Ontology Working Group March 6th 2015: Difference between revisions
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==Introductions to the working group:== | ==Introductions to the working group:== | ||
*''Léo Valette''- New Crop Ontology curator at the Crop Ontology team in Montpellier, thanks to the allocation of an [https://www.integratedbreeding.net/ 2015 IBP] grant. | *'''Léo Valette'''- New Crop Ontology curator at the Crop Ontology team in Montpellier, thanks to the allocation of an [https://www.integratedbreeding.net/ 2015 IBP] grant. | ||
- Background: Agronomist, with background in Information Technology | - Background: Agronomist, with background in Information Technology | ||
- Roles: | - Roles: | ||
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- Addition of new crops- e.g. Sunflower | - Addition of new crops- e.g. Sunflower | ||
*''Rosemary Shrestha''- Germplasm Data Coordinator, CIMMYT | *'''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 learnontology building with OBO-Edit- developed the wheat and Maize trait ontologies | - Background: Plant Pathology, molecular biology, joined CIMMYT in 2008 to develop ontologies on the GCP project with Elizabeth Arnaud. Worked with Jaiswal group to learnontology building with OBO-Edit- developed the wheat and Maize trait ontologies | ||
Revision as of 18:58, 10 March 2015
Friday March 6th
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 learnontology 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
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: [1]
- Kate Dreher, data manager, CIMMYT
- Maize descriptors- Maize finder, central system
- Collaborating with Mary Scheaffer- MaizeGDB
Crop Research Ontology (http://www.cropontology.org/ontology/CO_715/Crop%20Research)
- RS, being expanded to include the variables for environment and agronomy, etc - Needs to be harmonized with the EO and ENVO - How is it being used???
- Question: How to best deal with units and scales?
- Unit Ontology: