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  • The NCI Thesaurus & TDE

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    Sbo Chen
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    The NCI Thesaurus is a logic representation of NCI vocabulary stored in XML format. It has an is_a hierarchy called SuperConcept and uses kinds to group related concepts and roles to define relationships between concepts. Properties provide additional information about concepts. The thesaurus has a tree structure organized by kinds like diseases, genes, and proteins. Roles define uni-directional relationships between concepts and properties store descriptive information without inheritance. The thesaurus is developed asynchronously by multiple content editors and consolidated in an Oracle database.

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    The NCI Thesaurus is a logic representation of NCI vocabulary stored in XML format. It has an is_a hierarchy called SuperConcept and uses kinds to group related concepts and roles to define relationships between concepts. Properties provide additional information about concepts. The thesaurus has a tree structure organized by kinds like diseases, genes, and proteins. Roles define uni-directional relationships between concepts and properties store descriptive information without inheritance. The thesaurus is developed asynchronously by multiple content editors and consolidated in an Oracle database.

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    Download as PPT, PDF, TXT or read online from Scribd
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    9 views9 pages

    The NCI Thesaurus & TDE

    Uploaded by

    Sbo Chen
    The NCI Thesaurus is a logic representation of NCI vocabulary stored in XML format. It has an is_a hierarchy called SuperConcept and uses kinds to group related concepts and roles to define relationships between concepts. Properties provide additional information about concepts. The thesaurus has a tree structure organized by kinds like diseases, genes, and proteins. Roles define uni-directional relationships between concepts and properties store descriptive information without inheritance. The thesaurus is developed asynchronously by multiple content editors and consolidated in an Oracle database.

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    Attribution Non-Commercial (BY-NC)
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    of 9

    The NCI Thesaurus

    ►Description Logic representation of NCI vocabulary

    • xml based
    • is_a hierarchy (“SuperConcept”)
    • Kinds: disjoint groups of concepts
    • Roles: relationships between concepts
    • Properties: information about a concept
    NCI Thesaurus
    ► Research Orientation

    Disease

    Proteins Diagnosis Genes

    Prognosis

    Creates a knowledge base


    NCI Thesaurus
    Tree Structure ► Kinds
    • Anatomic Structures or Systems
    • Biological Processes
    • Chemicals and Drugs
    • Clinical or Research Activities; e.g. Treatment, Prevention, Screening
    • Diagnostic and Prognostic Factors; e.g. Biomarkers
    • Diagnostic, Therapeutic, or Research Equipment
    • Disease
    • Gene
    • Organisms
    • Proteins
    • Techniques
    • UWDA Digital Anatomist
    • NCI Thesaurus
    NCI Thesaurus
    ► Roles

    ► Unidirectional relationships between concepts


    • Circular arguments are not allowed
    • Restricted by Kind
    • Roles are inherited
    ► Minimum Set
    • Enough to allow all concepts to be discriminated
    • “Defining Roles”

    ► Maximum Set
    • Enough to represent all desired relationships
    • “Non-defining” or “Optional Roles”
    NCI Thesaurus
    ► Properties

    ► Specific information about a concept


    • Properties are not inherited
    • Stored as strings
    NCI Thesaurus Development
    • Asynchronous, distributed editing: Assignments or
    “Free-range” editing
    • Conflict detection & Database consolidation
    TDE
    TDE
    Content
    Editor
    (NCI) XML
    Work
    TDE
    TDE
    Content Manager
    Editor
    (KEVRIC) XML Oracle
    DBs
    TDE
    TDE
    Content XML
    Editor
    (Apelon)
    TDE Editor Screenshot
    NCI Thesaurus
    ► Gene Roles

    Defining Roles:
    • Gene_Has_Function
    • Gene_In_Chromosomal_Location

    Non-defining Roles:
    • Gene_Associated_With_Disease
    • Gene_Found_In_Organism
    • Gene_is_Biomarker_of
    • Gene_is_Biomarker_Type
    NCI Thesaurus
    ► Protein Roles

    Defining Roles:
    • Protein_Encoded_by_Gene
    • Protein_Has_Biochemical_Function
    • Protein_Plays_Role_In_Biological_Process

    Non-defining Roles:
    • Protein_Expressed_In_Tissue
    • Protein_Has_Associated_Anatomy
    • Protein_Has_Chemical_Classification
    • Protein_Has_Malfunction_Type
    • Protein_Has_Organism_Source
    • Protein_Has_Structural_Domain_Or_Motif
    • Protein_is_Biomarker_of
    • Protein_is_Biomarker_Type
    • Protein_is_Physical_Part_of
    • Protein_Malfunction_Associated_With_Disease

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