BIONT-BIORDF Collaboration

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BIONT-BIORDF Collaboration
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Use Case

• Show me the location of receptors that bind to a
  ligand which is a therapeutic agent in
  Parkinsons, Huntingtons disease in each of
  the dopaminergic neurons in the pars compacta,
  pars reticularis, substantia nigra.
• Spans the following domains
• Compartments of Neurons (Anatomy, Systems
  Physiology)
• Receptors on Neurons (Protein, Molecular Biology)
• Compounds that bind to Receptors (Pharmacology)
• Ligands associated with disease
  (Clinical/Medical)
• Spans the following Data Sources
• Neuron DB (SenseLab), RDF
• KI DB, OWL
• PubChem, TBD

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BIORDF Hackathon

• Data Sources
• Cocodat (SenseLab)
• KiDB
• Alan shows demo (at the end)

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Tasks for Demo

• Specify SPARQL queries against Parkinsons
  Disease Ontology
• Annotate Data Sources with
• Ontological relationships, e.g., receptor
  located_in neuron
• SPARQL queries to populate the relationships
• Create Merged Data Warehouse containing a
  pre-integrated database.
• Manually Decompose SPARQL query against
  ontology into SPARQL sub queries against
  individual data sources
• Merge RDF graphs
• User Interface?
• Update/refine Parkinsons Disease Ontology

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Architectural Alternatives

• Data Integrated vs Accumulation Warehousing
• Mediator approach
• Discuss Pros and Cons
• Demo April 2007
• Report could describe
• Approach for handling use case (as we implement
  it in the demo)
• Architectural Alternatives
• Value proposition of SW technologies for data
  integration, user interface and distribution?
• Alternatives for semantic web based
  representation of data
• Editorial Lead Don Doherty
• Deadline November 2006

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Next Steps

• Prepare Note in the November time frame
• Propose joint teleconferences/wiki pages and
  sessions to map out the tasks and set up a demo
• Determine the sophistication of the demo. To what
  extent should we implement the mediation
  architecture ? Or is just a simple hard coding of
  SPARQL queries enough ?
• Figure out potential clinical extensions based on
  Parkinsons guidelines identified by ACPP group

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BIONT Report

• Ontology Modeling and Mapping Issues
• Possible Collaboration with ACPP
• First Draft November 06
• Mapping across different ontologies such as
• Gene Ontology
• MeSH
• Neuro Names
• Enzyme Commission
• RIM
• Galen
• Editor Vipul Kashyap, Helen Chen?