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Outline

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Collaboration with various Task Forces: BioRDF, ACPP, SWAN. Use Cases ... SWAN. Scientific Publishing. Proposed Reorg? Discovery. BioRDF. BIONT. URIs. Rules ... – PowerPoint PPT presentation

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Title: Outline


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

4
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

5
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6
Ontologies
  • Biomedical Research
  • Parkinsons Disease Ontology
  • Clinical Reserch
  • Problem Oriented Medical Record Ontology
  • Study Data Tabulation Model
  • Clinical Practice
  • Detailed Clinical Models
  • ACPP Ontology

7
Parkinsons Disease Ontology
8
POMR Ontology
9
ACPP Ontology
10
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11
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

12
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

13
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

14
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..)?

15
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

16
Next Steps Clinical Observations Interoperability
  • Information Models
  • DCM
  • SDTM
  • BRIDG
  • Terminologies
  • Snomed
  • NCI Thesaurus
  • MedDRA
  • Re-use and alignment of these models for
    interoperability

17
Some tentative proposals
  • Two Organizations of Activity
  • Technology Driven Organization
  • BioRDF
  • BIONT
  • Application Driven Organization
  • ACPP
  • SWAN
  • Scientific Publishing

18
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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