PRO

Protein Ontology Kick-Off Meeting

The inaugural meeting of the Protein Ontology project will take place in Georgetown University on November 7-9, 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:

Wednesday, November 7

Arrival of Workshop Participants

Dinner for Workshop Participants [Time/Location to be Announced]

Thursday, November 8

Location:

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]

Friday, November 9

Location: ??

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)

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.

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.