The Species-specific crop ontology (Generation Challenge Programme): application and integration into the reference plant trait ontology to enable data mining on phenotypes : P0937

Arnaud Elizabeth, Shrestha Rosemary, Kulakow Peter, Bakare Moshood, Lopez-Montes Antonio, Ofodile Sam, Reddy Praveen, Prasad Peteti, Shah Trushar, Hash Charles Thomas, Weltzien-Rattunde Eva, Sissoko I., Guerrero Alberto Fabio, Simon Reinhard, Borja Borja Nikki Frances, Ramil Mauleon, Skofic Milko, Hazekamp Tom, McLaren Graham, Cooper Laurel, Jaiswal Pankaj, Menda Naama, Nelson Rex, Grant David, Bastow Ruth, Mueller Lukas, Rami Jean-François. 2013. The Species-specific crop ontology (Generation Challenge Programme): application and integration into the reference plant trait ontology to enable data mining on phenotypes : P0937. In : Plant and Animal Genome XXI conference, San Diego, USA, January 12-16 2013,. s.l. : s.n., Résumé, 1 p. Plant and Animal Genome conference. 21, San Diego, États-Unis, 12 January 2013/16 January 2013.

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Abstract : The Crop Ontology (CO) of the Generation Challenge Program (GCP) ( currently contains eleven crop-specific ontologies and has been developed for the Integrated Breeding Platform (IBP) ( 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 (; Agtrials, the Global Repository for Evaluation Trials of Climate Change, Agriculture and Food Security (CCAFS), a CGIAR Research Program ( ); and the EU-Sol BreedDB website ( 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;, the Trait Ontology (TO; the USDA-ARS SoyBase Database. (Résumé d'auteur)

Classification Agris : F30 - Plant genetics and breeding
U10 - Mathematical and statistical methods

Auteurs et affiliations

  • Arnaud Elizabeth, Bioversity International (FRA)
  • Shrestha Rosemary, CIMMYT (MEX)
  • Kulakow Peter, IITA (NGA)
  • Bakare Moshood, IITA (NGA)
  • Lopez-Montes Antonio, IITA (NGA)
  • Ofodile Sam, IITA (NGA)
  • Reddy Praveen, ICRISAT (IND)
  • Prasad Peteti, ICRISAT (IND)
  • Shah Trushar, ICRISAT (IND)
  • Hash Charles Thomas, ICRISAT (NER)
  • Weltzien-Rattunde Eva, ICRISAT (MLI)
  • Sissoko I., ICRISAT (MLI)
  • Guerrero Alberto Fabio, CIAT (COL)
  • Simon Reinhard, CIP (PER)
  • Borja Borja Nikki Frances, IRRI (PHL)
  • Ramil Mauleon, IRRI (PHL)
  • Skofic Milko, Bioversity International (ITA)
  • Hazekamp Tom
  • McLaren Graham
  • Cooper Laurel, IPPC (USA)
  • Jaiswal Pankaj, Oregon State University (USA)
  • Menda Naama, Boyce Thompson Institute for Plant Research (USA)
  • Nelson Rex, USDA (USA)
  • Grant David, USDA (USA)
  • Bastow Ruth
  • Mueller Lukas, Boyce Thompson Institute for Plant Research (USA)
  • Rami Jean-François, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-5679-3877

Source : Cirad - Agritrop (

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