The document discusses the development and use of the Generation Challenge Programme's (GCP) Crop Ontology. The Crop Ontology offers a standardized list of crop trait names, measurement methods, and scales to facilitate sharing of research information. It currently covers several major crops and continues to expand its content. The document introduces a new curation and annotation tool that allows users to upload and edit ontologies online through a web interface or API. It also describes how the Crop Ontology can integrate with other crop databases and field books to harmonize trait data annotation across various research projects and organizations. Plans are outlined to engage more crop communities, add additional traits, and further develop the online curation tool based on feedback.

1. How to contribute to and use the
GCP Crop Ontology,
A Reference Traits List ?
Use of the New Curation and
Annotation tool
Generation Challenge Programme, Global Research Meeting, 20th-26th September, Hyderabad, India
Elizabeth Arnaud, (Bioversity), Rosemary Shrestha (CIMMYT),
Matteis Luca (Bioversity), Milko Skofic (Bioversity)

2. Why a GCP Crop Ontology?
 Offer harmonized and structured list of traits
names, methods and scales
 Facilitate sharing of information between research
trials through field books
 Increase efficiency of trait information retrieval
and keyword-based queries
 Enable annotation for integration of research
documents, reports, and databases with ontological
terms

3. Current status of the Crop Ontology
Musa
Cassava
Anatomy, Structure & Phenotype of Crops
 Trait Measurement Methods and Scales
 Germplasm
Crop Leading
organization
Ontology Trait
Dictionaries
Number of
traits
Cassava IITA √ √ 123
Chickpea ICRSAT √ √ 51
Common beans CIAT √ 76
Cowpea ICRISAT √
Groundnuts ICRISAT √
Maize CIMMYT √ 177
Musa Bioversity √ 173
Potato CIP √ 210
Rice IRRI √ 220
Sorghum ICRISAT √ √ 70
Wheat CIMMYT √ 176
+

4. Trait Template & Dictionaries
• The Trait Template is used by ontology curators and
breeders to submit new trait lists
• Is a tool to get consensus on the trait to be submitted along
with definitions, categories and scales
• Excel files to be uploaded on the Tool

5. The New Curation and Annotation tool
 Crop curators can
 upload or create online ontologies
 Expend the content by adding terms and attributes like
photos, protocols, scale, scale value, scoring guidelines and
growth 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: https://github.com/lmatteis/Crop-
Ontology
Developers: Luca Matteis, Milko Skofic (Bioversity International)
Video realization: Valentina Barbiero (Bioversity International)
http://www.cropontology-curationtool.org/

6. The New Curation and Annotation tool
Homepage

7. Trait information with definition,
photos & measurement methods

8. Crop Ontology Annotation Tool
• The annotation tool matches the
content of the data file or trait
list with validated terms from
the ontology
• Curator can accept the match to
with local term
• Leading to the harmonization of
the annotation
• Result can be downloaded as
comma separated file (csv) that
can be uploaded into Excel or a
database.
• Still at the prototype level,
needs tests and feedback
http://www.cropontology-curationtool.org/annotation-tool

9. A reference Trait List
1. Integration with IB Field book
file:///Users/elisabeth/Documents/GCP%20GRM%202011/presentation/Agtrials%20crop%20otno.swf

10. 2. Integration with the
Global Agricultural Trial Repository
http://www.agtrials.org

11. Drought Recovery - (Rice)

12. 3. Integration with the
Crop Wild Relatives Ontology
European Crop Wild Relative Diversity Assessment and
Conservation Forum, EU funded
400 terms
representing in situ and ex situ
conservation status of Individual
taxa & their utilization potential
 PGRSecure project :
http://www.pgrsecure.bham.ac.uk/cont
acts

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 using
web service
 Integration in the online and offline configurable IB workflow
 Expend use cases with Agtrials
 Build a single working place

14. Crop Ontology Team since 2008
Developers
•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 descriptors
specialist), Richard Bruskiewich (GCP Bioinformatics, former Principle Investigator, IRRI),
Guy Davenport (GCP bioinformatics, CIMMYT), Graham McLaren (GCP sub-programme
on Crop information system, Leader), Martin SENGER (GCP Bioinformatics, formerly
IRRI), Theo van Hintum (SP4 leader, WUR)
Project PI– Elizabeth Arnaud (Bioversity International)
Crop ontology Coordinator - Rosemary Shrestha (CIMMYT)