Difference between revisions of "PRO Consortium Workshop 2019"

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m (Schedule: Wednesday, October 23, 2019)
m (Schedule: Thursday, October 24, 2019)
 
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'''Venue''':  
 
'''Venue''':  
:Protein Informatics Resource
+
:Protein Information Resource
 
:Georgetown University Medical Center  
 
:Georgetown University Medical Center  
:3300 Whitehaven Street, NW, Suite 1200
+
:Suite 1300
 +
:3300 Whitehaven Street NW (Milton Harris Building),  
 
:Washington, DC 20007, USA
 
:Washington, DC 20007, USA
 +
 +
For '''logistic questions''' please call BS at (716) 361-5100
 +
 +
'''Parking''' is available [https://buffalo.app.box.com/v/PRO-parking-map here] ($11 per day)
 +
 +
'''Zoom''': https://georgetown.zoom.us/j/3531468363
 +
  
  
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The goals of this meeting are:
 
The goals of this meeting are:
*1. To plan the future of the PRO
+
*1. To describe the future of PRO in light of the aims of the upcoming grant proposal:
*2. To foster PRO's collaborations with other initiatives
+
::(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==
 
==Schedule: Wednesday, October 23, 2019==
  
'''8:30 Breakfast'''
+
:8:15 Breakfast
  
'''Introductory Session: The Landscape of the Protein Ontology'''
+
'''Advancing disease understanding with site information: PRO and UniProtKB'''
  
 
''Chair: Darren Natale''
 
''Chair: Darren Natale''
  
:9:00 Introduction
+
:8:45 Logistics and introductions (Barry Smith)
 +
:9:00 [https://buffalo.box.com/s/9k3mnsy2ddodun7wje10ud9fe1dzuepg Meeting objectives] (Darren Natale)
 +
:9:20 [https://buffalo.box.com/s/2ge3p0ae5x6dd8oidks6vh4xgms9ichu General introduction to PRO] (Darren Natale)
 +
:9:35 [https://buffalo.box.com/v/Ruttenberg-PRO-Sites PRO sites] (Alan Ruttenberg)
 +
:9:45 [https://buffalo.box.com/s/og1tusat1l4ucbbhm51wd6zh539dxfyk PRO Sites] (Darren Natale)
  
:10:30-10:45 Break
+
:10:15-10:30 Break
  
'''Single-Cell RNA Sequence'''
+
'''Uncovering disease mechanisms: connecting site annotations to ontologies'''
 
+
''Chair: Alexander Diehl''
+
''Chair: Judith Blake''
 
+
:10:45 Introduction
+
  
 +
:10:30 [https://buffalo.box.com/s/d93kobo8dh0alyb5ykkina6e1nw81s5p UniProtKB Feature Viewer] (Alexander Bateman)
 +
:11:00 [https://buffalo.box.com/s/ylbpwqz19y7cvxuwhg2eqg40yzxq7mr5 UniProtKB's molecular impact information] (Harold Drabkin) - connecting feature line information to ontologies
 +
:11:30 [https://buffalo.box.com/s/42fky2o87di08dk4q943t52l4ktpovi0 Disease Ontology] (Melody Swen) - introduction to DO and how it can be used to go from UniProtKB variants to disease identifiers
 +
:12:00 [https://buffalo.box.com/v/PRO-meeting-BFO-OGMS Basic Formal Ontology and Ontology for General Medical Science] (Barry Smith) - introduction to OGMS and to the new ISO/IEC 21838 top-level ontology standard
 +
 
:12:30-13:30 Lunch
 
:12:30-13:30 Lunch
  
'''Sources of Information for PRO'''
+
'''Uncovering disease mechanisms: connecting variants to diseases'''
  
''Chair: Cecilia Arighi''
+
''Chair: Judith Blake''
 
+
:13:30 Introduction
+
:13:30 [https://buffalo.box.com/s/p640nyu246h7736k7xt8sbkak6twffoz Mouse models of human disease] (Li Ni)
 +
:14:00 [https://buffalo.box.com/s/jo07sdssyn52fj89j3stn63aucx6a5yv Extracting variant / disease associations from text] (Cecilia Arighi)
 +
:14:30 [https://buffalo.box.com/s/d1qbf10l14lv31bnnpg2i17oi1re49r6 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
 
:15:00-15:30 Break
  
'''Disease and Underlying Mechanisms'''
+
:15:30 [https://buffalo.box.com/s/6kdes4lhv1s0rz89fn6tm943jxb3ajca Leveraging PRO in EuPathDB, OrthoMCL, and NIAGADS Genomics] (Chris Stoeckert)
 
+
:16:00 [https://buffalo.box.com/s/ygac6ictkvsfqvx79snsl8jxgejewyiz Protein aggregates] (Lauren Wishnie)
:15:30 Introduction
+
:16:30 Close of Day 1
 
+
Representatives from DO and OGMS
+
 
+
Sites, mutations at sites, and biochemical activity
+
 
+
:17:30 Close of Day 1
+
  
 
:18:00 Working dinner
 
:18:00 Working dinner
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==Schedule: Thursday, October 24, 2019==
 
==Schedule: Thursday, October 24, 2019==
  
:8:45 Introduction
+
[https://docs.google.com/document/d/1PiVxUQcEjsMlbudSGbxkVKwg3ib7KFnRyvHgv-CpUa4/edit?ts=5db0bc19 Googledocs discussion page from Day 1]
  
'''Variants'''
+
:8:15 Breakfast
  
''Chair: ??''
+
'''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 [https://buffalo.box.com/s/x66k2vdtw0cjnqvl2npklofj92pi08bm Reactome's disease pathways] (Peter d'Eustachio) - how they can be used with PRO to make new proteoform/disease associations
 +
:9:30 [https://buffalo.box.com/s/pptezlimqnxqd7maxamw2aa9ke33nla3 Using DTO and PRO for Drug target discovery] (Stephan Schürer)
 +
:10:00 [https://buffalo.box.com/s/xvaekv096s5pmwhium9c73jwmc2xn45x Connecting diseases to epitopes and proteins] (Randi Vita)
  
:10:30-11:00 Break
+
:10:30-10:45 Break
  
'''The PRO and Drug Discovery'''
+
'''Cell type discovery: proteoform expression and clinically-relevant cell types'''
  
''Chair: Judith Blake''
+
''Chair: Alexander Diehl''
  
:11:00  
+
:10:45 [https://buffalo.box.com/s/0sexse2ofjo7nl96d0dy4qahtvkgbhic Cell Ontology and its use of PRO] (Alexander Diehl)
 +
:11:05 Proteoform-based cell type dictionary (Alexander Diehl)
 +
:11:30 [https://buffalo.box.com/s/q5qpc7v0dsfi0kiksc6id4r5k89yysdz ImmPort and its use of PRO] (Patrick Dunn)
 +
:12:00 [https://buffalo.box.com/s/y2lcjgvha37ls6xmxx829qah4x6enbwy Communicating and cataloging proteoforms within the Blood Proteoform Atlas] (Paul Martin Thomas and Richard Dann LeDuc)
 +
:12:30-13:00 Lunch
  
:12:30-1:30 Lunch
+
:13:00 [https://buffalo.box.com/s/gvmwx3nzb24p30kz1xrqaqvot8wlnm00 Sequences beyond the Central Dogma: describing, quality controlling, exchanging, and visualizing proteoforms with concrete chemical semantics using BpForms/BcForms] (Jonathan Karr)
 +
:13:30 TBD
 +
:13:45 PRO grant working session
  
:13:30 Working Session on Grant Proposal
+
:15:00 Close of meeting
 
+
:15:00 Close
+
  
 
----
 
----
Line 80: Line 110:
 
== '''Participants''' ==
 
== '''Participants''' ==
  
 +
:Cecilia Arighi (Delaware / PRO)
 
:Alexander Bateman (EBI)*
 
:Alexander Bateman (EBI)*
:Alexander Diehl (Buffalo)
 
:Cecilia Arighi (Delaware / PRO)
 
 
:Judith Blake (JAX)
 
:Judith Blake (JAX)
 
:Peter d'Eustachio (NYU)
 
:Peter d'Eustachio (NYU)
 
:Alexander Diehl (Buffalo)
 
:Alexander Diehl (Buffalo)
:? Harold Drabkin (JAX)
+
:Harold Drabkin (JAX)
:Michelle Giglio (Baltimore)
+
:Patrick Dunn (ImmPort)
:Yongqun (Oliver) He (Michigan)
+
 
