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)


* Introductions to the working group:
* Link to recording- Video: [[File:OntologyWG video 3-6-15.mp4|thumbnail|none|OntologyWG_video_3-6-15.mp4]]
**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.  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. Léo will provide '''help desk for the use of the TD Template''', '''trait alignment''' and the use of the '''web site.'''
* Link to recording- Audio: [[File:OntologyWG audio 3-6-15.m4a|thumbnail|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 [https://www.integratedbreeding.net/ 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 [https://www.integratedbreeding.net/15/breeding-management-system 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
- improve content of trait dictionaries
- Curation, redefining the guidelines, improving the template
- Curation, redefining the guidelines, improving the template
- Agronomist, with background in Information
 
- 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, GCP project with Elizabeth and worked with Jaiswal group to learn to use OBO-Edit  
- 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: 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
 
- Field and nurseries data is stored in the crop research ontology
- Field and nurseries data is stored in the crop research ontology
* Mapping to PO, TO terms in the maize and wheat ontologies


* Presentation from Montpellier meeting
- 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
 
===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


* Introduction to the wheat and maize ontologies- status?
=== Crop Research Ontology [http://www.cropontology.org/ontology/CO_715/Crop%20Research Crop Research Ontology]===
* * Under revision- currently cross-referencing to PO and TO
* RS: being expanded to include the variables for environment and agronomy, etc
* * Collaborating with Mary Scheaffer
* Integrated with the maize field book to describe treatments
* Harmonization with the reference ontologies
* 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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