PRO Consortium Workshop 2019

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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