Alzforum / Protein Ontology Kick-Off Meeting

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Date and Venue

October 4-5, Buffalo, NY

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 Alzheimers Disease (AD) researchers in a maximally effective way. We will focus primarily on extending the Protein Ontology (PRO), on applying the PRO to annotation of AD research results, and on creating PRO-based application ontologies for AD research.

The project forms part of the NIGMS-funded Protein Ontology initiative.

Topics to be addressed at the meeting will include

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.

Very Tentative Schedule

Tuesday, October 4

9:30am

  • Introduction to the project; introduction of project personnel
  • Introduction to the AD research problems to be addressed
  • Introduction to ontology for scientists

10:30am Break

11:00am

  • Short tutorial on the Protein Ontology and associated web tools (including feedback)
  • Review of proteomics information tools, resources used by AD researchers, unmet needs

12:30pm Lunch

1:30pm AD-relevant variants, complexes, aggregates

6:00pm Dinner

Wednesday, October 5

9:00am Case Studies

12:30pm Lunch

1:30pm Case Studies

2:30pm Project planning

3:30pm Main meeting ends

Technical session for selected participants during rest of day.

Intending Participants

  • Cecilia Arighi (University of Delaware)
  • Peter d'Eustachio (NYU School of Medicine, New York)
  • Alex Diehl (University at Buffalo)
  • Darren Natale (Georgetown University Medical Center, Washington DC)
  • Alan Ruttenberg (University at Buffalo)
  • Barry Smith (University at Buffalo)
  • Kinga Szigati (University at Buffalo)
  • Michael Wolfe (Harvard Medical School, Boston)
  • Cathy Wu (University of Delaware)
  • Elizabeth Wu (Alzforum, Boston)
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