:Natarajan Kannan (Georgia)
 
:Natarajan Kannan (Georgia)
 +
:Jonathan Karr (MSSM)
 
:Richard LeDuc (Northwestern)
 
:Richard LeDuc (Northwestern)
 +
:Yu Lin (FDA)
 
:Birgit Meldal (EBI)*
 
:Birgit Meldal (EBI)*
:Darren Natale (Georgetown)
+
:Darren Natale (Georgetown/PRO)
:? Li Ni (JAX)
+
:Li Ni (JAX)
::Karen Ross (Delaware)  
+
:Karen Ross (Georgetown/PRO)  
 
:Alan Ruttenberg (Buffalo)
 
:Alan Ruttenberg (Buffalo)
 
:Stephan Schürer (Miami)
 
:Stephan Schürer (Miami)
 +
:Henry Schaefer (ImmPort)
 
:Barry Smith (Buffalo)  
 
:Barry Smith (Buffalo)  
 
:Christian Stoeckert (Penn)
 
:Christian Stoeckert (Penn)
 +
:Melody Swen (Baltimore)
 
:Paul Martin Thomas (Northwestern)
 
:Paul Martin Thomas (Northwestern)
 
:Randi Vita (San Diego)
 
:Randi Vita (San Diego)
 +
:Lauren Wishnie (Buffalo)
 
:Cathy Wu (Delaware / PRO)
 
:Cathy Wu (Delaware / PRO)
 +
:Sara Yang (NIST)
  
 
*=online
 
*=online
 
  
 
Please contact [mailto:phismith@buffalo.edu Barry Smith] for further information.
 
Please contact [mailto:phismith@buffalo.edu Barry Smith] for further information.

Latest revision as of 10:59, 24 October 2019

Date: October 23-24, 2019

Venue:

Protein Information Resource
Georgetown University Medical Center
Suite 1300
3300 Whitehaven Street NW (Milton Harris Building),
Washington, DC 20007, USA

For logistic questions please call BS at (716) 361-5100

Parking is available here ($11 per day)

Zoom: https://georgetown.zoom.us/j/3531468363


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)
9:35 PRO sites (Alan Ruttenberg)
9:45 PRO Sites (Darren Natale)
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 Swen) - introduction to DO and how it can be used to go from UniProtKB variants to disease identifiers
12:00 Basic Formal Ontology and Ontology for General Medical Science (Barry Smith) - introduction to OGMS and 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)
16:30 Close of Day 1
18:00 Working dinner

Schedule: Thursday, October 24, 2019

Googledocs discussion page from Day 1

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 diseases 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)
11:05 Proteoform-based cell type dictionary (Alexander Diehl)
11:30 ImmPort and its use of PRO (Patrick Dunn)
12:00 Communicating and cataloging proteoforms within the Blood Proteoform Atlas (Paul Martin Thomas and Richard Dann LeDuc)
12:30-13:00 Lunch
13:00 Sequences beyond the Central Dogma: describing, quality controlling, exchanging, and visualizing proteoforms with concrete chemical semantics using BpForms/BcForms (Jonathan Karr)
13:30 TBD
13:45 PRO grant working session
15:00 Close of meeting

Participants

Cecilia Arighi (Delaware / PRO)
Alexander Bateman (EBI)*
Judith Blake (JAX)
Peter d'Eustachio (NYU)
Alexander Diehl (Buffalo)
Harold Drabkin (JAX)
Patrick Dunn (ImmPort)
Natarajan Kannan (Georgia)
Jonathan Karr (MSSM)
Richard LeDuc (Northwestern)
Yu Lin (FDA)
Birgit Meldal (EBI)*
Darren Natale (Georgetown/PRO)
Li Ni (JAX)
Karen Ross (Georgetown/PRO)
Alan Ruttenberg (Buffalo)
Stephan Schürer (Miami)
Henry Schaefer (ImmPort)
Barry Smith (Buffalo)
Christian Stoeckert (Penn)
Melody Swen (Baltimore)
Paul Martin Thomas (Northwestern)
Randi Vita (San Diego)
Lauren Wishnie (Buffalo)
Cathy Wu (Delaware / PRO)
Sara Yang (NIST)
  • =online

Please contact Barry Smith for further information.

Sponsors

The Protein Ontology Consortium
National Center for Ontological Research