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 seminar

Tuesday March 31st

Attending: LC, BS, EA, PJ, LV

Topic: Planteome Ontology Meeting

Time: Mar 31, 2015 8:00 AM (GMT-7:00) Pacific Time (US and Canada)

Join from PC, Mac, iOS or Android: https://zoom.us/j/106572348

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 draft 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.

Budget for collaboration is available for 1 year

The Labex NUMEV offers the opportunity to obtain the funding for a 1-year postdoc, starting in May 2015 for joining Clément Jonquet’s lab and testing NCBO technology with the Crop ontology project. The postdoc profile needs to be urgently submitted in order to start in May.

Possible interaction with Planteome

This project is a prospective project and must take into consideration the newly NSF-awarded Planteome project. The interactions with Planteome can be assessed along the Bioportal project lifetime. We give hereunder some examples of such collaboration but we propose to hold a videoconference with the Planteome Principal Investigators sometime in March or early April to present our project idea and see if it would be feasible to collaborate in developing technical solutions.

• In the context of Planteome, the Crop Ontology will align the crop concepts validated by the agricultural community to the plant reference ontologies. We propose to test how the Bioportal technology could support this work?

• Planteome will enhance the web tool developed by Chris Mungall, Berkeley, called TermGenie, which uses patterns and reasoning to create new terms for an ontology. The Bioportal Plant group project could test the tool and see if it could be integrated into a workflow with the Bioportal local instance.

• An annotation tool already exists within the Bioportal. Planteome will also develop an annotation pipeline so this Bioportal project could contribute to the test of the Planteome pipeline to identify the best technical solutions.

• The Wheat Data Interoperability Group has already made suggestions for testing the Bioportal instance and they are also interested by the ontologies of Planteome and using the Crop Ontology concepts.

Comments and Discussion:

Overall, the consensus was the following:

• The LIRMM Bioportal instance would be useful in expanding access to the ontologies to a wider base of users, especially ontology users who are already using the NCBO version of Bioportal.
• The CO user base is familiar with the existing site, Trait Template (spreadsheet), and workflow, so those should be maintained.
• Some tools that would be useful may be the Mapping, Annotator, and the viewer (seems to be missing?), although there are questions as to whether or not they would be effective, as the real work of the ontology revisions and cross referencing needs to be done.
• In order for it to be useful, we would need to have an instance with only the plant-related ontologies, rather than having to use the sub-group for searches and mapping. The ontologies need to be properly referenced and updated automatically.
• The Planteome is still in early stages at this point and we have much work to do on both the reference ontologies and the crop-specific application ontologies. We cannot commit to using this portal, but are interested in seeing the development of it and will assess it in about a year to see if we should have a more formal collaboration.

Action: Elizabeth will draft a response and share it with LC, PJ and BS for input. Then we will send it to them

2. Update of Rice Trait Ontology- Leo

• Leo has been working on cross-referencing the terms in the CGIAR Rice Trait Ontology (http://www.cropontology.org/ontology/CO_320/Rice) to the reference Plant Trait Ontology, in collaboration with Ruaraidh Sackville Hamilton, Head of the Genetic Resource Unit, IRRI.
• Of the traits he has looked at, about 95% have a corresponding terming the TO, although he level of granularity varies.
• The current working version of the CGIAR Rice Trait Ontology is not being posted to the CO website, so it was suggested that it would be a good practice to keep the working copies of the CO ontologies in the Planteome SVN. LC and JE will set up the needed folders and work with Leo, EA and any of the other curators to set up access to it.

3. Other Updates:

Next meeting- Tuesday April 7th 8am PDT