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)

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

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

+

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

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/

The New Curation and Annotation tool Homepage

Trait information with definition, photos & measurement methods

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

A reference Trait List 1. Integration with IB Field book

file:///Users/elisabeth/Documents/GCP%20GRM%202011/presentation/Agtrials%20crop%20otno.swf

2. Integration with the Global Agricultural Trial Repository

http://www.agtrials.org

Drought Recovery - (Rice)

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/contacts

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

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)