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This page provides a summary on the species, data sources and URI patterns.

AgroLD includes data on the following species on:

  • Arabidopsis thaliana (NCBI Taxon ID: 3702)
  • Oryza species:
    • Oryza barthii (NCBI Taxon ID: 65489)
    • Oryza brachyantha (NCBI Taxon ID: 4533)
    • Oryza glaberrima (NCBI Taxon ID: 4538)
    • Oryza meridionalis (NCBI Taxon ID: 40149)
    • Oryza sativa (NCBI Taxon ID: 4530)
      • Oryza sativa indica (NCBI Taxon ID: 39946)
      • Oryza sativa japonica (NCBI Taxon ID: 39947)
  • Sorghum bicolor (NCBI Taxon ID: 4558)
  • Triticum species:
    • Triticum aestivum (NCBI Taxon ID: 4565)
    • Triticum urartu (NCBI Taxon ID: 4572)
  • Zea mays (NCBI Taxon ID: 4577)

Ontologies in AgroLD:

The OWL versions of the ontologies have been loaded to AgroLD. The original namespaces and URIs have been retained.

Ontology Website Example(s)
Gene Ontology (GO) http://geneontology.org/ http://purl.obolibrary.org/obo/GO_0008150
Plant Ontology (PO) http://planteome.org/ http://purl.obolibrary.org/obo/PO_0025131
Plant Trait Ontology (TO) http://purl.obolibrary.org/obo/TO_0000387
Plant Environment Ontology (EO) http://purl.obolibrary.org/obo/EO_0007359
Sequence Ontology (SO) http://www.berkeleybop.org/ontologies/ http://purl.obolibrary.org/obo/SO_0000104
Phenotype and Attribute Ontology (PATO) http://purl.obolibrary.org/obo/PATO_0000462
NCBI Taxonomy http://purl.obolibrary.org/obo/NCBITaxon_4565
Evidence code Ontology http://purl.obolibrary.org/obo/ECO_0000033

Data sources in AgroLD:

Data source Information Website Note
Gramene Gene, QTL, Pathways and ontology associations (PO, TO and EO) www.gramene.org In the future versions, ontology associations will be taken from the Planteome project (http://planteome.org/)
GOA Gene Ontology associations www.ebi.ac.uk/GOA
UniprotKB Protein Information www.uniprot.org
GreenPhylDB Web resource for phylogenetic-based approach to predict homologous relationships. www.greenphyl.org
Oryza Tag Line Database consists of phenotypic data resulting from the evaluation of the Génoplante rice insertion line library. oryzatagline.cirad.fr
OryGenesDB Database for sequence information resulting from the T-DNA and Ds flanking sequence tags FSTs. Also contains information on cDNA full length, EST and Markers orygenesdb.cirad.fr
TropGeneDB Database for genomic, genetic and phenotypic information about tropical crops. tropgenedb.cirad.fr

Species specific break down of the data sources:

Data
Sources
Crop species
Oryza species Triticum species A.thaliana S.bicolor Z.mays
Ontology associations GOA
Gramene-PO
Gramene-TO      
Gramene-EO        
Gramene-gene
Gramene-QTL        
Gramene-Cyc,pathways  
UniprotKB
OryGenesDB      
Oryza Tag Line        
TropGeneDB        
GreenPhylDB  

Graph Names:

The RDF graphs have a common name-space: http://www.southgreen.fr/agrold/

The list of graphs are follows:

  • http://www.southgreen.fr/agrold/eco
  • http://www.southgreen.fr/agrold/eo
  • http://www.southgreen.fr/agrold/go
  • http://www.southgreen.fr/agrold/gramene.cyc
  • http://www.southgreen.fr/agrold/gramene.genes
  • http://www.southgreen.fr/agrold/gramene.qtl
  • http://www.southgreen.fr/agrold/greenphyldb
  • http://www.southgreen.fr/agrold/ncbitaxon
  • http://www.southgreen.fr/agrold/orygenesdb.a.thaliana
  • http://www.southgreen.fr/agrold/orygenesdb.o.s.indica
  • http://www.southgreen.fr/agrold/orygenesdb.o.s.japonica
  • http://www.southgreen.fr/agrold/otl
  • http://www.southgreen.fr/agrold/pato
  • http://www.southgreen.fr/agrold/po
  • http://www.southgreen.fr/agrold/protein.annotations
  • http://www.southgreen.fr/agrold/qtl.annotations
  • http://www.southgreen.fr/agrold/so
  • http://www.southgreen.fr/agrold/to
  • http://www.southgreen.fr/agrold/tropgenedb
  • http://www.southgreen.fr/agrold/uniprot.plants

URIs:

To make AgroLD Linked Data compliant, de-referenceable stable URIs provided by Identifiers.org (http://identifiers.org/), Ontobee (www.ontobee.org) and canonical stable URIs provided UniprotKB are used.

Datasets that are not included in these registries, new URIs were minted the identifiers for these datasets take the form:

http://www.southgreen.fr/agrold/[resource_namespace]/[identifier]
Example:
http://www.southgreen.fr/agrold/biocyc.pathway/CALVIN-PWY

Similarly, properties, would be of the form:

http://www.southgreen.fr/agrold/[vocabulary]/[property]
Example:
http://www.southgreen.fr/agrold/vocabulary/expressed_in