PRO Consortium Workshop 2019: Difference between revisions

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


:8:30 Breakfast
:8:15 Breakfast


'''PRO as a framework for advancing disease understanding'''
'''Advancing disease understanding with site information: PRO and UniProtKB'''


''Chair: Darren Natale''
''Chair: Darren Natale''


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


:10:30-10:45 Break
:10:15-10:30 Break


'''Disease mechanisms: connecting clinically-relevant protein sequence variations with their impact on underlying molecular mechanisms. Part 1'''
'''Uncovering disease mechanisms: connecting site annotations to ontologies'''
''Chair: Judith Blake''
''Chair: Judith Blake''


:10:45 Mouse models of human disease (TBD)
:10:30 UniProtKB Feature Viewer (Alexander Bateman)
:11:15 UniProt
:11:00 UniProtKB's molecular impact information (Harold Drabkin) - connecting feature line information to ontologies
::UniProt (Alexander Bateman)
:11:30 Disease Ontology (Melody Swan) - introduction to DO and how it can be used to go from UniProtKB variants to disease identifiers
::UniProtKB's molecular impact information (Harold Drabkin?)
: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
:::There is a need for standardization of information found on UniProtKB's mutation feature lines. Currently this information is provided as free text. It needs to be connected to various ontologies, including the GO. For example, some mutation might abolish some function that could be described using GO.
:12:30-13:30 Lunch
:12:30-13:30 Lunch


'''Disease mechanisms: connecting clinically-relevant protein sequence variations with their impact on underlying molecular mechanisms. Part 2'''
'''Uncovering disease mechanisms: connecting variants to diseases'''
 
::Chair: Judith Blake''
   
   
:13:30
:13:30 Mouse models of human disease (TBD)
::Disease Ontology (Melody Swan)
:14:00 Extracting variant / disease associations from text (Cecilia Arighi)
::Ontology for General Medical Science (Barry Smith)
:14:00 Discovering molecular mechanisms underlying disease (Karen Ross, Natarajan Kannan) - the PRO/ProKinO/NeXtProt work as a model for what's to come
::Discovering molecular mechanisms underlying disease (Karen Ross, Natarajan Kannan)
 
:15:00-15:30 Break


:15:30-16:00 Break
:15:30 TBD
 
:TBD Protein aggregates (Lauren Wishnie)
 
 
:17:30 Close of Day 1
:17:00 Close of Day 1


:18:00 Working dinner
:18:00 Working dinner
Line 61: Line 66:
''Chair: Peter d'Eustachio''   
''Chair: Peter d'Eustachio''   
 
 
:8:45 Connecting proteins to disease using disease pathways (Peter d'Eustachio)
:8:45 Introduction to Day 2 theme / 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
::Drug targets (Stephan Schürer)
:9:30 Using DTO and PRO for Drug target discovery (Stephan Schürer)
::Connecting antibodies to epitopes and proteins (Randi Vita)
10:00 Connecting antibodies to epitopes and proteins (Randi Vita)


:10:30-11:00 Break
:10:30-10:45 Break


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


''Chair: Alexander Diehl''
''Chair: Alexander Diehl''


:11:00 Introduction (Alexander Diehl)
:10:45 Cell Ontology and its use of PRO (Alexander Diehl)
 
:11:10 ImmPort and its use of PRO (Patrick Dunn)
::scRNA from KPMP (Oliver He)
:11:40 The Kidney Precision Medicine Project (Oliver He) - with an emphasis on how scRNA can detect new isomoforms
::Proteoform-based cell type dictionary (Alex Diehl)  
:12:05 Proteoform-based cell type dictionary (Alex Diehl)  


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


:13:30 Working Session (on Grant Proposal)
:13:30 TBD - includes PRO grant working session


:15:00 Close
:16:00 Close of meeting


----
----

Revision as of 16:02, 20 August 2019

Date: October 23-24, 2019

Venue:

Protein Informatics Resource
Georgetown University Medical Center
3300 Whitehaven Street, NW, Suite 1200
Washington, DC 20007, USA


Goals

The goals of this meeting are:

  • 1. To plan the future of the PRO
  • 2. To foster PRO's collaborations with other initiatives

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
12:30-13:30 Lunch

Uncovering disease mechanisms: connecting variants to diseases

Chair: Judith Blake
13:30 Mouse models of human disease (TBD)
14:00 Extracting variant / disease associations from text (Cecilia Arighi)
14:00 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 TBD
TBD 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 / 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)
12:30-1:30 Lunch
13:30 TBD - includes 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)
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 Barry Smith for further information.

Sponsors

The Protein Ontology Consortium
National Center for Ontological Research
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