Alzforum / Protein Ontology Kick-Off Meeting

The Alzforum / Protein Ontology collaboration is a driving biological project of the NIGMS-funded Protein Ontology initiative.

Goals of the meeting

The goal of this meeting is to initiate a project to create a protein information resource that will address the needs of Alzheimer's Disease (AD) researchers in a maximally effective way. The focus of the meeting will be directed primarily towards identifying these needs through discussion with specialists in different aspects of AD research. The intended long-term outcome will take the form of elaborations and extensions of the Protein Ontology (PRO), of new applications of the ontology to annotation of AD research results, and of new PRO-based software tools to support AD research.

Date and Venue

October 4-5, 2011, Hotel Indigo, Buffalo, NY

Topics to be addressed

Protein Variants

How can we most effectively represent information pertaining to the variants associated with AD and to the relations between them; for example, what level of specificity of descriptions of variants would best address the requirements of AD researchers? In the case of APP, for example, what are the genetic variants of relevance to APP? How should the Protein Ontology deal with such variants in order to assist researchers?

Aggregates of proteins / Protein complexes

What are the different kinds of aggregates and complexes relevant to AD, how do AD researchers treat them?

We envisage two case studies in the course of the meeting, both of which will be designed to serve as guidance for Protein Ontology developers in the initial phases of the project:

1. Protein case study: Perform a detailed review of one class of proteins important to AD research, chosen to be part of the research agenda of at least one of the AD scientists, to bring all participants up to the same level of understanding about what is known. Issues to be addressed will include:

importance of recording non-protein constituents

multimerism

relations to disease hypotheses

kinds of evidence

research plan

protein knowledge queries that would aid the AD researchers

protein knowledge queries that would help others retrieve AD research results

2. Protein complex case study: In addition to the issues addressed above as these arise for protein complexes, this case study will address in addition: criteria for being a complex - what amount of stability is necessary, component stoichiometry and structure, modifications/changes to complexes and associated functional changes.

Schedule

Monday, October 3

From 7:00pm Dinner / Informal Reception, Blue Fire Restaurant, Marriott Hotel (next door to Indigo Hotel)

Tuesday, October 4

8:30am Continental Breakfast

9:30am Moderator: Darren Natale

• Alan Ruttenberg: Introduction to the project; introduction of project personnel
• Dominic Walsh: Introduction to Alzheimer's Disease Research
• Barry Smith: Introduction to Ontology for Biomedical Scientists
• Cathy Wu: Introduction to the Protein Ontology

10:30am Refreshment Break

11:00am Moderator: Elizabeth Wu

• Discussion of Proteomics Information Tools and Resources Used by AD Researchers
• Identification of Unmet Needs

12:30pm Lunch

1:30pm Moderator: Barry Smith

• Cecilia Arighi: Short Tutorial on the PRO Website and Associated Tools
• AD-Relevant Variants, Complexes, Aggregates

3:00pm Refreshment Break

3:30 Moderator: Darren Natale

• Tim Danford: On Using Exons to Define Isoforms
• Discussion of Epitope Identification
• Barry Smith: Introduction to the OBO Foundry
• Alan Ruttenberg: Reasoning with PRO and Other OBO Foundry Ontologies

6:00pm Dinner: Byblos Restaurant, 270 Campbell Blvd, Getzville, NY 14068. Directions

Wednesday, October 5

8:30am Continental Breakfast

9:00am Darren Natale: Review of Existing PRO Coverage of AD-Related Proteins

9:30am Fahim Imam: Neuroscience Information Framework (NIF)

10:00am Paolo Ciccarese: Annotation of Neuroscientific Data

10:30am Refreshment Break

11:00am Case Studies

Sample Questions

• What is APP695
• Give me all recorded phosphorylation sites involving APP

Using Alzforum as a Starting Point for Queries: What Goes Wrong?

12:30pm Lunch

1:30pm Case Studies

Topics for discussion: Animal Models

2:30pm Project planning

3:30pm Main meeting ends / Refreshment Break

Technical session for selected participants during rest of day.

6:00pm Dinner

Participants

• Cecilia Arighi (PRO / University of Delaware)
• Paolo Ciccarese (Massachusetts General Hospital / Harvard Medical School, Boston)
• Alexander Cox (University at Buffalo)
• Kelly Anne Dakin (Alzforum, Boston)
• Paresh Dandona (University at Buffalo)
• Timothy Danford (Novartis, Boston)
• Peter D'Eustachio (Reactome / NYU School of Medicine, New York)
• Alexander Diehl (CL, GO / University at Buffalo)
• Fahim Imam (NIF / University of California at San Diego)
• Mark Jensen (University at Buffalo)
• Darren Natale (PRO / Georgetown University Medical Center, Washington DC)
• Mark Ressler (University at Buffalo)
• Caryn-Amy Rose (Alzforum, Boston)
• Alan Ruttenberg (University at Buffalo)
• Barry Smith (University at Buffalo)
• Kinga Szigati (University at Buffalo)
• Dominic M. Walsh (Brigham & Women's Hospital, Harvard Institutes of Medicine, Boston)
• Michael Wolfe (Brigham & Women's Hospital, Center for Neurologic Diseases, Boston)
• Cathy Wu (PRO / University of Delaware)
• Elizabeth Wu (Alzforum, Boston)