Protein Ontology Workshop

Venue: Conference Room #1300, Harris Building, Georgetown University, 3300 Whitehaven Street NW, Washington DC 20007.

Date: June (17)-18-19, 2014. The meeting will begin with an informal reception in the Holiday Inn, Georgetown, on Tuesday, June 17 and conclude at 4pm on June 19.

---

Goals

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 resources, including the UniProtKB and the Protein Data Bank

Themes:

Neurological disease, immunology, cancer

Protein-based disease/phenotype representation

PRO and UniProt

Persons interested in participating should contact Barry Smith as soon as possible.

Schedule: Wednesday, June 18, 2014

8:00 Continental Breakfast

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

12:00 Lunch

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

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

17:05 Alexander Cox (Buffalo): Neurofibrillary Tangles and Amyloid Plaques: The Treatment of Protein Aggregates in the Protein Ontology

17:30 Close

18:00 Working Dinner

Schedule: Thursday, June 19th, 2014

8:00 Continental breakfast

9:00 Donna Maglott (NIH): PRO and Medical Genetics resources at NCBI

9:45 Claire Donovan (EBI): Ontologies at the EBI

10:30 Break

10:45 Paul Martin Thomas (Northwestern): Descriptive and Quantitative Top Down Proteomics

11:30 Jonathan Bona and Alan Ruttenberg (Buffalo): UniProt Accessions - Issues of Tracking and Stability

12:30 Lunch

13:30 Judith Blake (Jackson Lab) and Barry Smith (Buffalo):

• 1. Ontologies, Databases, Knowledgebases: How Should They Interoperate?
• 2. Relations linking Proteins to Diseases

14:30 Break

14:45 Gilbert S. Omenn (Michigan): The Human Proteome Project

16:00 Close

---

Participants

Cecilia Arighi (Georgetown)

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)

Donna Duffield (NIH / NLM / NCBI)

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)

Please contact Barry Smith for further information.

Sponsors

The Protein Ontology Consortium

National Center for Biomedical Ontology

National Center for Ontological Research