Child pages
  • Protein_Ontology_Kick-Off_Meeting
Skip to end of metadata
Go to start of metadata

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.


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]


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]



Cecilia ArighiGeorgetown University Medical
Judith BlakeThe Jackson
James W BrownNC State
Lindsay CowellDuke Institute for Genome Sciences &
Harold DrabkinThe Jackson
Karen EilbeckUniversity of
Gopal GopinayhraoCold Spring Harbor
Zhangzhi HuGeorgetown University Medical
Suzanna LewisLawrence Berkeley National
Jerry LiNIGMS /
Hongfang LiuGeorgetown University Medical
Chris MungallLawrence Berkeley National
Darren NataleGeorgetown University Medical
Alan RuttenbergScience
Richard ScheuermannUT Southwestern Medical Center at
Barry SmithSUNY at
John WestbrookRutgers, The State University of New
Cathy WuGeorgetown University Medical


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]

  • No labels