Alzforum / Protein Ontology Kick-Off Meeting
Venue
October 4-5, Buffalo, NY
Goals of the meeting
The goal of this meeting is to initiate a project that is designed to lead to the creation of a protein information resource that will address the needs of Alzheimers Disease (AD) researchers in a maximally effective way.
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 What are the different kinds of aggregates of protein 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 os 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 the AD researchers think their colleagues ought to be able to do that would retrieve their own 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. <-- SPECIFIC RELEVANCE TO AD NOT CLEAR
Tentative Schedule
9:30am
- Introduction to the project; introduction of project personnel
- Introduction to the AD research problems to be addressed
- Introduction to ontology-based ontology for scientists
10:30am Break
11:00am
Variants: How to relate variants, and collect requirements for the level of specificity needed in descriptions of variants to meet the needs of AD researchers. (This is one of several pending issues unresolved in the Neurocommons Semantic Resources
Different kinds of aggregates of protein relevant to AD, how do people treat them
Start with APP, what are all the genetic variants? How does PRO deal with that? How do variants relate.
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's 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 the AD researchers think their colleagues ought to be able to do that would retrieve their own results
Complexes: Same issues as above, but for protein complexes. To address in addition: criteria for being a complex - what amount of stability necessary, component stoichiometry and structure, modifications/changes to complexes and associated functional changes.
- Based on above analysis set project goals for 3 months, 6 months, 1 year.
Intending Participants
- Cecilia Arighi (Delaware)
- Peter d'Eustachio (New York)
- Alex Diehl (Buffalo)
- Darren Natale (Washington)
- Alan Ruttenberg (Buffalo)
- Kinga Szigati (Buffalo)
- Barry Smith (Buffalo)
- Cathy Wu (Delaware)
- Elizabeth Wu (Boston)