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GRM 2011: Introduction to the crop ontology tool


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GRM 2011: Introduction to the crop ontology tool

  1. 1. How to contribute to and use theGCP Crop Ontology,A Reference Traits List ?Use of the New Curation andAnnotation toolGeneration Challenge Programme, Global Research Meeting, 20th-26th September, Hyderabad, IndiaElizabeth Arnaud, (Bioversity), Rosemary Shrestha (CIMMYT),Matteis Luca (Bioversity), Milko Skofic (Bioversity)
  2. 2. Why a GCP Crop Ontology? Offer harmonized and structured list of traitsnames, methods and scales Facilitate sharing of information between researchtrials through field books Increase efficiency of trait information retrievaland keyword-based queries Enable annotation for integration of researchdocuments, reports, and databases with ontologicalterms
  3. 3. Current status of the Crop OntologyMusaCassavaAnatomy, Structure & Phenotype of Crops Trait Measurement Methods and Scales GermplasmCrop LeadingorganizationOntology TraitDictionariesNumber oftraitsCassava IITA √ √ 123Chickpea ICRSAT √ √ 51Common beans CIAT √ 76Cowpea ICRISAT √Groundnuts ICRISAT √Maize CIMMYT √ 177Musa Bioversity √ 173Potato CIP √ 210Rice IRRI √ 220Sorghum ICRISAT √ √ 70Wheat CIMMYT √ 176+
  4. 4. Trait Template & Dictionaries• The Trait Template is used by ontology curators andbreeders to submit new trait lists• Is a tool to get consensus on the trait to be submitted alongwith definitions, categories and scales• Excel files to be uploaded on the Tool
  5. 5. The New Curation and Annotation tool Crop curators can upload or create online ontologies Expend the content by adding terms and attributes likephotos, protocols, scale, scale value, scoring guidelines andgrowth stages for scoring traits Anyone can post a comment. API available for any application to ‘programmatically’ create,read, update and delete terms NoSQL Database The tool is on the Cloud to improve the access performance Code documented on GitHub: Luca Matteis, Milko Skofic (Bioversity International)Video realization: Valentina Barbiero (Bioversity International)
  6. 6. The New Curation and Annotation toolHomepage
  7. 7. Trait information with definition,photos & measurement methods
  8. 8. Crop Ontology Annotation Tool• The annotation tool matches thecontent of the data file or traitlist with validated terms fromthe ontology• Curator can accept the match towith local term• Leading to the harmonization ofthe annotation• Result can be downloaded ascomma separated file (csv) thatcan be uploaded into Excel or adatabase.• Still at the prototype level,needs tests and feedback
  9. 9. A reference Trait List1. Integration with IB Field bookfile:///Users/elisabeth/Documents/GCP%20GRM%202011/presentation/Agtrials%20crop%20otno.swf
  10. 10. 2. Integration with theGlobal Agricultural Trial Repository
  11. 11. Drought Recovery - (Rice)
  12. 12. 3. Integration with theCrop Wild Relatives OntologyEuropean Crop Wild Relative Diversity Assessment andConservation Forum, EU funded400 termsrepresenting in situ and ex situconservation status of Individualtaxa & their utilization potential PGRSecure project :
  13. 13. Plans for end 2011 & 2012 Ontology Curation and use Community of Practice for Data Management and Breeders Content extension A trait dictionary for each crop with methods & scales Check online content with breeders Add Common Beans, Cowpea and Groundnut, Germplasm Methods Multilingual versions of trait names & definitions Tool Development Take GRM feedback into account  ON LINE SURVEY Synchronize crop ontology curation tool with the IBP Field Book usingweb service Integration in the online and offline configurable IB workflow Expend use cases with Agtrials Build a single working place
  14. 14. Crop Ontology Team since 2008Developers•Luca Matteis (Bioversity)•Milko Skofic (Bioversity)•Hector Sanchez (CIMMYT)• Martin Senger (CRIL)• Mauleon Ramil (CRIL-IRRI)Curators of the Crop-specific Ontology•Jayashree Balaji (ICRISAT, Sorghum & Chickpea)•Ibrahima Sissoko (ICRISAT, Sorghum)•Prasad Peteti (ICRISAT, Groundnut & Chickpea)•Praveen Reddy (ICRISAT, Sorghum )•Stephanie Channeliere (Bioversity, Musa)•Jean Piette Horry (CIRAD, Musa)•Peter Kulakow (IITA, Cassava)• Moshood Bakare Agba (IITA, Cassava)•Nikki Frances Borja (IRRI, Rice)•Rosemary Shrestha (CIMMYT, Maize & Wheat)•Reinhard Simon (CIP, Potato)Acknowledgements to: Adriana Alercia, (Bioversity International, Crop descriptorsspecialist), Richard Bruskiewich (GCP Bioinformatics, former Principle Investigator, IRRI),Guy Davenport (GCP bioinformatics, CIMMYT), Graham McLaren (GCP sub-programmeon Crop information system, Leader), Martin SENGER (GCP Bioinformatics, formerlyIRRI), Theo van Hintum (SP4 leader, WUR)Project PI– Elizabeth Arnaud (Bioversity International)Crop ontology Coordinator - Rosemary Shrestha (CIMMYT)