View source for PRO Consortium Workshop 2019

'''Date''': October 23-24, 2019

'''Venue''': 
:Protein Information Resource
:Georgetown University Medical Center 
:3300 Whitehaven Street, NW, Suite 1300 
:Washington, DC 20007, USA


==Goals==

The goals of this meeting are:
*1. To describe the future of PRO in light of the aims of the upcoming grant proposal: 
::(a) represent proteoforms of clinical interest 
::(b) connect sequence variations with molecular mechanisms using semantic web technologies 
::(c) link disease biomarker, antibody, and drug target information to appropriate proteoforms
::(d) connect proteoform expression profiles to cell types
::(e) enhance PRO quality control and distribution mechanisms.

*2. To describe PRO's collaborating projects and how they fit into PRO.

*3. To discuss implementation plans, especially with respect to collaborations.

==Schedule: Wednesday, October 23, 2019==

:8:15 Breakfast

'''Advancing disease understanding with site information: PRO and UniProtKB'''

''Chair: Darren Natale''

:8:45 Logistics and introductions (Barry Smith)
:9:00 Meeting objectives (Darren Natale)
:9:20 General introduction to PRO (Darren Natale)	
:9:45 PRO sites (Alan Ruttenberg)

:10:15-10:30 Break

'''Uncovering disease mechanisms: connecting site annotations to ontologies'''
	
''Chair: Judith Blake''

:10:30 UniProtKB Feature Viewer (Alexander Bateman)
:11:00 UniProtKB's molecular impact information (Harold Drabkin) - connecting feature line information to ontologies
:11:30 Disease Ontology (Melody Swan) - introduction to DO and how it can be used to go from UniProtKB variants to disease identifiers
:12:00 Ontology for General Medical Science (Barry Smith) - introduction to OGMS and how it can be used to standardize UniProt Feature Table (FT) information (includes introduction to the new ISO/IEC 21838 top-level ontology standard)
	
:12:30-13:30 Lunch

'''Uncovering disease mechanisms: connecting variants to diseases'''

''Chair: Judith Blake''
 
:13:30 Mouse models of human disease (Li Ni)
:14:00 Extracting variant / disease associations from text (Cecilia Arighi)
:14:30 Discovering molecular mechanisms underlying disease (Karen Ross, Natarajan Kannan) - the PRO/ProKinO/NeXtProt work as a model for what's to come

:15:00-15:30 Break

:15:30 Leveraging PRO in EuPathDB, OrthoMCL, and NIAGADS Genomics (Chris Stoeckert)
:16:00 Protein aggregates (Lauren Wishnie)
 	
:17:00 Close of Day 1

:18:00 Working dinner

==Schedule: Thursday, October 24, 2019==

:8:15 Breakfast

'''Clinical discovery: connecting clinically-relevant information to proteoforms and complexes'''
 		 	
''Chair: Peter d'Eustachio''  
 		 	
:8:45 Introduction to Day 2 theme (Darren Natale) / Logistics (Barry Smith)
:9:00 Reactome's disease pathways (Peter d'Eustachio) - how they can be used with PRO to make new proteoform/disease associations
:9:30 Using DTO and PRO for Drug target discovery (Stephan Schürer)
:10:00 Connecting antibodies to epitopes and proteins (Randi Vita)

:10:30-10:45 Break

'''Cell type discovery: proteoform expression and clinically-relevant cell types'''

''Chair: Alexander Diehl''

:10:45 Cell Ontology and its use of PRO (Alexander Diehl)
:11:10 ImmPort and its use of PRO (Patrick Dunn)
:11:40 The Kidney Precision Medicine Project (Oliver He) - with an emphasis on how scRNA can detect new isomoforms
:12:05 Proteoform-based cell type dictionary (Alex Diehl) 

:12:30-13:30 Lunch

:13:30 Communicating and cataloging proteoforms within the Blood Proteoform Atlas (Paul Martin Thomas and Richard Dann LeDuc)
:14:00 PRO grant working session

:16:00 Close of meeting

----

== '''Participants''' ==

:Alexander Bateman (EBI)*
:Alexander Diehl (Buffalo)
:Cecilia Arighi (Delaware / PRO)
:Judith Blake (JAX)
:Peter d'Eustachio (NYU)
:Alexander Diehl (Buffalo)
:Harold Drabkin (JAX)
:Patrick Dunn (ImmPort)
:Yongqun (Oliver) He (Michigan)
:Natarajan Kannan (Georgia)
:Richard LeDuc (Northwestern)
:Yu Lin (FDA)
:Birgit Meldal (EBI)*
:Darren Natale (Georgetown)
:Li Ni (JAX)
:Karen Ross (Georgetown) 
:Alan Ruttenberg (Buffalo)
:Stephan Schürer (Miami)
:Henry Schaefer (ImmPort)
:Barry Smith (Buffalo) 
:Christian Stoeckert (Penn)
:Melogy Swan (Baltimore)
:Paul Martin Thomas (Northwestern)
:Randi Vita (San Diego)
:Lauren Wishnie )
:Cathy Wu (Delaware / PRO)

*=online


Please contact [mailto:phismith@buffalo.edu Barry Smith] for further information.

== '''Sponsors''' ==
 
:[http://pir.georgetown.edu/pro/ The Protein Ontology Consortium]
:[http://ncor.buffalo.edu National Center for Ontological Research]