Ontology Working Group meeting: Tuesday, Feb 10th, 2015

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

Link to audio recording: File:Planteome ontologies 2-10-15.m4a

• Meetings will be held using Zoom (https://www.zoom.us/) - we are in the process of getting it set up
• Wiki is set up and notes will be kept here, need to login to access

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.

Long term goal is to integrate the CO vocabularies with the reference ontologies.

• Part of the Integrated Breeding Platform
• Common vocabularies are used to integrate data from breeders field book
• Was started as part of the Generation Challenge Program (GCP), which has run out of funding. The GCP Pantheon webiste (http://pantheon.generationcp.org/index.php) will be shut down soon and so that information needs to be moved somewhere else. Could perhaps go the the GCP Wiki page?

• 18 crops (http://www.cropontology.org/) 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: http://www.cropontology.org/ontology/CO_334/Cassava

• 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- http://www.cropontology.org/api
• make 'Permalink' to individual terms pages
• Formats include csv, OBO, SKOS, RDF, Trait Template v4
• Ones in blue are OBO based
• Terms are translated into various languages, as synonyms

Terms have a unique identifier:

• CO_###:#######

Questions and Discussion:

• Goal is to keep the web-based tool for user access, in some form.
• Database behind it is No-SQL based
• Integration with future versions of Term Genie
• We will need a technical call as we we move towards integration at GitHub
• The Trait Ontology is not displayed here as it was confusing to the users.
• Identified an issue where curators/users can upload an ontology without any quality control.

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

• At the PAG meeting- Rice, wheat and Maize were identified as the best candidates to start on
• The PO is well set up to provide entity terms for these as they are important crop/model species
• The TO has some of the needed terms, but will need additional work

Fill in some details of the Rice, Wheat and Maize vocabs here:

3. Transition to GitHub Repository

Planteome Ontologies on GitHub

• This will be very useful for editting and versioning, then the relased version can be pushed out to Crop Ontology site

4. Hiring at Bioversity, OSU and NYBG

• Bioversity Curator position is advertised on the Bioversity Jobs page:

You can view it here: Position Description: Post Doctoral Fellow, Crop Ontology, MPL

• Ontology Curator Position at OSU: In progress....

• Ontology Curator Position at NYBG: In progress....

5. Possible Ontology development workshop this spring

Time is quite short, maybe consider a web-conferencing strategy to start, new people are being added to project at OSU, NYBG, CO

6. White paper on plant phenotyping standards

See details on All Hands Call Feb 6th