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.

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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, Conference Room 4200), Washington DC on December 2-4, 2007. This is an internal meeting.
+Details of this event are now posted [https://pir5.georgetown.edu/wiki/Protein_Ontology_Kick-Off_Meeting here].
-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
-:30pm  Dinner for Workshop Participants [Location to be Announced]
-'''Monday, December 3'''
-:00am-10:00am Session 1: Introduction to the Protein Ontology (Cathy Wu)
-:00am-10.30am Coffee
-.30am-12:15pm Session 2: The Protein Ontology within the OBO Foundry (Barry Smith)
-*with presentation by Lindsay Cowell on OBO Foundry Methodologies
-:15pm-1:30pm Lunch
-:30pm-3:30pm Session 3: The Protein Ontology and Its Neighbors (Darren Natale)
-*with presentation by James W. Brown on the RNA Ontology and by Richard H. Scheuermann on HLA Proteins
-.30pm-4:00pm Coffee
-:00pm-5:00pm Session 4: PRO, GO and GO Annotations (Chris Mungall)
-*with presentation by Harold Drabkin
-:30pm Dinner [Location to be Announced]
-'''Tuesday, December 4'''
-:30am Continental Breakfast
-:00am-10:15am Session 5: Ontologies and Databases (Alan Ruttenberg)
-*with presentation by John Westbrook on the Protein DataBase (PDB)
-:15am-10.30am Coffee
-:30am-12:30pm Session 6: The Protein Ontology and Its Users (Judith Blake)
-:30pm-1:30pm Lunch
-:30pm-4:00pm Session 7: Next Steps (Suzanna Lewis)
-== Relations between PRO and the Gene Ontology ==
-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 GO (The Gene Ontology)'''
-The Gene Ontology term 'cellular component' is defined as meaning: the part of a cell or its extracellular environment in which a gene product is located. The following gloss is provided:
-The GO-CC ontology accordingly defines parts of a cell or its extracellular environment in which gene products are located. This includes the cell itself, it's parts, both internal and external (endoplasmic reticulum, extracellular matrix), organelles and macromolecular
-complexes of various sizes and compositions, including protein complexes.
-GO will contain terms for attributes of protein entities, including
-*1. terms for the molecular functions proteins perform
-*2. terms for the biological processes in which proteins are involved
-*3. terms for parts of cells (or the extracellular environment) in which proteins can be located, including terms for complexes of protein molecules.
-GO will not contain terms for individual protein entities, and will not contain terms for transient multi-protein associations.
-Protein complexes are defined by GO as: any protein group composed of two or more subunits, which may or may not be identical [in type]. This definition includes homodimers, but not single protein molecules. As an operational criterion, the GO excludes unstable or
-random assemblages of parts.
-The GO will frequently describe the typical constituents of a protein complex in a free text description embedded in a definition of some other term, but not explicitly using ''part_of'' links. Protein complex members can also be extracted from annotations of gene products, but this information may be incomplete and yields only organism-specific protein sequence
-identifiers.
-==Relations between PRO and Other Neighbor Ontologies==
-'''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 (Georgetown University Medical Center)
-Judith Blake (The Jackson Laboratory)
-Vivien Bonazzi (NHGRI / NIH)
-James W Brown (Department of Microbiology, NC State University)
-Lindsay Cowell (Duke Institute for Genome Sciences & Policy)
-Harold Drabkin (The Jackson Laboratory)
-Karen Eilbeck (Eccles Institute of Human Genetics, University of Utah)
-Zhangzhi Hu (Georgetown University Medical Center)
-Suzanna Lewis (Lawrence Berkeley National Lab)
-Jerry Li (NIGMS / NIH)
-Hongfang Liu (Georgetown University Medical Center)
-Chris Mungall (Lawrence Berkeley National Lab)
-Darren Natale (Georgetown University Medical Center)
-Alan Ruttenberg (Science Commons)
-Richard Scheuermann (The University of Texas Southwestern Medical Center at Dallas)
-Barry Smith (University at Buffalo)
-John Westbrook (Rutgers, The State University of New Jersey)
-Cathy Wu (Georgetown University Medical Center)
-== 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.[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

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