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Protein Ontology Kick-Off Meeting

The inaugural meeting of the Protein Ontology project will take place in Georgetown University (Harris Building, Monday 3: Conference Room 1300, Tuesday 4: Conference Room 4200), Washington DC on December 2-4, 2007. This is an internal meeting.

The goals of the meeting are:

  • to present the PRO ontology and to subject it to preliminary critique;
  • to clarify the relations between PRO and its neighbor ontologies, between PRO and the representations in protein sequence databases, and between PRO and GO sequence annotations;
  • to establish plans for PRO's further development, dissemination and use.

Agenda

Sunday, December 2

  • Arrival of Workshop Participants

6:30pm Dinner for Workshop Participants (Red Ginger [1]; Meet in Hotel Lobby at 6:15pm)

Monday, December 3

Location: Conference Room 1300

8:30am Continental Breakfast

9:00am-10:00am Session 1: Introduction to the Protein Ontology (Cathy Wu)

10:00am-10.30am Break

10.30am-12:15pm Session 2: The Protein Ontology within the OBO Foundry (Barry Smith)

  • presentation by Lindsay Cowell on OBO Foundry Methodologies

12:15pm-1:30pm Lunch

1:30pm-3:30pm Session 3: The Protein Ontology and Its Neighbors (Darren Natale)

  • presentation by James W. Brown on the RNA Ontology
  • presentation by Karen Eilbeck on the Sequence Ontology
  • presentation by Richard H. Scheuermann on HLA Proteins

3.30pm-4:00pm Break

4:00pm-5:00pm Session 4: PRO, GO and GO Annotations (Chris Mungall)

  • presentation by Harold Drabkin on GO Annotation to Protein Isoforms

6:30pm Dinner (Heritage India [2]; Meet in Hotel Lobby at 6:15pm)

Tuesday, December 4

Location: Conference Room 4200

8:30am Continental Breakfast

9:00am-10:15am Session 5: Ontologies and Databases (Alan Ruttenberg)

  • presentation by John Westbrook on the Representation of Protein Structure and Experiment in the Protein Data Bank (PDB)

10:15am-10.30am Break

10:30am-12:30pm Session 6: The Protein Ontology and Its Users (Judith Blake)

  • presentation by Bill Bug on PRO and SO in Neuropathology and Neuropharmacology
  • presentation by Gopal Gopinathrao on Reactome and the Future of PRO

12:30pm-1:30pm Lunch

1:30pm-4:00pm Session 7: Next Steps (Suzanna Lewis)

Documents (pre-workshop)

DocumentRevision DateRelevant to
Framework for a Protein Ontology27 Nov 2007Session 1
PRO.obo (beta version)30 Nov 2007Session 1
PRO neighbors - list30 Nov 2007Sessions 2, 3, 4, 6
PRO neighbors - relations29 Nov 2007Sessions 1, 3, 4
PRO neighbors - boundaries29 Nov 2007Sessions 2, 4

Documents (new)

Issues to address [3]

PRO diagram revision [4]

Presentations

Blake [5]

Brown [6]

Bug [7]

Cowell [8]

Drabkin [9]

Eilbeck [10]

Gopinayhrao [11]

Lewis [12]

Mungall [13]

Natale [14]

Ruttenberg [15]

Scheuermann [16]

Smith [17]

Westbrook [18]

Wu [19]

 

Participants

NameInstitutionE-mail 
Cecilia ArighiGeorgetown University Medical Centercna5@georgetown.edu
Judith BlakeThe Jackson Laboratoryjblake@informatics.jax.org
James W BrownNC State UniversityJames_brown@ncsu.edu
William BugUCSDbbug@speakeasy.org
Lindsay CowellDuke Institute for Genome Sciences & Policylgcowell@duke.edu
Harold DrabkinThe Jackson Laboratoryhjd@informatics.jax.org
Karen EilbeckUniversity of Utaheilbeck@fruitfly.org
Gopal GopinayhraoCold Spring Harbor Labgopinath@cshl.edu
Zhangzhi HuGeorgetown University Medical Centerzh9@georgetown.edu
Suzanna LewisLawrence Berkeley National Labsuzi@berkeleybop.org
Jerry LiNIGMS / NIHlij@nigms.nih.gov
Hongfang LiuGeorgetown University Medical Centerhl224@georgetown.edu
Chris MungallLawrence Berkeley National Labcjm@fruitfly.org
Darren NataleGeorgetown University Medical Centerdan5@georgetown.edu
Alan RuttenbergScience Commonsalanruttenberg@gmail.com
Richard ScheuermannUT Southwestern Medical Center at Dallasrichard.scheuermann@utsouthwestern.edu
Barry SmithSUNY at Buffalophismith@buffalo.edu
John WestbrookRutgers, The State University of New Jerseyjwest@rcsb.rutgers.edu
Cathy WuGeorgetown University Medical Centerwuc@georgetown.edu

 

Protein Ontology Specific Aims

The Protein Ontology (PRO) project is funded by NIGMS / NIH Grant 1 R01 GM080646-01, PI: Cathy Wu.

The Aims of the project are:

Aim 1. Develop a Protein Evolution (ProEvo) ontology to describe proteins based on evolutionary relationships. In essence, ProEvo will reflect protein families (using sequence or structure similarities) in an ontology framework.

Aim 2. Develop a Protein Forms (ProForm) ontology to represent the multiple protein end-products from a gene. This will include "normal" and mutant forms, forms derived from different splice variants, and cleaved and post-translationally modified products.

Aim 3. Specify the relationships between the ProEvo, ProForm and other OBO Foundry ontologies. Several ontologies provide qualities that can be attributed to various forms of a protein or to an entire protein family. These qualities, in effect, can annotate the protein forms or families.

Aim 4. Disseminate PRO ontology, and demonstrate its usefulness in health-related research via scientific case studies.

Meeting Minutes

Complete Minutes

Condensed version with issues and action items[20]

More information about PRO

PRO Website

Darren A Natale, Cecilia N Arighi, Winona C Barker, Judith Blake, Ti-Cheng Chang, Zhangzhi Hu, Hongfang Liu, Barry Smith, and Cathy H Wu, "Framework for a Protein Ontology", BMC Bioinformatics 2007, 8(Suppl 9):S1. [21]

Darren A. Natale, Cecilia N. Arighi, Winona Barker, Judith Blake, Ti-Cheng Chang, Zhangzhi Hu, Hongfang Liu, Barry Smith, and Cathy H. Wu, "Framework for a Protein Ontology", Proceedings of the First International Workshop on Text Mining in Bioinformatics, 2006, p. 29-36.[22]

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