PRO-PO-GO Meeting

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PRO-PO-GO: International Coordination Meeting for Ontology-Based Efforts for Plant Biology

A meeting 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 9am on May 15 and conclude at 4pm on May 16.


Contents

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

File:cROP.jpg



Schedule

Wednesday, May 15, 2013

8:00 Registration and continental breakfast

9:00 From the OBO Foundry to cROP Slides

Webex recording Webex download link Note: No audio

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) Slides
CHEBI and Natural Products of Plant Origin (Janna Hastings) Slides
Cells
GO-Cellular Component (Alex Diehl)
Cell Type Ontology (CL) (Alex Diehl)
Use of PRO in defining Cell Types (Alex Diehl)
Diehl Slides
Plant Cell branch of the Plant Ontology (PO) (Laurel Cooper)
Organisms
Plant Ontology (PO) (Laurel Cooper)
Cooper Slides

10:30 Break

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

Webex Streaming recording link Webex Download recording link

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?
Need for mechanisms of alerting each other to changes in ontology structure, e.g term obsoletions
  • Use of PO for relevant GO logical definitions (Tanya Berardini) Slides
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 Webex Session #2

Streaming recording link Download recording link

Phenotypic Quality Ontology (PATO) (George Gkoutos) Slides
Automated tools to help construction of Trait Ontologies (Chris Mungall) Slides
The treatment of population phenotypes and use of the Population and Community Ontology (PCO) (Ramona Walls) Slides
Plant Trait Ontology (TO) (Pankaj Jaiswall/Laurel Cooper) Slides

14:30 Break

15:00 Critical remarks on PATO and TO (Barry Smith) Slides Streaming recording link

Webex Download recording link

Defining Disease Across Organisms (Judith Blake)Slides
Defining Disease
Disease as a Subtype of Stress (Pankaj Jaiswal/Laurel Cooper) Slides
Plant Stresses and the Plant Environment Ontology (EO)
Plant Disease Ontology
Plant Infectious Disease Ontology (Ramona Walls) slides


17:30 Close

18:00 Working Dinner in the Ramada Inn Restaurant

Thursday, May 16th, 2013

8:00 Continental breakfast

9:00 PRO and UniProt Streaming recording link Download recording link Note: Audio only, variable quality

The Representation of Proteins in UniProtKB (Claire O'Donovan) Slides
The Integration of the Protein Ontology and UniProtKB (Cathy Wu) Slides

10:30 Break

10:45 Ontologies Across Species

Streaming recording link Download recording link Note: Audio quite poor

Top-Down Proteomics (Paul Martin Thomas) Slides
Maintaining Ontologies as They Scale Across Multiple Species (Darren Natale) Slides
Interface Points between the cROP plant ontologies and the Protein Ontology (Cathy Wu) Slides
Species-Neutral vs. Multi-Species Ontology (Barry Smith) Slides

12:30 Lunch

13:30 Documenting Success Stories and On-Going Projects (Dennis W. Stevenson) Slides

Streaming recording link:Part One Download recording link: Part One Warning- large file!

GO Annotation of 23 Plant Genomes in Ensembl Plants (Dan Bolser) Slides
The iPlant Ontology Strategy (Ramona Walls) Slides
Morphobank (Ramona Walls and Dennis Stevenson)

Streaming recording link:Part Two Download recording link: Part Two Warning- large file!

AISO: Annotation of Image Segments using Ontologies (Justin Preece) Webex Session #3 Slides
Plant Phenotype Pilot Project (Laurel Cooper) Slides
Bioportal Slices (Trish Whetzel) Slides

16:00 Close


Participants

PO Consortium

Laurel Cooper (Oregon)
Pankaj Jaiswal (Oregon)
Justin Preece (Oregon)
Barry Smith (Buffalo)
Dennis Wm. Stevenson (New York Botanical Gardens)

GO Consortium

Judith Blake (JAX)
Jane Lomax (EBI)
Chris Mungall (Berkeley)
Tanya Berardini (Stanford)
Eva Huala (Stanford)

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)

Top-Down Proteomics

Paul Martin Thomas (Northwestern)

Ensembl Plants

Dan Bolser (EBI)

CHEBI

Janna Hastings (EBI / Geneva)

PATO

George Gkoutos (Cambridge)

Immune Epitope Database

James Overton

Arabidopsis Information Portal

Christopher D. Town (J. Craig Venter Institute)

The iPlant Collaborative

Ramona Walls

TAIR

Tanya Berardini (Stanford)
Eva Huala (Stanford)

NCBO

Trish Whetzel (Stanford)

Other participants:

Alexander Cox (Buffalo)
Mark Jensen (Buffalo)
Patrick Ray (Buffalo)

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
National Center for Biomedical Ontology
National Center for Ontological Research
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IN DISCUSSION