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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:

SPECIES

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
FALDO: Feature Annotation Location Description Ontology http://biohackathon.org/resource/faldo http://biohackathon.org/resource/faldo#ExactPosition
The Interaction Network Ontology (INO) https://github.com/INO-ontology/ino http://purl.obolibrary.org/obo/INO_0000111
The OBO Relations Ontology (RO) https://github.com/oborel/obo-relations http://purl.obolibrary.org/obo/RO_0002408
The Semanticscience Integrated Ontology (SIO) https://github.com/MaastrichtU-IDS/semanticscience http://semanticscience.org/resource/SIO_000061
ORTH - the orthology ontology https://qfo.github.io/OrthologyOntology http://purl.org/net/orth#OrthologsCluster
VOCAB - the AgroLD schema Schema http://purl.org/net/orth#OrthologsCluster

Data sources in AgroLD:

Data source Information Website Notes Species Ontologies used
Ensembl plants Gene, Orthologs plants.ensembl.org This resource host several genome of plant species and gather their annotations All GO, SO, RO, SIO
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/) R,A, W, S, M GO, PO, TO, EO
GOA Gene Ontology associations www.ebi.ac.uk/GOA All RO,GO,SIO
UniprotKB Protein Information www.uniprot.org All GO,RO,SIO
GreenPhylDB Web resource for phylogenetic-based approach to predict homologous relationships. www.greenphyl.org 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. oryzatagline.cirad.fr R PO, TO
Rice Genome Hub Genes, annotations, Ontology associations rice-genome-hub.southgreen.fr R GO,SIO,FALDO,RO,SO
TropGeneDB Database for genomic, genetic and phenotypic information about tropical crops. tropgenedb.cirad.fr R GO, TO, PO
Oryzabase Genes, ontology associations, publications shigen.nig.ac.jp/rice/oryzabase R GO,PO,TO
Interpro Classification of protein families www.ebi.ac.uk/interpro All GO
RAPdb The Rice annotation project rapdb.dna.affrc.go.jp R GO,SIO,FALDO,RO,SO
MSU RGAP MSU Rice genome annotation project rice.plantbiology.msu.edu R GO,SIO,FALDO,RO,SO
RiceNetDB Gene networks database bis.zju.edu.cn R GO
StringDB Protein-Protein interactions network database string-db.org R,A GO

Datasets:

Datasets releases are available through Zenodo under CC BY 4.0 licence at DOI:10.5281/zenodo.4694518

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/qtaro.genes
  • http://www.southgreen.fr/agrold/qtaro.qtl
  • http://www.southgreen.fr/agrold/rap.msu
  • http://www.southgreen.fr/agrold/greenphyldb
  • http://www.southgreen.fr/agrold/uniprot.plants
  • http://www.southgreen.fr/agrold/gramene.qtl
  • http://www.southgreen.fr/agrold/tropgenedb
  • http://www.southgreen.fr/agrold/ensembl.plants
  • http://www.southgreen.fr/agrold/protein.annotations
  • http://www.southgreen.fr/agrold/qtl.annotations
  • http://www.southgreen.fr/agrold/msu.genes
  • http://www.southgreen.fr/agrold/gramene.cyc
  • http://www.southgreen.fr/agrold/sniplaydb
  • http://www.southgreen.fr/agrold/oryzabase.genes
  • http://www.southgreen.fr/agrold/ricenetdb
  • http://www.southgreen.fr/agrold/rapdb
  • http://www.southgreen.fr/agrold/genome.hub
  • http://www.southgreen.fr/agrold/plantftdb
  • http://www.southgreen.fr/agrold/interpro
  • http://www.southgreen.fr/agrold/cegresources
  • http://www.southgreen.fr/agrold/ncbitaxon
  • http://www.southgreen.fr/agrold/faldo
  • http://www.southgreen.fr/agrold/ino
  • http://www.southgreen.fr/agrold/ro
  • http://www.southgreen.fr/agrold/go
  • http://www.southgreen.fr/agrold/vocabulary
  • http://www.southgreen.fr/agrold/so
  • http://www.southgreen.fr/agrold/sio
  • http://www.southgreen.fr/agrold/eco
  • http://www.southgreen.fr/agrold/pato
  • http://www.southgreen.fr/agrold/po
  • http://www.southgreen.fr/agrold/to

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