PRO Consortium Workshop 2017
Date: October 11-12, 2017
Venue: The Jackson Lab, Bar Habor, Maine
Goals
The goals of this meeting are:
- 1. To review the current state of the Protein Ontology and its relation to other protein-related information resources, especially UniProt and GO
- 2. To assess progress in the use of advanced computational techniques, including Natural Language Processing, in the development of the PRO
- 3. To examine the actual and potential contribution of PRO to the understanding of disease across organisms
- 4. To review PRO's role in the field of immunology informatics
- 5. To advance the treatment of protein-related clinical and translational data from the perspective of consistency, discoverability and support for diagnosis
- 6. To evaluate competing approaches to PRO annotation
Schedule: Tuesday, October, 10, 2017
19:00 Informal reception for early arrivals in conference hotel
Schedule: Wednesday, October, 11, 2017
8:45 Introductory Session: The Landscape of the Protein Ontology
- Cathy Wu: Protein Ontology: Its current state and future development
- Sites, PTMs
- Susan Gregurick: NIH 2018 Priorities in Data Science and Computational Science
9:45 PRO and Related Resources
- Karen Ross: PRO Collaborations (ProKinO, NeXtProt ...)
- Erich Baker and Elissa Chesler: GeneWeaver
- Cindy Smith: The Alliance of Genome Resources
10:45 Break
11:00 PRO and Informatics
- Kimberley VanAuken: Noctua
- Julie Cowart: Writing SPARQL queries for PRO
- Alan Ruttenberg: Enhanced SPARQL queries for PRO
- Cecilia Arighi: The role of NLP in PRO curation
12:30 Lunch
13:30 PRO and Disease
Chair: Darren Natale
- Judith Blake: Disease Ontology -- overview of available resources
- Chris Mungall: MONARCH
- Elissa Chesler: MGI effort to combine variant data with disease forms; Genereader resource, PRO IDs for variants
14:30 Break
14:45 PRO and Disease (Continued)
- Peter McGarvey: Genome Annotation, ClinGen and PRO
- Peter d'Eustachio : PRO and Reactome
- Alexander Diehl: PRO and the Antibody Ontology
- Alexander Diehl: PRO and the Cell Ontology
- HIPC, cell populations, the Antibody Panel Ontology, Cell types vs. cell states -- when do combinations of protein markers
16:00 Break
16:15 The Value of PRO Annotations in Enabling Interconnection of Biomedical Ontologies and Databases
- This session will include a debate between Alan Ruttenberg, Chris Mungall, David Hill and Darren Natale on the proper representation of PRO annotations
18:00 Working dinner
Schedule: Thursday, October 12, 2017
8:00 Continental breakfast
8:45 GO, PRO and UniProt: How they should work together
Chair: Cathy Wu
- Alex Bateman (EBI)
10:30 Break
10:45 Maria Martin (EBI) TBD
12:00 Lunch
12:45 Debate: How genes are referenced in OBO Foundry and in PRO: why do they differ?
Chair: TBD
- Participants: Chris Mungall, Darren Natale, Alan Ruttenberg (will be moved to working dinner if space needed)
14:00 Close of Plenary Sessions
14:00 Working group meetings
17:00 Close
Participants
*=online
- Cecilia Arighi (Delaware / PRO)*
- Erich Baker (Baylor)
- Alex Bateman (EBI)*
- Judith Blake (JAX)
- Chuming Chen (Delaware)*
- Elissa Chesler (JAX)
- Julie Cowart (Delaware)*
- Peter d'Eustachio (NYU)*
- Alexander Diehl (Buffalo)
- Harold Drabkin (JAX)
- Susan Gregurick (NIH / NIGMS)*
- David Hill (JAX)
- Stanley Laulederkind (Medical College of Wisconsin)
- Peter McGarvey (Georgetown)
- Chris Mungall (LBNL)
- Darren Natale (Georgetown)
- Li Ni (JAX)
- Karen Ross (Delaware)*
- Alan Ruttenberg (Buffalo)
- Cynthia Smith (JAX)
- Barry Smith (Buffalo)
- Kimberley VanAuken (CalTech)
- Laurens Wilming (JAX)
- Cathy Wu (Delaware / PRO)
Please contact Barry Smith for further information.
