Outline

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Outline

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

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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

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Use Cases

• Parkinsons Disease Use Case
• Combined AD PD Use Case
• Patient Recruitment Use Case

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Use Case Parkinsons Disease

• Description of Parkinsons 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

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Ontologies

• Biomedical Research
• Parkinsons Disease Ontology
• Clinical Reserch
• Problem Oriented Medical Record Ontology
• Study Data Tabulation Model
• Clinical Practice
• Detailed Clinical Models
• ACPP Ontology

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Parkinsons Disease Ontology
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POMR Ontology
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ACPP Ontology
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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

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Design Issues in Parkinsons 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 Parkinsons 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

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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 (skosConcept)
• Careful use of partial and complete class axioms
• Clear seperation of temporal semantics
• Exhaustive disjointeness

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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..)?

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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

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Next Steps Clinical Observations Interoperability

• Information Models
• DCM
• SDTM
• BRIDG
• Terminologies
• Snomed
• NCI Thesaurus
• MedDRA
• Re-use and alignment of these models for
  interoperability

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Some tentative proposals

• Two Organizations of Activity
• Technology Driven Organization
• BioRDF
• BIONT
• Application Driven Organization
• ACPP
• SWAN
• Scientific Publishing

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Proposed Reorg?

• Discovery
• BioRDF
• BIONT
• URIs
• Rules ...
• Development
• BioRDF
• BIONT
• URIs
• Rules
• Secondary Uses Of Healthcare Data
• BioRDF
• BIONT
• URIs
• Rules