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Protein Ontology (PRO) workshop 2016

Created by Cecilia Arighi, last modified on Nov 28, 2016


When and Where

Dates: November 14-15, 2016
Venue: 3300 Whitehaven NW., Harris Building, Georgetown University, Washington DC 20007.

This is a close meeting, attendance is by invitation.

Mission and workshop objectives

PRO mission is to enable protein-disease understanding by presenting knowledge about proteins in biological context richly and accurately for both human understanding and computational reasoning.

Workshop objectives

1Creation and implementation of strategies to enable researchers to curate PRO branches in collaboration with PRO experts
2Identification of relationships and biological contexts (e.g., kinase-substrate, proteoform-disease) to describe relations of proteins to disease
3Curation of terms needed to address use cases
4Construction of semantic queries to address use cases

1- PTM/variants and disease. One of the aims in PRO is to provide comprehensive coverage of proteoforms in their biological context. More specifically create a comprehensive representation of known proteoforms that integrates proteomic evidence of clinical variants and PTMs with rich relationships and biological contexts (e.g., kinase-substrate, proteoform-disease). To work on this topic ProKinO, MGI, NeXtProt and Reactome groups were recruited.

2- epitopes, antibodies, proteoforms and disease. The immunology community is keenly interested in ontological terms for key immune-related proteins such as cell surface markers, cytokines, transcription factors, and the highly variable antigen receptors. In some cases, these requests highlight the need for development of the PRO framework, e.g., to allow the proper mapping between the antibody and the set of recognized proteins. To work on this topic, the Immport and IEDB groups were recruited.

Agenda

https://drive.google.com/open?id=0B4QyLB3JI6qRR05pQUgxdEthQzQ

Day 1 (Conference Room 1300)

8:30-9:00 Breakfast

9:00-9:15 PRO mission and workshop objectives (Cathy Wu)

9:15-9:35 PRO Ontological Framework (Darren Natale)

9:35-10:45 Accessing PRO scientific content: this session will introduce some resources to access PRO data

9:35-10:00 PRO website [includes overview of the website and demonstration of scientific content] (Cecilia Arighi)
10:00-10-25 SPARQL queries [includes demonstration of federated query using UniProt as example] (Chuming Chen)
10:25-10:45 iPTMnet [includes how PRO is consumed by iPTMnet and enriches its content] (Karen Ross)

10:45-11:00 COFFEE BREAK

11:00-12:30 Projectís introductions: 15 min presentations from each resource to provide a general information, followed by workshop-related questions about the intended outcome of the workshop and how PRO could assist to achieve such outcome.

11:00-11:15 ProKinO (Kannan Natarajan)
11:15-11:30 NeXtProt (Pascale Gaudet)
11:30-11:45 Reactome (Peter D'Eustachio)
11:45-12:00 MGI (Cynthia Smith)
12:00-12:15 Immport (Alex Diehl)
12:15-12:30 IEDB (Randi Vita)

12:30-1:30 LUNCH

1:30-2:00 Intro to use cases. This section will layout the most relevant issues and use cases to be discussed in different working sessions. By the end of the day, each group should give a presentation of the major outcomes of the discussion. (Cecilia Arighi)

2:00-3:00 Session 1-General session. This section intends to get (hopefully) a consensus opinion on common topics of interest, so we can provide our recommendation to the ontology community. Moderators should have a proposal ready to be discussed.

2:00-2:20 Connecting proteoforms/complexes and disease. How to relate protein and complexes to disease. Moderators: Judith Blake, Peter D'Eustacchio, Cynthia Smith
2:20-2:40 Connecting peptides/epitopes and proteins.How to relate peptides and epitopes to proteins. Moderators: Alex Diehl, Darren Natale
2:40-3:00Representation of variants and isoforms. How to relate variants and isoforms. Moderators: Karen Ross, Harold Drabkin

3:00-3:15 COFFEE BREAK

3:15-4:45 Parallel group sessions. For the proposed questions/use cases the discussion should include: who has the data and how to connect to such data, and a proposal of federated queries/scientific questions from each group.

