Crop Ontology towards the semantic integration of open

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www.cropontology.org
Crop Ontology
towards the semantic
integration of open plant
trait data
Elizabeth Arnaud, Luca Matteis, Rosemary Shrestha,
Milko Skofic, Laurel Cooper, Pankaj Jaiswal, PierreYves Chibon, Mark Wilkinson, Richard Bruskiewich,
Graham McLaren
Problem
Breeders 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 breeders
breeding = ”the art and science
of changing the traits of plants
in order to produce desired
characteristics in given
environments.”
salinity tolerance
16 crops...
Banana
Barley
Cassava
Chickpea
Common bean
Cowpea
Groundnut
Maize
Pearl Millet
Pigeon pea
Potato
Rice
Sorghum
Soybean
Wheat
Yam
Semantics
From OBO to RDF/SKOS
resolvable 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 using
Crop Ontology?
FAO- Open AGRIS
FAO- Open AGRIS
1) Integrated Breeding Platform
https://www.integratedbreeding.net/
2) Genotyping Data Management
System
https://code.google.com/p/icrisat-gdms/
3) Global Agricultural Trial Repository of the
Climate Change For Agriculture and Food
Security Programme
http://www.agtrials.org/
4) Cassava International Database
http://www.cassavabase.org/
Contacts
Peter Kulakow, IITA
Jean-Luc Jannink, Cornell
Lukas Muller, BTI
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
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
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