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:

• 1. To inform members of the Protein, Plant, Gene Ontology and related communities of developments in their respective ontologies in order to promote cross-ontology coordination. 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 species of organisms
• 3. To contribute to the cROP (Common Reference Ontologies for Plants) initiative
• 4. To contribute to the ontological understanding of phenotype and disease across organisms.
• 5. To identify potentially fruitful applications which enhanced ontology coordination might bring.

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Draft Schedule

Wednesday, May 15, 2013

8:15 Registration and continental breakfast

9:00 From the OBO Foundry to cROP (Common Reference Ontologies for Plants)

Outline of the cROP Framework (Pankaj Jaiswal)

Yellow = cROP ontologies for plants; Blue = general reference ontologies; Pink = to be developed by cROP

Overview of general ontologies used within the cROP Framework

Molecules:

Protein Ontology (PRO) (Cathy Wu)

CHEBI (Janna Hastings)

Cells

GO-Cellular Component (Alex Diehl)

Cell Type Ontology (CL) (Alex Diehl)

Use of PRO in defining Cell Types

Plant cell branch of the Plant Ontology (PO)

Presentations should focus on:

Current or planned treatment of multiple organism types

Important applications of these ontologies

Experiences in the use of these ontologies in coordination

10:30 Break

10:45 The Coordinating Role of the Gene Ontology (Jane Lomax)

Questions to be addressed include:

How does the GO view the division of labor with regard to describing Biological Processes (BPs) which are not within the scope of the GO BP ontology especially in regard to stage ontologies such as the cell life cycle ontology or the PO plant development stage ontology?

How are growth and development terms to be dealt with across organisms?

What are the lessons learned from the GO's experience in coordinating with other ontologies using GO terms in definitions?

12:00 Lunch

13:00 Traits and Phenotypes

Phenotypic Quality Ontology (PATO)

Includes treatment of population phenotypes and of the Population and Community Ontology (PCO) (Ramona Walls)

Plant Trait Ontology (TO) (Pankaj Jaiswal)

Critical remarks on PATO and TO (Barry Smith)

14:30 Break

15:00 Defining Disease Across Organisms (Judith Blake)

Defining Disease

The Plant Disease Ontology and the Plant Infectious Disease Ontology (Ramona Walls)

Use of PRO in defining diseases

17:00 Close

18:00 Working Dinner

Thursday, May 16th, 2013

8:15 Continental breakfast

9:00 The Coordinating Role of the Protein Ontology

PRO and Model Organism Research: Maintaining Ontologies Across Multiple Species

PRO and UniProt

10:30 Break

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

12:30 Lunch

13:30 Documenting Success Stories in Application of Annotated Genome Data

This is a discussion of ontology annotations; we will alert attendees to bring success stories regarding use of annotations in areas such as

Diversity research (Inter-Species)

Discovering similarities and dissimilarities within organisms (Intra-Species)

Identification of species for forensic purposes

What are the structures involved in given biological processes (for example pollination)?

What are the biological processes involved in phenomena such as disease)?

16:00 Close

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Participants will include:

PO Consortium

Laurel Cooper (Oregon)

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)

Darren Natale (Georgetown)

Alan Ruttenberg (Buffalo)

Cell Ontology

Alex Diehl (Buffalo)

BFO

Stefan Schulz (Graz)

Selja Seppälä (Buffalo)

UniProt

Claire O'Donovan (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)

William Hogan (Arkansas)

Mark Jensen (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