Difference between revisions of "PRO"

Latest revision as of 10:49, 19 November 2007

Protein Ontology Kick-Off Meeting

Details of this event are now posted here.

@@ Line 1: / Line 1: @@
 == Protein Ontology Kick-Off Meeting ==
-The inaugural meeting of the Protein Ontology project will take place in Georgetown University, 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.
+Details of this event are now posted [https://pir5.georgetown.edu/wiki/Protein_Ontology_Kick-Off_Meeting here].
-A draft program is as follows (names of proposed moderators for each session are given in parentheses):
-'''December 2'''
-Arrival of Workshop Participants
-Dinner for Workshop Participants
-'''December 3'''
-:30am 	Continental Breakfast
-:00am-10:30am	Session 1: Introduction to the Protein Ontology (Cathy Wu)
-:45am-12:15pm	Session 2: The Protein Ontology and Its Neighbors (Darren Natale)
-:15pm- 1:30pm	Lunch
-:30pm- 3:00pm	Session 3: The Protein Ontology within the OBO Foundry (Barry Smith)
-:30pm- 5:00pm	Session 4: Protein Ontology and Protein Data (Chris Mungall and Alan Ruttenberg)
-:00pm	Dinner [Location to be Announced]
-'''December 4'''
-:30am 		Continental Breakfast
-:00am-10:30am 	Session 5: The Protein Ontology and Its Users 1 (Helen Berman)
-:45am-12:15pm	Session 6: The Protein Ontology and Its Users 2 (Judith Blake)
-:30pm- 4:00pm	Session 8: Next Steps (Suzanna Lewis)
-----
-== 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 [http://obofoundry.org 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.[http://pir.georgetown.edu/pirwww/about/doc/tmbio19-natale.pdf]

Difference between revisions of "PRO"

Latest revision as of 10:49, 19 November 2007

Protein Ontology Kick-Off Meeting

Navigation menu

Search