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 developing a public-facing Bioportal Instance for the Crop Ontology:

File:TestingBioPortal with CO.pdf

Key Points and Project description:

Who is involved:

• 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)

From the proposal: Customizing an instance of the Bioportal behind the Crop Ontology web site

• The NCBO Bioportal is a well-known repository for biomedical ontologies. Its functionalities have been progressively extended, with a new release in February 2015 that aims at improving the user experience when accessing registered ontologies and using it for annotations. An instance of the Bioportal is currently being customized at the University of Montpellier, in the context of the SIFR and IBC projects (in collaboration with Pierre Larmande).

• This project is essentially a feasibility study for maintaining and supporting a local Bioportal instance for plants, and reusing the recent technologies and services of the NCBO BioPortal, such as hosting, search, mappings, versioning, annotation, REST endpoint, visualization.
• The main objective is to enable straightforward use of plant related ontologies, freeing researchers to deal with complex knowledge engineering issues and to concentrate on biological challenges and conducting field trips.

A quick prototype of the BioPortal Plant Group is available at: http://bioportal.lirmm.fr

• NCBO technology is domain-independent and open source. The NCBO Bioportal virtual appliance is available for the community allowing to set up a local ontology repository and eventually customize it: http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance

• We have already set-up a local instance of BioPortal on a LIRMM server. It is a prototype that currently hosts French terminologies (for the SIFR project) and English plant related ontologies (around 15) aggregated for the IBC project and testing for INRA. As part of the Wheat Data Interoperability Working Group activities, a group of users will be identified (e.g. IRD, INRA, CIRAD, Bioversity) to use and test the prototype with the Wheat terms and user needs: http://bioportal.lirmm.fr.

As an illustration of what could be done, we have developed an ontology group for Crop-related ontologies, provisionally called the "CROP" group.

2. Update of Rice trait ontology- Leo