Group 1- PTM/variants and disease.

Moderator: Judith Blake
Participants: Karen Ross, Cathy Wu, Cynthia Smith, Harold Drabkin, Pascale Gaudet, Kannan Natarajan, Liang-Chin Huang and Peter D'Eustacchio

- PTM-variants and disease
What are variants affecting phosphorylation site (gain or loss)?
What proteoforms and complexes would be affected?
What pathways would be affected?
Connected to what disease?
What are variants affecting kinase function?
What targets would be affected?
What pathways would be affected?
Connected to what disease?

- Isoforms-variants and connection to disease in mouse and human
Connecting mouse and human isoforms and variants to allelic information in MGI, disease models and human disease
Connecting functional annotation of variants

Group 2- Epitopes/antibodies and disease

Moderator: Cecilia Arighi
Participants: Darren Natale, Alex Diehl and Randi Vita

MHC related proteins
Epitopes/proteins and antibodies in autoimmune disease
Cytokines

Group 3 Ė Semantic integration

Moderator: Chuming Chen
Participants: Alan Ruttenberg, Krys Kochut

4:45-5:30 Wrap up session day 1

4:45-4:55 Presentation group 1
4:55-5:05 Presentation group 2
5:05-5:15 Presentation group 3
5:15-5:30 General Discussion that should lead to action items and regrouping for day 2

6:30 Working Dinner at Cafe Divan, 1834 Wisconsin Ave, NW. Washington, DC 20007

Day 2 (Conference Room 4300)

8:30-9:00 Breakfast

9:00-10:30 Group session (cont). For the proposed questions/use cases the discussion should now model different cases. If possible, apply to real case.

Group 1- PTM/variants and disease. (cont)
Moderator: Cathy Wu
Participants: TBD after day 1

PTM-variants and disease
Isoforms-variants and connection to disease in mouse and human

Group 2- epitopes/antibodies and disease (cont.)

Moderator: Cecilia Arighi
Participants: TBD after day 1

MHC related proteins
Epitopes/proteins and antibodies in autoimmune disease
Cytokines

10:30-10:45 COFFEE BREAK

10:45-12:30 Breakout sessions to streamline data integration

    1ProkinO ontology development as an extension of PRO (Alan Ruttenberg, Darren Natale and Kannanís group)
2NeXtProt and IEDB modified peptides and epitopes, respectively, and link to proteins in iPTMnet and PRO (Cathy Wu, Randi Vita and Pascale Gaudet)
3MGI-PRO establish workflow for variants in MGI to PRO IDs and annotation. Modeling with Noctua (Cecilia Arighi and MGI group)

12:30-1:30 LUNCH

1:30-2:30 Presentation of breakout session

1:30-1:45 ProkinO ontology development as an extension of PRO
1:45-2:00 NeXtProt and IEDB modified peptides and epitopes, respectively, and link to proteins in iPTMnet and PRO
2:00-2:15 MGI-PRO establish workflow for variants in MGI to PRO IDs and annotation. Modeling with Noctua?
2:15-2:30 General discussion

2:30-2:45 COFFEE BREAK

2:45-4:00 Wrap up use case sessions and next steps

- Review of meeting objectives and their outcome
- Planning for manuscripts
Manuscript 1-proteoforms/complexes->noctua modeling
Manuscript 2-epitopes/antibodies/proteoforms
-
Next steps

End of workshop


Participants

On Site:

EIDBRandi Vita
ProKinOKannan Natarajan
ProKinOLiang-Chin Huang
ProKinOKrys Kochut
ProKinODaniel McSkimming
JAXHarold Drabkin
JAXJudith Blake
JAXCynthia Smith
ReactomePeter D'Eustacchio
Buffalo/ImmportAlex Diehl
BuffaloAlan Ruttenberg
NeXtprotPascale Gaudet
PIRDarren Natale
PIRChuming Chen
PIRKaren Ross
PIRCecilia Arighi
PIRCathy Wu
University of DelawareJulie Cowart (remotely)
University of MiamiStephan Schurer (remotely)