PRO

Protein Ontology Kick-Off Meeting

The inaugural meeting of the Protein Ontology project will take place in Georgetown University (Harris Building, Conference Room 4200), Washington DC on December 2-4, 2007. This is an internal meeting. Its goals are: to subject the PRO ontology to preliminary critique, and to establish plans for its further development, dissemination and use.

A draft program is as follows (names of proposed moderators for each session are given in parentheses):

December 2

Arrival of Workshop Participants

6:00pm Dinner for Workshop Participants [Location to be Announced]

December 3

8:30am Continental Breakfast

9:00am-10:30am Session 1: Introduction to the Protein Ontology (Cathy Wu)

10:45am-12:15pm Session 2: The Protein Ontology and Its Neighbors (Darren Natale)

12:15pm-1:30pm Lunch

1:30pm-3:00pm Session 3: The Protein Ontology within the OBO Foundry (Barry Smith)

3:30pm-5:00pm Session 4: Protein Ontology and Protein Data (Chris Mungall and Alan Ruttenberg)

6:00pm Dinner [Location to be Announced]

December 4

8:30am Continental Breakfast

9:00am-10:30am Session 5: The Protein Ontology and Its Users 1 (Helen Berman)

10:45am-12:15pm Session 6: The Protein Ontology and Its Users 2 (Judith Blake)

12:15pm-1:30pm Lunch

1:30pm-4:00pm Session 8: Next Steps (Suzanna Lewis)

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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, ProMod 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.

Relations between PRO and Its Neighbor Ontologies

One goal of the meeting is to clarify the relations between PRO and those OBO Foundry ontologies with which it has the potential to overlap.

Relations between PRO and SO (The Sequence Ontology) SO will contain

• 1. terms for features of sequences of protein molecules
• 2. terms for qualities of features of sequences of protein molecules
• 3. terms for variants of sequences of protein molecules

Relations between PRO and RNAO (The RNA Ontology)

RNAO will contain terms for evolutionary relations (like homology) between different RNA molecules and parts of homologous RNA -- homology at the motif or nucleotide level -- with the goal of representing such relations in databases and in multiple sequence alignments.

Relations between RNAO and SO

• SO will contain terms for 1-dimensional features of sequences.
• RNAO will contain terms for 2- and 3-dimensional features of sequences.

Participants

Cecilia Arighi

Judith Blake

James W Brown

Lindsay Cowell

Harold Drabkin

Karen Eilbeck

Zhangzhi Hu

Jerry Li

Hongfang Liu

Chris Mungall

Darren Natale

Alan Ruttenberg

Richard Scheuermann

Barry Smith

John Westbrook

Cathy Wu

Literature

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.[1]