Reactome pathways for arahy.Tifrunner.gnm1
arahy.Tifrunner.gnm1.ann1.CCJH.legfed_v1_0.M65K.pathway.tsv
Plant Reactome pathways for arahy.Tifrunner.gnm2
arahy.Tifrunner.gnm2.ann1.4K0L.legfed_v1_0.M65K.pathway.tsv
Plant Reactome pathways for araip.K30076.gnm1
araip.K30076.gnm1.ann1.J37m.pathway.tsv
Protein models for the aradu.V14167.gnm1 genome
aradu.V14167.gnm1.ann1.cxSM.protein.faa
Protein models for the arahy.Tifrunner.gnm1 genome
arahy.Tifrunner.gnm1.ann1.CCJH.protein_primaryTranscript.faa
Protein models for the arahy.Tifrunner.gnm2 genome
arahy.Tifrunner.gnm2.ann1.4K0L.protein_primaryTranscript.faa
Protein models for the araip.K30076.gnm1 genome
araip.K30076.gnm1.ann1.J37m.protein.faa
Synteny between aradu.V14167.gnm1 and other species.
aradu.V14167.gnm1.ann1.x.aradu.V14167.gnm1.ann1.gff
Synteny between aradu.V14167.gnm1 and other species.
aradu.V14167.gnm1.ann1.x.araip.K30076.gnm1.ann1.gff
Synteny between aradu.V14167.gnm1 and other species.
aradu.V14167.gnm1.ann1.x.glyma.Wm82.gnm2.ann1.gff
Synteny between aradu.V14167.gnm1 and other species.
aradu.V14167.gnm1.ann1.x.lupan.Tanjil.gnm1.ann1.gff
Synteny between aradu.V14167.gnm1 and other species.
aradu.V14167.gnm1.ann1.x.medtr.A17_HM341.gnm4.ann2.gff
Synteny between aradu.V14167.gnm1 and other species.
aradu.V14167.gnm1.ann1.x.phavu.G19833.gnm1.ann1.gff
Synteny between aradu.V14167.gnm1 and other species.
aradu.V14167.gnm1.ann1.x.phavu.G19833.gnm2.ann1.gff
Synteny between aradu.V14167.gnm1 and other species.
aradu.V14167.gnm1.ann1.x.vigra.VC1973A.gnm6.ann1.gff
Synteny between araip.K30076.gnm1 and other species.
araip.K30076.gnm1.ann1.x.aradu.V14167.gnm1.ann1.gff
Synteny between araip.K30076.gnm1 and other species.
araip.K30076.gnm1.ann1.x.araip.K30076.gnm1.ann1.gff
Synteny between araip.K30076.gnm1 and other species.
araip.K30076.gnm1.ann1.x.glyma.Wm82.gnm2.ann1.gff
Synteny between araip.K30076.gnm1 and other species.
araip.K30076.gnm1.ann1.x.lupan.Tanjil.gnm1.ann1.gff
Synteny between araip.K30076.gnm1 and other species.
araip.K30076.gnm1.ann1.x.medtr.A17_HM341.gnm4.ann2.gff
Synteny between araip.K30076.gnm1 and other species.
araip.K30076.gnm1.ann1.x.phavu.G19833.gnm1.ann1.gff
Synteny between araip.K30076.gnm1 and other species.
araip.K30076.gnm1.ann1.x.phavu.G19833.gnm2.ann1.gff
Synteny between araip.K30076.gnm1 and other species.
araip.K30076.gnm1.ann1.x.vigra.VC1973A.gnm6.ann1.gff
mRNA models for the aradu.V14167.gnm1 genome
aradu.V14167.gnm1.ann1.cxSM.transcript.fna
mRNA models for the arahy.Tifrunner.gnm1 genome
arahy.Tifrunner.gnm1.ann1.CCJH.transcript_primaryTranscript.fna
mRNA models for the arahy.Tifrunner.gnm2 genome
arahy.Tifrunner.gnm2.ann1.4K0L.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
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.
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