Ontology Working Group March 6th 2015: Difference between revisions
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= | =Agenda Items:= | ||
Agenda Items: | |||
Who: EA, LC, BS, CM, along with new folks: Rosemary Shrestha, Léo Valette, (both from the CGIAR) | Who: EA, LC, BS, CM, along with new folks: Rosemary Shrestha, Léo Valette, (both from the CGIAR) | ||
* Link to recording- Video: [[File:OntologyWG video 3-6-15.mp4|thumbnail|none|OntologyWG_video_3-6-15.mp4]] | |||
* Link to recording- Audio: [[File:OntologyWG audio 3-6-15.m4a|thumbnail|OntologyWG audio 3-6-15.m4a]] | |||
==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: | ||
- Collaborate with each crop curator and with Julian Pietragalla (IBP) to maintain quality Trait Dictionaries for the [https://www.integratedbreeding.net/15/breeding-management-system Breeding Management System] and expend the Crop Ontology to new crops. | - Collaborate with each crop curator and with Julian Pietragalla (IBP) to maintain quality Trait Dictionaries for the [https://www.integratedbreeding.net/15/breeding-management-system Breeding Management System] and expend the Crop Ontology to new crops. | ||
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*'''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 | - 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 | - Role at CIMMYT: Germplasm Data Coordinator- to bring the maize and wheat data into the CIMMYT databases, rolling out to the IBP | ||
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=== Crop Research Ontology [http://www.cropontology.org/ontology/CO_715/Crop%20Research Crop Research Ontology]=== | === Crop Research Ontology [http://www.cropontology.org/ontology/CO_715/Crop%20Research Crop Research Ontology]=== | ||
* RS: being expanded to include the variables for environment and agronomy, etc | * RS: being expanded to include the variables for environment and agronomy, etc | ||
* Integrated with the maize | * Integrated with the maize field book to describe treatments | ||
* Needs to be harmonized with the EO and ENVO | * Needs to be harmonized with the EO and ENVO | ||
* trait methods and scales | * trait methods and scales | ||
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** [http://www.obofoundry.org/cgi-bin/detail.cgi?id=unit Unit Ontology] | ** [http://www.obofoundry.org/cgi-bin/detail.cgi?id=unit Unit Ontology] | ||
* IWIS2 | |||
IWIS2 | |||
* No query tools | * No query tools | ||
* Wheat descriptors, moving to IBP fieldbook | * Wheat descriptors, moving to IBP fieldbook | ||
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Comments: | Comments: | ||
* Barry Smith- Suggestion of ontology building | * Barry Smith- Suggestion of ontology building seminar | ||
= | ===Back to the [[Planteome_Ontology_Development_and_Coordination_Working_Group]] page=== | ||
Latest revision as of 23:30, 20 April 2015
Agenda Items:
Who: EA, LC, BS, CM, along with new folks: Rosemary Shrestha, Léo Valette, (both from the CGIAR)
- Link to recording- Video: File:OntologyWG video 3-6-15.mp4
- Link to recording- Audio: File:OntologyWG audio 3-6-15.m4a
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?
- 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