Planteome Ontology Development and Coordination Working Group

Participants

• Jaiswal Lab (Oregon, OSU): Laurel Cooper (Project coordinator, Curator), Pankaj Jaiswal (PI), Justin Elser (System Admin), new curator to be added
• Mungall Group (Lawrence Berkeley National Laboratory): Chris Mungall (Co-PI, AmiGO2, Gene Ontology)
• CGIAR Consortium (Montpellier, France and CG centers around the world): Elizabeth Arnaud (Co-PI, Crop Ontology), Léo Valette (Curator, IBP + CO), Marie Angelique Laporte (Ontology Engineer)
  • Rosemary Shrestha (Wheat Traits, CIMMYT, Mexico, Curator), Kate Dreher (Maize Traits, CIMMYT, Mexico, Curator),
• New York Botanic Garden (Bronx, NY): Dennis W. Stevenson (Co-PI), new curator to be added
• Barry Smith, University at Buffalo (Ontology Consultant)
• Georgios Gkoutos, University of Aberystwyth, UK (Senior Personnel, PATO), new curator to be added

Goals and Objectives:

1. Develop a set of common reference ontologies to describe major knowledge domains of plant biology, comprising plant phenotype and traits, environments, and biotic and abiotic stresses, including plant diseases.

The project will provide a suite of reference and interoperable ontologies (Figure-1) relevant to the knowledge domain of plant biology required for annotating and describing the experiments, data sets, tagging published papers, and images.

These ontologies include the Plant Ontology (PO); Trait Ontology (TO), Environment Ontology (EO) and Plant Stress Ontology (PSO) to be developed by the cROP project and will associate them to the existing reference ontologies for relevant knowledge domains (Figure-1 Table-1) being developed and funded by other resources.

The Planteome project will also contribute to and enhance the existing reference ontologies, developed and maintained by the proposal partners. A network of national and international collaborators, representing major plant genomics resources, large-scale phenotype and genome annotation projects (Appendix-A3), will apply the set of reference ontologies to empower researchers to build their hypotheses, query, discover and analyze the plant genomics and genetics data sets.

• Plant Trait Ontology (TO)
• Plant Environment Ontology (EO)
• Plant Ontology (PO)
• Plant Stress Ontology (PSO)
• Coordination with the Phenotypic Qualities Ontology (PATO)
• Building references with the Crop Ontology (CO) as a resource of concepts for cROP

2. Develop standards, workflows and tools for ontology development, curation and improved annotation of genes, genomes, phenotype and germplasm.

2.1 Collaborative approaches on ontology development and annotation:

• Transition to OWL Format
• Introduction of Elk reasoner and Continuous Integration (CI) system
• Development of TermGenie tool for TO and PO
• Use of Inferred graph completion

2.2 Improving ontology-based annotations for plant genomes and develop quality assessment matrix:

GOstruct method

2.3 Annotating orphan plant genomes and maintaining reference genome annotations.

Details TBA

Ontology Working Group Meetings:

Goal is to hold these meetings on a bi-weekly basis on Tuesday 8 am PST (GMT -8) Please check for your specific local time, if you are not sure here is a handy site: http://www.timeanddate.com/worldclock/meeting.html. I apologize if this time does not work for everyone.

Ontology Working Group_Meetings- Jan 2015

Ontology Working Group_Meetings- Feb 2015

Ontology Working Group March 6th 2015

Ontology Working Group Meeting Tuesday March 31st

Ontology Working Group GitHub Meeting, Tuesday April 3rd, 2015

Ontology Working Group Meeting, Tuesday April 7th, 2015

Ontology Working Group Meeting, Tuesday April 28th, 2015

Ontology Working Group Meeting, Tuesday May 12th, 2015

Ontology Working Group Meeting, Tuesday May 26th, 2015

Ontology Development Resources and Workshops

Links to current versions of the Ontologies:

Plant Trait Ontology (TO)

TO-Dev AmiGO Browser

TO-Dev on Planteome Browser

Link to most recent changes on SVN: Link to most recent changes on SVN

Crop Ontology Pages:

http://www.cropontology.org/