Ontology Working Group Meetings- Feb 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 (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