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

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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 Barry Smith for further information.

Sponsors

The Protein Ontology Consortium

National Center for Ontological Research