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BIONT-BIORDF Collaboration

BIONT-BIORDF Collaboration. Use Case. Show me the location of receptors that bind to a ligand which is a therapeutic agent in {Parkinson’s, Huntington’s} disease in each of the dopaminergic neurons in the {pars compacta, pars reticularis, substantia nigra}. Spans the following domains

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BIONT-BIORDF Collaboration

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  1. BIONT-BIORDF Collaboration

  2. Use Case • Show me the location of receptors that bind to a ligand which is a therapeutic agent in {Parkinson’s, Huntington’s} 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

  3. BIORDF Hackathon • Data Sources: • Cocodat (SenseLab) • KiDB • Alan shows demo (at the end)

  4. Tasks for Demo • Specify SPARQL queries against Parkinson’s 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 Parkinson’s Disease Ontology

  5. 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

  6. 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 Parkinson’s guidelines identified by ACPP group

  7. 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?

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