Ontology Working Group Meetings- Feb 2015

Tuesday, Feb 10th, 2015

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

• 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

Tuesday, Feb 17th, 2015

Who: PJ, LC, CM,

1. Discussion of the GitHub Repository: https://github.com/Planteome

• Intro to the GitHub- site for the Planteome
  • Procedure will be to do a check out. Two-step commit process: make changes and then commit locally, then do a "push" to synchronize with the server version.
  • Branching: It is different than forking

• What is 'Forking': (we probably won't need to be doing this)
  • You can copy a version of the ontology into your own user space to make local changes, changes can be made there, and then a make a "pull request"
  • Administrator can review the pull request and look at the difs, and select the parts that are accepted. Can also be voted on by the project members
  • Works best if the files are easily "diffable", OBO works well, OWL not so well suited for this. Possible changes coming to OWL to make this work better.
  • Different than doing a check out

2. Overview and update on the Plant Trait Ontology - The trait Ontology can be accessed in various ways:

• TO-Dev AmiGO Browser
• TO-Dev on Planteome Browser
• Link to TO on SVN

• Work done on the TO in the last few years:
  • Changes are stored on the SVN, with notes as to what the nature of the changes is

• • Chris has done some work on setting up Logical Definitions (also called Cross Products)
    • Cross products are a way to 'decompose' the TO terms into the element entities (from PO, GO, ChEBI or other ontology) and qualities (from PATO).
  • This allows Automatic classification by the reasoner -

• Example: ligule length (TO:0000024)
  • ligule- PO:0020105 (is_a cardinal organ part; part_of vascular leaf)
  • length-

• BATTO- now called "OBA"- Ontology of Biological Attributes

3. Recent work with Mary Schaeffer of MaizeGDB which was presented at the PAG Conference (https://pag.confex.com/pag/xxiii/webprogram/Paper14937.html)in January.

4. Links to the up-to-date versions (live and dev) of the Plant Trait Ontology: Planteome_Ontology_Development_and_Coordination_Working_Group#Ontology_Development_Resources_and_Workshops