Protein Ontology Workshop

Date: June 18-19, 2014.

Venue: Georgetown University's Harris Building is about 3 miles from Union Station, and 1.5 miles from the Woodley Park subway station. The DC Circulator Georgetown Line services the Holiday Inn Georgetown the Union Station train station. If you arrive via the Woodley Park subway station, the hotel provides free shuttle service. The cost is just $1.

There is a GU shuttle that stops at the Harris building. From the GU campus, look for the Wisconsin Ave Shuttle, which stops at the Epicurean Restaurant.

Parking is available at the Holiday Inn, which is half a block from Georgetown University's Harris Building. There is also parking directly underneath the Harris Building ($20 per day), and another one at the end of the road ($9 per day).

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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

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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.

Sponsors

The Protein Ontology Consortium

National Center for Biomedical Ontology

National Center for Ontological Research