Ontology Working Group Meetings- Feb 2015

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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 (e.g.) : Maize Ontology (http://www.cropontology.org/ontology/CO_322/Maize)

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

Relations:

  • is_a
  • part _of
  • method_of
  • scale _of
  • derived_from

Availability and Formats::

  • Download from www.cropontology.org
  • API
  • Formats include csv, OBO, SKOS, RDF
  • Ones in blue are OBO based

Terms have a unique identifier:

  • CO_###:#######


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

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