Protein Ontology Workshop
Date: June 18-19, 2014
Venue: Georgetown University
Goals and outcomes
The goals of this meeting are:
- 1. To contribute to the ontological understanding of phenotype and disease across organisms
- 2. To advance the treatment of protein-related clinical and translational data from the perspective of consistency, discoverability and support for diagnosis
- 3. To advance coordination between the Protein Ontology and other protein-related information resources
Desired outcomes are of two sorts:
- Relating to disease:
- We will seek greater clarity as to
- - how proteomic information in general and the PRO in particular can help us to understand the relationship between genotype and phenotype, for example in understanding disease etiology
- - which relations we should use in linking the protein entities represented in the PRO to disease entities
- - which are the important entities on the protein side that need to be linked
- Relating to PRO's interactions with external resources:
- UniProt: Draft of policies/recommendations regarding accession/site tracking for UniProt and PRO
- IntAct: Identify points of agreement and discrepancy in curation pipelines and resolve as appropriate. Reach agreements for example on reciprocal links and accession issues
Schedule: Wednesday, June 18, 2014
Chair: Barry Smith
8:45 Cathy Wu (Delaware/Georgetown): Current Status and Future Goals of the Protein Ontology
9:45 Peter d'Eustachio (NYU): PRO, Reactome and Disease Pathways
10:30 Break
10:45 Olivier Bodenreider (NLM): Ontologies in the NLM
11:25 Sirarat Sarntivijai (FDA): Using the Protein Ontology: The View from the Outside
11:55 Carol Bean (Stanford / NCBO): The Future of the Bioportal
12:15 Lunch
Chair: Peter d'Eustachio
13:00 Sandra Orchard (EBI): PRO and IntAct
14:00 Evan Bolton (NCBI): PubChemRDF: Towards a Semantic Description of PubChem
14:40 Lynn Schriml (Baltimore): Collaboration of PRO and PubChem with the Disease Ontology
15:20 Break
Chair: Darren Natale
15:40 Veerasamy “Ravi” Ravichandran (NIGMS): NIGMS and the Protein Ontology
16:00 John Westbrook (PDB): PRO Represention of Proteins Observed in 3D Experimental Structure Data
16:40 Alexander Diehl (Buffalo): PRO and the NIF / ImmPort Antibody Registries
17:20 Close
18:00 Working Dinner: Cafe Divan, 1834 Wisconsin Ave
Schedule: Thursday, June 19th, 2014
Venue: Conference Room #1300, Harris Building, Georgetown University, 3300 Whitehaven Street NW
8:00 Continental breakfast
Chair: Alexander Diehl
9:00 Donna Maglott (NIH): PRO and Medical Genetics resources at NCBI
9:40 Paul Martin Thomas (Northwestern): Descriptive and Quantitative Top Down Proteomics
10:20 John Garavelli (Delaware): Use Cases for Modified Protein Interactions (for UniProt, PRO and proteomics)
10:30 Break
10:45 Alexander Cox (Buffalo): Neurofibrillary Tangles and Amyloid Plaques: The Treatment of Protein Aggregates in the Protein Ontology
11.15 Alan Ruttenberg and Jonathan Bona (Buffalo): Issues surrounding coordination of UniProtKB and the Protein Ontology
12:30 Lunch
Chair: Cecilia Arrighi
13:30 Judith Blake (Jackson Lab): Ontologies, Databases, Knowledgebases: How Should They Interoperate?
14:00 Barry Smith (Buffalo): Introduction to the Relation Ontology
14:15 Darren Natale: Relations linking Proteins to Diseases
14:30 Break
14:45 Gilbert S. Omenn (Michigan): The Human Proteome Project
16:00 Close
Participants
- Cecilia Arighi (Delaware / PRO)
- Carol Bean (NCBO / Stanford)
- Judith Blake (JAX)
- Olivier Bodenreider (NIH / NLM / LHC)
- Evan Bolton (NIH / NCBI)
- Jonathan Bona (Buffalo)
- Karen Christie (JAX)
- Alexander Cox (Buffalo)
- Peter d'Eustachio (NYU / Reactome)
- Alex Diehl (Buffalo)
- Harold Drabkin (JAX)
- Gang Fu (NCBI / NIH)
- John S. Garavelli (Delaware)
- Donna Maglott (NIH / NLM / NCBI)
- John Mattison (Global Alliance for Genomics and Health)
- Darren Natale (Georgetown)
- Claire O'Donovan (EBI / UniProt)
- Gilbert S. Omenn (Michigan)
- Sandra Orchard (EBI / IntAct)
- Veerasamy “Ravi” Ravichandran (NIH / NIGMS)
- Karen Ross (Delaware)
- Alan Ruttenberg (Buffalo)
- Sirarat Sarntivijai (FDA)
- Selja Seppälä (Buffalo)
- Lynn Schriml (Baltimore)
- Barry Smith (Buffalo)
- Paul Martin Thomas (Top Down Proteomics / Northwestern)
- John Westbrook (PDB / Rutgers)
- Cathy Wu (Delaware / PRO)
Please contact Barry Smith for further information.
