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Outline

This project aims to establish best practices for creating and implementing ontologies in biomedical research, focusing on Parkinson's Disease and Clinical Research. It includes use cases, collaborations with BioRDF, and modeling issues.

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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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