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.
