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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.

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The NCI Thesaurus


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    1. 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

    2. NCI Thesaurus ► Research Orientation Disease Diagnosis Proteins Genes Prognosis Creates a knowledge base

    3. 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

    4. 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”

    5. NCI Thesaurus ► Properties • ► Specific information about a concept • Properties are not inherited • Stored as strings

    6. TDE NCI Thesaurus Development • Asynchronous, distributed editing: Assignments or “Free-range” editing • Conflict detection & Database consolidation ContentEditor(NCI) WorkManager XML TDE OracleDBs ContentEditor(KEVRIC) XML TDE ContentEditor(Apelon) XML

    7. TDE Editor Screenshot

    8. 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

    9. 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