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