The NCI Thesaurus Description Logic representation of NCI

The NCI Thesaurus ►Description Logic representation of NCI vocabulary • xml based • is_a hierarchy (“Super. Concept”) • Kinds: disjoint groups of concepts • Roles: relationships between concepts • Properties: information about a concept

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

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) Content Editor (KEVRIC) Content Editor (Apelon) XML XML Work Manager Oracle DBs

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