PRO-PO-GO Meeting

PRO-PO-GO: Challenges of Ontology Coordination Across Organisms

A meeting designed to promote the coordination of the Gene, Protein, and Plant Ontologies and of other reference ontologies used in plant biology

Venue: Ramada Inn, Amherst, NY 14221

Date: May 15-16, 2013. The meeting will start at 10am on May 15 and conclude at 4pm on May 16.

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Goals

The goals of this meeting are to enhance coordination in ontology development and use in relation to plant genomics, proteomics and related fields. The meeting is designed:

• 1. to inform members of the Protein, Plant, Gene Ontology communities of developments in each of these ontologies, and in related ontologies such as the CL (Cell), TO (Plant Trait), ENVO (Environment), PATO (Phenotype) and IDO-Plant (Plant Infectious Disease) ontologies. Specifically:

a. to enhance the PO treatment of plant-related proteins

b. to address issues concerning reuse of GO terms to describe plant-related proteins, for example as concerns treatment of plant life cycle and development stages

• 2. to address general issues which arise when ontologies need to be extended to cover multiple model organisms
• 3. to contribute to the cROP (Common Reference Ontologies for Plants) initiative
• 4. To contribute to the ontological understanding of phenotype and disease in all model organisms.
• 5. to identify potentially fruitful applications which enhanced ontology coordination might bring.

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Draft Schedule

Wednesday, May 15, 2013

10:00 From the OBO Foundry to cROP

Outline of the cROP Framework (Pankaj Jaiswal)

Overview of Ontologies including Examples of Applications

General Ontologies within the cROP Framework: CHEBI, CL, EnvO, GO, PATO, PCO, PRO

Plant Ontologies within the cROP framework: PO, TO, EO, Plant IDO, Plant Disease

12:30 Lunch

13:30

Promoting the Use of cROP Terms for Cross-Ontology Integration

The Coordinating Role of the Gene Ontology

How to manage the relations between the GO:Biological Process and the PO:Development Stage ontologies

15:00 Break

15:30 Phenotype and Disease in Model Organism

Defining Phenotype: PATO and Beyond

Defining Disease

Thursday, May 16th, 2013

9:00 The Coordinating Role of the Protein Ontology

PRO and Model Organism Research: Maintaining Ontologies Across Multiple Species

PRO and UniProt

11:00 cROP Ontologies as Annotation Resources for New Plant Genomes

12:30 Lunch

13:30 Applications of Annotated Genomes

Diversity Research (Inter-Species)

Using Phylogenetic To Discover Similarities and Dissimilarities (Intra-Species)

Identification of Species for Forensic Purposes

What are the Structures Involved in Pollination

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Participants will include:

PO Consortium

Laurel Cooper (Oregon)

Maria A. Gandolfo (Cornell)

Pankaj Jaiswal (Oregon)

Barry Smith (Buffalo)

Dennis Wm. Stevenson (New York Botanical Gardens)

GO Consortium

Judith Blake (JAX)

Jane Lomax (EBI)

Chris Mungall (Berkeley)

PRO Consortium

Cathy Wu (Delaware)

Cecilia Arighi (Delaware)

Darren Natale (Georgetown)

Alan Ruttenberg (Buffalo)

Cell Ontology

Alex Diehl (Buffalo)

BFO

Stefan Schulz (Graz)

UniProt

Claire O'Donovan (EBI)

Maria Martin (EBI)

CHEBI

Janna Hastings (EBI, Geneva)

Arabidopsis Information Portal

Christopher D. Town (J. Craig Venter Institute)

The iPlant Collaborative

Ramona Walls

TAIR

Tanya Berardini (Stanford)

Eva Huala (Stanford)

Other participants:

Alexander Cox (Buffalo)

A limited number of places are available for additional participants. Please contact Barry Smith for further information.

Note that this meeting is co-located with the BFO 2.0 meeting, which will take place in Buffalo on May 13-14:

http://ncorwiki.buffalo.edu/index.php/2013_BFO_Meeting

Sponsors

The Plant Ontology

The Protein Ontology

The National Center for Biomedical Ontology