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


Please cite : Venkatesan A et al. (2018) Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy.
PLOS ONE 13(11): e0198270.

AgroLD includes data on the following species on:


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)
Plant Ontology (PO)
Plant Trait Ontology (TO)
Plant Environment Ontology (EO)
Sequence Ontology (SO)
Phenotype and Attribute Ontology (PATO)
NCBI Taxonomy
Evidence code Ontology
FALDO: Feature Annotation Location Description Ontology
The Interaction Network Ontology (INO)
The OBO Relations Ontology (RO)
The Semanticscience Integrated Ontology (SIO)
ORTH - the orthology ontology
VOCAB - the AgroLD schema Schema

Data sources in AgroLD:

Data source Information Website Note Species Ontologies used
Ensembl plants Gene, Orthologs This resource host several genome of plant species and gather their annotations All GO, SO, RO, SIO, FALDO
Gramene Gene, QTL, Pathways and ontology associations (PO, TO and EO) In the future versions, ontology associations will be taken from the Planteome project ( R,A, W, S, M GO, PO, TO, EO
GOA Gene Ontology associations All RO,GO,SIO
UniprotKB Protein Information All GO,RO,SIO
GreenPhylDB Web resource for phylogenetic-based approach to predict homologous relationships. R,A GO,RO,SIO,ORTH
Oryza Tag Line Database consists of phenotypic data resulting from the evaluation of the Génoplante rice insertion line library. R PO, TO
Rice Genome Hub Genes, annotations, Ontology associations R GO,SIO,FALDO,RO,SO
TropGeneDB Database for genomic, genetic and phenotypic information about tropical crops. R GO, TO, PO
Oryzabase Genes, ontology associations, publications R GO,PO,TO
Interpro Classification of protein families All GO
RAPdb The Rice annotation project R GO,SIO,FALDO,RO,SO
MSU RGAP MSU Rice genome annotation project R GO,SIO,FALDO,RO,SO
RiceNetDB Gene networks database R GO
StringDB Protein-Protein interactions network database R,A GO


Datasets are available under cc By licence DOI

Graph Names:

The RDF graphs have a common name-space:

The list of graphs are available here


To make AgroLD Linked Data compliant, de-referenceable stable URIs provided by (, Ontobee ( 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:[resource_namespace]/[identifier]

Similarly, properties, would be of the form:[vocabulary]/[property]