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Outline

Outline. Goals Use Cases Ontologies Best Practices and Modeling Issues Collaboration with BioRDF Next Steps: Clinical Observations Interoperability. BIONT Goals. Develop best practices around crucial questions related to creation and use of ontologies: What is an ontology?

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Outline

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  1. Outline • Goals • Use Cases • Ontologies • Best Practices and Modeling Issues • Collaboration with BioRDF • Next Steps: • Clinical Observations Interoperability

  2. BIONT Goals • Develop best practices around crucial questions related to creation and use of ontologies: • What is an ontology? • How should one represent information in an ontology? • Ontology lifecycle: How should ontologies be created, used, accessed, maintained and evolved? • Develop use cases spanning the Bench to Bedside Spectrum • Identify best practices and methodologies in design and development of various ontologies across the Bench to Bedside Spectrum • Collaboration with various Task Forces: BioRDF, ACPP, SWAN

  3. Use Cases • Parkinson’s Disease Use Case • Combined AD – PD Use Case • Patient Recruitment Use Case

  4. Use Case: Parkinson’s Disease • Description of Parkinson’s Disease and Information Needs from different perspectives: • Systems Physiology View • Cellular and Molecular Biologist View • Clinical Researcher View • Clinical Guideline Formulator View • Clinical Decision Support Implementer View • Primary Care Clinical View • Neurologist View • Available at: • http://esw.w3.org/topic/HCLS/ParkinsonUseCase • Developed by: • Don Doherty • Ken Kawamato

  5. Ontologies • Biomedical Research • Parkinson’s Disease Ontology • Clinical Reserch • Problem Oriented Medical Record Ontology • Study Data Tabulation Model • Clinical Practice • Detailed Clinical Models • ACPP Ontology

  6. Parkinson’s Disease Ontology

  7. POMR Ontology

  8. ACPP Ontology

  9. Collaboration with BioRDF • Collaboration and contribution to the joint AD – PD Use Case • BIONT: • Top Down (Domain?) Ontology Construction • Driven by Use Case • BioRDF: • Bottom up (Data?) driven Ontology construction • Driven by the need to provide a thin layer to “integrate” the islands

  10. Design Issues in Parkinson’s Ontology • Using classes vs relationships • UHCL-1 transcribed_into Dardarin • Using instance-of vs subclasses • UHCL-1 subclass-of Gene vs UHCL-1 instance-of Gene • Granularity/Specificity of relationships • AllelicVariant causes Disease, vs LRR2KVariant causes Parkinson’s Disease • Uncertainty • The discovery that genetic mutations in the alpha synuclein gene could cause Parkinson's disease in families • Multiple Domains/Ranges • Property: associated_with, Domains: Pathway, Protein, Ranges: Cell, Biomarker • Default Values • Default function of proteosomal pathway is protein degradation • Ontology Inclusion and Modularization • NeuroNames, Enzyme Commission, MeSH • Higher Order Relationships • Association between a Gene and a Disease in the context of a Study

  11. Best Practices for POMR Ontology • Mappings to foundational ontologies to facilitate ontological commitment • Adoption of consient terminology for ontological constructs • Avoidance of constructs which denote cognitive representations (skos:Concept) • Careful use of partial and complete class axioms • Clear seperation of temporal semantics • Exhaustive disjointeness

  12. Problems and Issues for POMR Ontology • Expressing periodic time intervals with OWL Time • No known URI-based naming convention (or OWL export) for SNOMED CT terms • Lossy semantic transformation from HL7 to RDF • No feasible means of reasoning over very large ontologies (GALEN, DOLCE, etc..)?

  13. Hard issues • What level of model becomes a Java class? • How do you make models easy to use in Java? • Opposition to this level of detailed models • Modeling of concepts and quantitative values in a single language/paradigm • Huge diversity of modeling styles: how to be consistent? • Defining computable connections between model and externally defined terminology • Large number of models needed

  14. Next Steps: Clinical Observations Interoperability • Information Models • DCM • SDTM • BRIDG • Terminologies • Snomed • NCI Thesaurus • MedDRA • Re-use and alignment of these models for interoperability

  15. Some tentative proposals • Two Organizations of Activity • Technology Driven Organization • BioRDF • BIONT • Application Driven Organization • ACPP • SWAN • Scientific Publishing

  16. Proposed Reorg? • Discovery • BioRDF • BIONT • URIs • Rules ... • Development • BioRDF • BIONT • URIs • Rules • Secondary Uses Of Healthcare Data • BioRDF • BIONT • URIs • Rules …

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