Crop Ontologytowards the semantic

integration of open plant trait data

www.cropontology.org

Elizabeth Arnaud, Luca Matteis, Rosemary Shrestha, Milko Skofic, Laurel Cooper, Pankaj Jaiswal, Pierre-Yves Chibon, Mark Wilkinson, Richard Bruskiewich, Graham McLaren

ProblemBreeders databases use different names for the same trait, or same

trait name for different things.Data are often unstructured.They are NOT interoperable.

Knowledge domain for plant breedersbreeding = ”the art and science of changing the traits of plants in order to produce desired characteristics in given environments.”

salinity tolerance

16 crops...BananaBarleyCassavaChickpea Common bean Cowpea Groundnut Maize Pearl Millet

Pigeon peaPotatoRiceSorghumSoybeanWheat Yam

SemanticsFrom OBO to RDF/SKOSresolvable HTTP URIs

<http://www.cropontology.org/rdf/CO_324:0000002> a skos:Concept ; rdfs:label "Flag leaf weight"@en ; dc:creator _:b1 ; skos:definition "Weight of the flag leaf (the one just below the panicle)." ; skos:inScheme co:sorghum ; skosxl:prefLabel [ a skosxl:Label ; co:acronym [ a skosxl:Label ; skosxl:literalForm "FLGWT" ] ; skosxl:literalForm "Flag leaf weight"@en ] .

Linked Data

Work done by Marie-Angelique Laporte

Who’s usingCrop Ontology?

FAO- Open AGRIS

FAO- Open AGRIS FAO- Open AGRIS

1) Integrated Breeding Platform

https://www.integratedbreeding.net/

2) Genotyping Data Management

Systemhttps://code.google.com/p/icrisat-gdms/

3) Global Agricultural Trial Repository of

the Climate Change For Agriculture and

Food Security Programmehttp://www.agtrials.org/

4) Cassava International Database

ContactsPeter Kulakow, IITA

Jean-Luc Jannink, CornellLukas Muller, BTI

http://www.cassavabase.org/

5) EU-SOL BreeDB database

University of Wageningen, NDLPlant Breeding Programme

Annotations of web pages with the Crop Ontology terms

Contributed script for gettingCO in Ressource Description Framework (RDF) and using RDFa for annotations

Accessions report

Richard Finkers, Pierre Yves Chibon

https://www.eu-sol.wur.nl/

5) Plant Phenomics Ontology

Driven Database (PODD)

Crop Ontology will facilitate the discovery of plant trait data within the Linked Data cloud

Thanks!https://github.com/bioversity/Crop-Ontology