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
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 medsa.XinJiangDaYe.gnm1 genome
medsa.XinJiangDaYe.gnm1.ann1.RKB9.cds.fna
LINK
CDS models for the medtr.A17_HM341.gnm4 genome
medtr.A17_HM341.gnm4.ann2.G3ZY.cds_primaryTranscript.fna
LINK
CDS models for the medtr.R108_HM340.gnm1 genome
medtr.R108_HM340.gnm1.ann1.85YW.cds_primaryTranscript.fna
LINK
CDS models for the medtr.jemalong_A17.gnm5 genome
medtr.jemalong_A17.gnm5.ann1_6.L2RX.cds.fna
LINK
Gene model annotation for the medsa.XinJiangDaYe.gnm1 genome
medsa.XinJiangDaYe.gnm1.ann1.RKB9.gene_models_main.gff3
LINK
Gene model annotation for the medtr.A17_HM341.gnm4 genome
medtr.A17_HM341.gnm4.ann2.G3ZY.gene_models_main.gff3
LINK
Gene model annotation for the medtr.R108_HM340.gnm1 genome
medtr.R108_HM340.gnm1.ann1.85YW.gene_models_main.gff3
LINK
Gene model annotation for the medtr.jemalong_A17.gnm5 genome
medtr.jemalong_A17.gnm5.ann1_6.L2RX.gene_models_main.gff3
LINK
LIS datastore genomic FASTA file for Medicago sativa XinJiangDaYe gnm1
medsa.XinJiangDaYe.gnm1.12MR.genome_main.fna
LINK
LIS datastore genomic FASTA file for Medicago truncatula A17_HM341
medtr.A17_HM341.gnm4.2GZ9.genome_main.fna
LINK
LIS datastore genomic FASTA file for Medicago truncatula R108_HM340
medtr.R108_HM340.gnm1.XT6J.genome_main.fna
LINK
LIS datastore genomic FASTA file for Medicago truncatula jemalong_A17
medtr.jemalong_A17.gnm5.MVZ2.genome_main.fna
LINK
LIS gene families
legume.genefam.fam1.M65K.info_annot_ahrd.tsv
LINK
LIS gene family assignments for medsa.XinJiangDaYe.gnm1
medsa.XinJiangDaYe.gnm1.ann1.RKB9.legfed_v1_0.M65K.gfa.tsv
LINK
LIS gene family assignments for medtr.A17_HM341.gnm4
medtr.A17_HM341.gnm4.ann2.G3ZY.legfed_v1_0.M65K.gfa.tsv
LINK
LIS gene family assignments for medtr.R108_HM340.gnm1
medtr.R108_HM340.gnm1.ann1.85YW.legfed_v1_0.M65K.gfa.tsv
LINK
LIS gene family assignments for medtr.jemalong_A17.gnm5
medtr.jemalong_A17.gnm5.ann1_6.L2RX.legfed_v1_0.M65K.gfa.tsv
LINK
Medicago sativa organism and strain information.
description_Medicago_sativa.yml
LINK
Medicago sativa organism and strain information.
strains_Medicago_sativa.yml
LINK
Medicago truncatula organism and strain information.
description_Medicago_truncatula.yml
LINK
Medicago truncatula organism and strain information.
strains_Medicago_truncatula.yml
LINK
Plant Reactome pathways for medsa.XinJiangDaYe.gnm1 via gene family membership with R108_HM340.
medsa.XinJiangDaYe.gnm1.ann1.RKB9.legfed_v1_0.M65K.pathway.tsv
LINK
Plant Reactome pathways for medtr.A17_HM341.gnm4
medtr.A17_HM341.gnm4.ann2.G3ZY.pathway.tsv
LINK
Plant Reactome pathways for medtr.R108_HM340.gnm1 via gene family membership with R108_HM340.
medtr.R108_HM340.gnm1.ann1.85YW.legfed_v1_0.M65K.pathway.tsv
LINK
Plant Reactome pathways for medtr.jemalong_A17.gnm5 via gene family membership with R108_HM340.
medtr.jemalong_A17.gnm5.ann1_6.L2RX.legfed_v1_0.M65K.pathway.tsv
LINK
Protein models for the medsa.XinJiangDaYe.gnm1 genome
medsa.XinJiangDaYe.gnm1.ann1.RKB9.protein.faa
LINK
Protein models for the medtr.A17_HM341.gnm4 genome
medtr.A17_HM341.gnm4.ann2.G3ZY.protein_primaryTranscript.faa
LINK
Protein models for the medtr.R108_HM340.gnm1 genome
medtr.R108_HM340.gnm1.ann1.85YW.protein_primaryTranscript.faa
LINK
Protein models for the medtr.jemalong_A17.gnm5 genome
medtr.jemalong_A17.gnm5.ann1_6.L2RX.protein.faa
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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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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