Ontology Working Group Meetings- Feb 2015: Difference between revisions

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=Tuesday, Feb 10th, 2015=
=Tuesday, Feb 10th, 2015=
Who: PJ, EA, LC, JE, CM, BS


Topics for Discussion:
== 1. Coordination between the species-specific Crop Ontologies and the reference ontologies- PO, TO, GO etc==
 
PJ: Initial goal will be to work on improving and updating the TO
 
EA provided an overview of the Crop Ontology curation tool (http://www.cropontology.org/) and some background information about the ontologies and platform.
* Part of the Integrated Breeding Platform
* Common vocabularies are used to integrate data from breeders field book
* 18 crops represented in five sections:
** General Germplasm Ontology
** Phenotype and Trait Ontology
** Structural and Functional Genomic Ontology
** Location and Environmental Ontology
** Plant Anatomy & Development Ontology
 
Cassava Example:
* Based on OBO-Edit
* Excel-based template
* Visualized by the tool
 
Common Trait Classes:
* "Agronomic/Agronomical"
* Morphological
* Stress (Abiotic/Biotic Stresses)
* Phenological
* Quality
* Unit


1. Coordination between the species-specific Crop Ontologies and the reference ontologies- PO, TO, GO etc


2. Prioritizing the work on the species-specific Crop Ontologies- Rice, wheat and Maize
2. Prioritizing the work on the species-specific Crop Ontologies- Rice, wheat and Maize
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6.  White paper on plant phenotyping standards
6.  White paper on plant phenotyping standards
Notes from meeting:

Revision as of 23:52, 11 February 2015

Tuesday, Feb 10th, 2015

Who: PJ, EA, LC, JE, CM, BS

1. Coordination between the species-specific Crop Ontologies and the reference ontologies- PO, TO, GO etc

PJ: Initial goal will be to work on improving and updating the TO

EA provided an overview of the Crop Ontology curation tool (http://www.cropontology.org/) and some background information about the ontologies and platform.

  • Part of the Integrated Breeding Platform
  • Common vocabularies are used to integrate data from breeders field book
  • 18 crops represented in five sections:
    • General Germplasm Ontology
    • Phenotype and Trait Ontology
    • Structural and Functional Genomic Ontology
    • Location and Environmental Ontology
    • Plant Anatomy & Development Ontology

Cassava Example:

  • Based on OBO-Edit
  • Excel-based template
  • Visualized by the tool

Common Trait Classes:

  • "Agronomic/Agronomical"
  • Morphological
  • Stress (Abiotic/Biotic Stresses)
  • Phenological
  • Quality
  • Unit


2. Prioritizing the work on the species-specific Crop Ontologies- Rice, wheat and Maize

3. Transition to GitHub repository

4. Hiring at Bioversity, OSU and NYBG

5. Possible Ontology development workshop this spring

6. White paper on plant phenotyping standards


Notes from meeting:

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