Ontology Working Group March 6th 2015: Difference between revisions
| Line 29: | Line 29: | ||
Link to Rosemary's Presentation: [https://docs.google.com/viewer?a=v&pid=sites&srcid=Y2d4Y2hhbmdlLm9yZ3xjcm9wb250b2xvZ3ljb21tdW5pdHl8Z3g6ZjQ2NDBmMmQ1ZGFhY2Fl Maize and Wheat Data Management and Annotation Activities] | Link to Rosemary's Presentation: [https://docs.google.com/viewer?a=v&pid=sites&srcid=Y2d4Y2hhbmdlLm9yZ3xjcm9wb250b2xvZ3ljb21tdW5pdHl8Z3g6ZjQ2NDBmMmQ1ZGFhY2Fl Maize and Wheat Data Management and Annotation Activities] | ||
- | * Status- Under revision- currently cross-referencing to PO and TO | ||
* Harmonization with the reference ontologies | * Harmonization with the reference ontologies | ||
* Germplasm terms: from the [http://www.cropontology.org/ontology/CO_010/Germplasm GCP germplasm Onotlogy] | |||
- Not currently being used in the IBP | |||
- passport Info, multi-crop passport descriptors | |||
- GeneBank- needs to be linked to terms | |||
* Maize trait Ontology: [http://www.cropontology.org/ontology/CO_322/Maize] | |||
- 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? | * Question: How to best deal with units and scales? | ||
- Unit Ontology: | |||
=Tuesday March 10th= | =Tuesday March 10th= | ||
Revision as of 18:54, 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 Onotlogy
- 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: