Ontology Working Group March 6th 2015: Difference between revisions

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=Friday March 6th=
=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)


* Introduction 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. 
* Link to recording- Video: [[File:OntologyWG video 3-6-15.mp4|thumbnail|none|OntologyWG_video_3-6-15.mp4]]
**Role-   Léo will 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. This work will also benefit the NSF-awarded project 'Planteome'. Léo will provide help desk for the use of the TD Template, trait alignment and the use of the web site. Léo is already well known from some of you as last year he contributed to the feasibility study about integrating Participatory Varietal Selection methods in the Crop Ontology.
* Link to recording- Audio: [[File:OntologyWG audio 3-6-15.m4a|thumbnail|OntologyWG audio 3-6-15.m4a]]


* Rosemary- Data Coordinator, CIMMYT
==Introductions to the working group:==
* Introduction to the working group, role?
*'''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. 
* Presentation from Montpellier meeting
- Background: Agronomist, with background in Information Technology
* Invite others from data management team?  
 
* Introduction to the wheat and maize ontologies- status?
- Roles:
* * Under revision- currently cross-referencing to PO and TO
- 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.
* * Collaborating with Mary Scheaffer
 
- 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: [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 Ontology]===
* 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 Maize trait Ontology]===
* Managed by 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 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?
* Question: How to best deal with units and scales?
** Unit Ontology
** [http://www.obofoundry.org/cgi-bin/detail.cgi?id=unit Unit Ontology]
 
* Crop Research Ontology- RS, being expanded to include the variables for environment and agronomy,
** Needs to be harmonized with the EO and ENVO
** How is it being used???


* planning a Protege/BFO online webinar-workshop?
* 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


=Tuesday March 10th=
2013 Review: Conversion to SKOS


=Tuesday March 17th=
Comments:
* Barry Smith- Suggestion of ontology building seminar


=Tuesday March 24th=
===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)

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:

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
  • 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

Back to the Planteome_Ontology_Development_and_Coordination_Working_Group page

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