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 treatment of plant-related proteins in the Protein Ontology

b. To address issues concerning reuse of GO terms to describe plant-related entities, for example in the 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.

cROP: Common Reference Ontologies for Plants

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

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Draft Schedule

Tuesday, May 14, 6pm: Dinner (details will follow)

Wednesday, May 15, 2013

8:00 Registration and continental breakfast

9:00 From the OBO Foundry to cROP

Outline of the cROP Framework (Pankaj Jaiswal)

Overview of cROP ontologies

Presentations will focus on:

• Current or planned treatment of multiple organism types
• Important applications of these ontologies
• Experiences in the use of these ontologies in coordination (prototypically via use of terms from coordinating ontologies in cross-product definitions)

Molecules:

Protein Ontology (PRO) (Cathy Wu)

CHEBI and Natural Products of Plant Origin(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) (Laurel Cooper)

Organisms

Plant Ontology (PO) (Laurel Cooper)

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?

What is the strategy and timeline for integrating PO into cross-product definitions of plant-relevant BPs (analogous to the way in which CHEBI, CL and PRO are currently being used)?

12:00 Lunch

13:00 Traits and Phenotypes

Phenotypic Quality Ontology (PATO) (Chris Mungall)

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

Plant Trait Ontology (TO) (Pankaj Jaiswall/Laurel Cooper)

Critical remarks on PATO and TO (Barry Smith)

14:30 Break

15:00 Defining Disease Across Organisms (Judith Blake)

Defining Disease

Disease as a Subtype of Stress (Pankaj Jaiswal/Laurel Cooper)

Plant Stresses and the Plant Environment Ontology (EO)

Plant Disease Ontology

Plant Infectious Disease Ontology (Ramona Walls)

17:30 Close

18:00 Working Dinner in the Ramada Inn Restaurant

Thursday, May 16th, 2013

8:15 Continental breakfast

9:00 The Coordinating Role of the Protein Ontology

PRO and UniProt (Cathy Wu and Claire O'Donovan)

Protein Annotations, UniProt/Ensembl (Claire O'Donovan and Dan Bolser)

10:30 Break

11:00 Ontologies Across Species

Maintaining Ontologies as They Scale Across Multiple Species (Darren Natale)

Species-Neurtal vs. Multi-Species Ontology (Barry Smith)

Interface Points between the cROP plant ontologies and the Protein Ontology (Cathy Wu)

12:30 Lunch

13:30 Documenting Success Stories (Dennis W. Stevenson)

Participants are invited to bring success stories regarding use of ontology-based annotations in areas such as

Diversity research (Inter-Species)

Discovering similarities and dissimilarities within organisms (Intra-Species)

Identification of species for forensic purposes

Identification of the structures involved in given biological processes (for example pollination)

Identification of the processes involved in phenomena such as disease

16:00 Close

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Participants

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)

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.

Sponsors

The Plant Ontology

The Protein Ontology

The National Center for Biomedical Ontology