The species-specific crop ontology (Generation Challenge Programme): Application and integration into the reference plant trait ontology to enable data mining on phenotypes.

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dc.creatorArnaud, Elizabeth
dc.creatorShrestha, R.
dc.creatorKulakow, Peter A.
dc.creatorBakare, M.
dc.creatorLópez Montes, Antonio José
dc.creatorOfodile, S.
dc.creatorReddy T.P.
dc.creatorPrasad, P.
dc.creatorShah, Tushaar
dc.creatorHash, C.T.
dc.creatorWeltzien, Eva
dc.creatorSissoko, I.
dc.creatorGuerrero, Alberto F.
dc.creatorSimon, R.
dc.creatorBorja Borja, N.F.
dc.creatorRamil, M.
dc.creatorMatteis, L.
dc.creatorSkofic, M.
dc.creatorHazekamp, T.
dc.creatorMcLaren, G.
dc.creatorCooper, Laurel D.
dc.creatorJaiswal, P.
dc.creatorMenda, N.
dc.creatorNelson, R.
dc.creatorGrant, D.
dc.creatorBastow, R.
dc.creatorMueller, L.
dc.creatorRami, J.F.
dc.date2013
dc.date2015-03-11T12:04:51Z
dc.date2015-03-11T12:04:51Z
dc.date.accessioned2026-06-27T18:00:19Z
dc.descriptionThe Crop Ontology (CO) of the Generation Challenge Program (GCP) (http://cropontology.org/) currently contains eleven crop-specific ontologies and has been developed for the Integrated Breeding Platform (IBP) (https://www.integratedbreeding.net/) by several CGIAR centers. The CO provides validated trait names used by crop communities of practice (CoP) for harmonizing the annotation of phenotypic and genotypic data and thus supporting data accessibility and discovery through web queries. The trait information is completed by the description of the measurement methods and scales and images. The trait dictionaries used to produce the Integrated Breeding (IB) fieldbooks are synchronized with the CO terms for automatic annotation of the phenotypic data measured in the field. The CO acts as a trait name server for various sites and databases: the Genotyping Data Management System (GDMS); the cassava database at Cornell University (http://cassavadb.org); Agtrials, the Global Repository for Evaluation Trials of Climate Change, Agriculture and Food Security (CCAFS), a CGIAR Research Program (http://agtrials.org ); and the EU-Sol BreedDB website (https://www.eu-sol.wur.nl/). The vision will be presented of a species-neutral and overarching Reference Plant Trait Ontology to support data annotation, integration and data mining across species, which has resulted from the successful collaboration between the CO project, the Plant Ontology (PO; http://www.plantontology.org/), the Trait Ontology (TO;http://www.gramene.org/plant_ontology/) the USDA-ARS SoyBase Database (http://www.soybase.org/), the Solanaceae Genomic Network (http://solgenomics.net/), and GarNet (http://www.garnetcommunity.org.uk/).
dc.identifierhttps://hdl.handle.net/10568/57036
dc.identifier.urihttp://hdl.handle.net/123456789/152150
dc.languageen
dc.rightsLimited Access
dc.sourceArnaud, E.; Shrestha, R.; Kulakow, P.; Bakare, M.; Lopez Montes, A.; Ofodile, S.; Reddy T.P.; Prasad, P.; Shah, T.; Hash, C.T.; Weltzien-Rattunde, E.; Sissoko, I.; Guerrero, A.F.; Simon, R.; Borja Borja, N.F.; Ramil, M.; Matteis, L.; Skofic, M.; Hazekamp, T.; McLaren, G.; Cooper, L.; Jaiswal, P.; Menda, N.; Nelson, R.; Grant, D.; Bastow, R.; Mueller, L.; Rami, J.F. 2013. The species-specific crop ontology (Generation Challenge Programme): Application and integration into the reference plant trait ontology to enable data mining on phenotypes. Final abstracts guide. 21. International Plant & Animal Genome Conference. San Diego, California (USA). 12-16 Jan 2013. California (USA). PAG.
dc.subjectpotatoes
dc.subjectontology
dc.subjectphenotypes
dc.titleThe species-specific crop ontology (Generation Challenge Programme): Application and integration into the reference plant trait ontology to enable data mining on phenotypes.
dc.typeConference Paper

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