PRO - Revision history

Phismith: Replacing page with '== Protein Ontology Kick-Off Meeting == Details of this event are now posted [https://pir5.georgetown.edu/wiki/Protein_Ontology_Kick-Off_Meeting here].'

2007-11-19T18:49:15Z

Replacing page with '== Protein Ontology Kick-Off Meeting == Details of this event are now posted [https://pir5.georgetown.edu/wiki/Protein_Ontology_Kick-Off_Meeting here].'

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2007-11-19T16:30:31Z

Agenda

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2007-11-06T16:57:41Z

Participants

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2007-11-06T15:19:12Z

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2007-11-05T15:15:36Z

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2007-11-05T15:12:03Z

Participants

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2007-10-31T13:17:32Z

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2007-10-31T13:17:11Z

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2007-10-30T19:54:12Z

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2007-10-30T19:16:42Z

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← Older revision		Revision as of 18:49, 19 November 2007
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	== Protein Ontology Kick-Off Meeting ==		== 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
−
−	~~6:30pm Dinner for Workshop Participants [Location to be Announced; Meet in Hotel Lobby at 6:15pm]~~
−
−	~~'''Monday, December 3'''~~
−
−	~~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)~~
−
−	*with 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)~~
−
−	*with presentations by James W. Brown on the RNA Ontology, Karen Eilbeck on the Sequence Ontology and Richard H. Scheuermann on HLA Proteins
−
−	~~3.30pm-4:00pm Break~~
−
−	~~4:00pm-5:00pm Session 4: PRO, GO and GO Annotations (Chris Mungall)~~
−
−	*with presentation by Harold Drabkin on GO Annotation to Protein Isoforms
−
−	~~6:30pm Dinner [Location to be Announced; Meet in Hotel Lobby at 6:15pm]~~
−
−	~~'''Tuesday, December 4'''~~
−
−	~~8:30am Continental Breakfast~~
−
−	~~9:00am-10:15am Session 5: Ontologies and Databases (Alan Ruttenberg)~~
−
−	*with presentation by John Westbrook on the Protein DataBase (PDB)
−
−	~~10:15am-10.30am Break~~
−
−	~~10:30am-12:30pm Session 6: The Protein Ontology and Its Users (Judith Blake)~~
−
−	*with presentation by Bill Bug on PRO and SO in Neuropathology and Neuropharmacology
−
−	~~12:30pm-1:30pm Lunch~~
−
−	~~1:30pm-4:00pm Session 7: Next Steps (Suzanna Lewis)~~
−
−	*with presentation by Gopal Gopinathrao on Reactome and the Future of PRO
−
−	~~== 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)~~
−
−	~~William Bug (Drexel University College of Medicine)~~
−
−	~~Lindsay Cowell (Duke Institute for Genome Sciences & Policy)~~
−
−	~~Harold Drabkin (The Jackson Laboratory)~~
−
−	~~Karen Eilbeck (Eccles Institute of Human Genetics, University of Utah)~~
−
−	~~Gopal Gopinayhrao (Cold Spring Harbor Lab)~~
−
−	~~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]~~

@@ Line 38: / Line 38: @@
 :00pm-5:00pm Session 4: PRO, GO and GO Annotations (Chris Mungall)
-*with presentation by Harold Drabkin
+*with presentation by Harold Drabkin on GO Annotation to Protein Isoforms
 :30pm Dinner [Location to be Announced; Meet in Hotel Lobby at 6:15pm]

← Older revision		Revision as of 16:57, 6 November 2007
Line 120:		Line 120:

	Karen Eilbeck (Eccles Institute of Human Genetics, University of Utah)		Karen Eilbeck (Eccles Institute of Human Genetics, University of Utah)
		+
		+	Gopal Gopinayhrao (Cold Spring Harbor Lab)

	Zhangzhi Hu (Georgetown University Medical Center)		Zhangzhi Hu (Georgetown University Medical Center)

← Older revision		Revision as of 15:19, 6 November 2007
Line 59:		Line 59:

	1:30pm-4:00pm Session 7: Next Steps (Suzanna Lewis)		1:30pm-4:00pm Session 7: Next Steps (Suzanna Lewis)
		+
		+	*with presentation by Gopal Gopinathrao on Reactome and the Future of PRO

	== Relations between PRO and the Gene Ontology ==		== Relations between PRO and the Gene Ontology ==

← Older revision		Revision as of 15:15, 5 November 2007
Line 17:		Line 17:

	'''Monday, December 3'''		'''Monday, December 3'''
		+
		+	8:30am Continental Breakfast

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

← Older revision		Revision as of 15:12, 5 November 2007
Line 108:		Line 108:

	James W Brown (Department of Microbiology, NC State University)		James W Brown (Department of Microbiology, NC State University)
		+
		+	William Bug (Drexel University College of Medicine)

	Lindsay Cowell (Duke Institute for Genome Sciences & Policy)		Lindsay Cowell (Duke Institute for Genome Sciences & Policy)

@@ Line 52: / Line 52: @@
 :30am-12:30pm Session 6: The Protein Ontology and Its Users (Judith Blake)
-*with presentation by Bill Bug on PRO and SO in Neuropharmacology and Neuropathology
+*with presentation by Bill Bug on PRO and SO in Neuropathology and Neuropharmacology
 :30pm-1:30pm Lunch

← Older revision		Revision as of 13:17, 31 October 2007
Line 51:		Line 51:

	10:30am-12:30pm Session 6: The Protein Ontology and Its Users (Judith Blake)		10:30am-12:30pm Session 6: The Protein Ontology and Its Users (Judith Blake)
		+
		+	*with presentation by Bill Bug on PRO and SO in Neuropharmacology and Neuropathology

	12:30pm-1:30pm Lunch		12:30pm-1:30pm Lunch

@@ Line 14: / Line 14: @@
 *Arrival of Workshop Participants
-:30pm  Dinner for Workshop Participants [Location to be Announced]
+:30pm  Dinner for Workshop Participants [Location to be Announced; Meet in Hotel Lobby at 6:15pm]
 '''Monday, December 3'''
@@ Line 20: / Line 20: @@
 :00am-10:00am Session 1: Introduction to the Protein Ontology (Cathy Wu)
-:00am-10.30am Coffee
+:00am-10.30am Break
 .30am-12:15pm Session 2: The Protein Ontology within the OBO Foundry (Barry Smith)
@@ Line 30: / Line 30: @@
 :30pm-3:30pm Session 3: The Protein Ontology and Its Neighbors (Darren Natale)
-*with presentation by James W. Brown on the RNA Ontology, Karen Eilbeck on the Sequence Ontology and Richard H. Scheuermann on HLA Proteins
+*with presentations by James W. Brown on the RNA Ontology, Karen Eilbeck on the Sequence Ontology and Richard H. Scheuermann on HLA Proteins
-.30pm-4:00pm Coffee
+.30pm-4:00pm Break
 :00pm-5:00pm Session 4: PRO, GO and GO Annotations (Chris Mungall)
@@ Line 38: / Line 38: @@
 *with presentation by Harold Drabkin
-:30pm Dinner [Location to be Announced]
+:30pm Dinner [Location to be Announced; Meet in Hotel Lobby at 6:15pm]
 '''Tuesday, December 4'''
@@ Line 48: / Line 48: @@
 *with presentation by John Westbrook on the Protein DataBase (PDB)
-:15am-10.30am Coffee
+:15am-10.30am Break
 :30am-12:30pm Session 6: The Protein Ontology and Its Users (Judith Blake)