Ontology Working Group March 6th 2015

Friday March 6th, 2015

Agenda Items: Who: EA, LC, BS, CM, along with new folks: Rosemary Shrestha, Léo Valette, (both from the CGIAR)

Introductions to the working group:

• Léo Valette- New Crop Ontology curator at the Crop Ontology team in Montpellier, thanks to the allocation of an 2015 IBP grant.

- Background: Agronomist, with background in Information Technology - Roles: - Collaborate with each crop curator and with Julian Pietragalla (IBP) to maintain quality Trait Dictionaries for the Breeding Management System and expend the Crop Ontology to new crops.

- Provide help desk for the use of the TD Template, trait alignment and the use of the web site.

- improve content of trait dictionaries

- Curation, redefining the guidelines, improving the template

- Addition of new crops- e.g. Sunflower

• Rosemary Shrestha- Germplasm Data Coordinator, CIMMYT

- Background: Plant Pathology, molecular biology, joined CIMMYT in 2008 to develop ontologies on the GCP project with Elizabeth Arnaud. Worked with Jaiswal group to learn ontology building with OBO-Edit- developed the wheat and Maize trait ontologies

- Role at CIMMYT: Germplasm Data Coordinator- to bring the maize and wheat data into the CIMMYT databases, rolling out to the IBP

- Field and nurseries data is stored in the crop research ontology

- Mapping to PO, TO terms in the maize and wheat ontologies

Introduction to the Wheat and Maize Ontologies: Rosemary

Presentation from March 2014 Montpellier meeting:

• Link to Rosemary's Presentation: Maize and Wheat Data Management and Annotation Activities
• Status- Under revision- currently cross-referencing to PO and TO
• Harmonization with the reference ontologies

Germplasm terms: from the GCP Germplasm Ontology

• Not currently being used in the IBP
• passport Info, multi-crop passport descriptors
• GeneBank- needs to be linked to terms

Maize Trait Ontology: Maize trait Ontology

• Managed by Kate Dreher, data manager, CIMMYT
• Maize descriptors- Maize finder, central system
• Collaborating with Mary Scheaffer- MaizeGDB

Crop Research Ontology Crop Research Ontology

• RS: being expanded to include the variables for environment and agronomy, etc
• Integrated with the maize field book to describe treatments
• Needs to be harmonized with the EO and ENVO
• trait methods and scales

• Question: How to best deal with units and scales?
  • Unit Ontology

• IWIS2
• No query tools
• Wheat descriptors, moving to IBP fieldbook
• Study info etc- described by the CR ontology
• Links to CO terms in the fieldbook

2013 Review: Conversion to SKOS

Comments:

• Barry Smith- Suggestion of ontology building semianbr

Tuesday March 31st

Attending: LC, BS, EA, PJ, LV

1. Proposal for using the Bioportal Instance for the Crop Ontology:

File:TestingBioPortal with CO.pdf

^{Key Points:}

• Testing the Bioportal Technology with the Crop Ontology Project description – Montpellier, March 2015.

Collaborators:

Clement Jonquet – jonquet@lirmm.fr (University of Montpellier)

Pierre Larmande – pierre.larmande@ird.fr (Institute of Research for Developing Countries and IBC project)

Elizabeth Arnaud – e.arnaud@cgiar.org (Bioversity-France)

Patrick Valduriez – patrick.valduriez@inria.fr (INRIA, ZENITH Team)

Pascal Neveu - pascal.neveu@supagro.inra.fr (French National Institute of Agronomy)

2. Update of Rice trait ontology- Leo