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Crop Ontology towards the semantic integration of open plant trait data

Crop Ontology towards 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.

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Crop Ontology towards the semantic integration of open plant trait data

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  1. 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

  2. ProblemBreeders databases use different names for the same trait, or same trait name for different things.Data are often unstructured.They are NOT interoperable.

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

  4. salinity tolerance

  5. 16 crops... Banana Barley Cassava Chickpea Common bean Cowpea Groundnut Maize Pearl Millet Pigeon pea Potato Rice Sorghum Soybean Wheat Yam

  6. 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 ] .

  7. Linked Data

  8. Work done by Marie-Angelique Laporte

  9. Who’s using Crop Ontology?

  10. FAO- Open AGRIS FAO- Open AGRIS

  11. 1) Integrated Breeding Platform https://www.integratedbreeding.net/

  12. 2) Genotyping Data Management System https://code.google.com/p/icrisat-gdms/

  13. 3) Global Agricultural Trial Repository of the Climate Change For Agriculture and Food Security Programme http://www.agtrials.org/

  14. 4) Cassava International Database http://www.cassavabase.org/ Contacts Peter Kulakow, IITA Jean-Luc Jannink, Cornell Lukas Muller, BTI

  15. 5) EU-SOL BreeDB database https://www.eu-sol.wur.nl/ Accessions report Annotations of web pages with the Crop Ontology terms Contributed script for getting CO in Ressource Description Framework (RDF) and using RDFa for annotations Richard Finkers, Pierre Yves Chibon University of Wageningen, NDL Plant Breeding Programme

  16. 5) Plant Phenomics Ontology Driven Database (PODD)

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

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

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