The NCI Thesaurus:

A Controlled Vocabulary

Of NCI Functions

Gilberto FragosoCenter for BioinformaticsNational Cancer Institute

National Institutes of Health (U.S.)

Overview

• Center for Bioinformatics (NCICB)• Mission• Supported NCI Activities • http://ncicb.nci.nih.gov

• NCI Thesaurus

• Challenges & Issues

• Support NCI Bioinformatics/Research Activities Cancer Genome Annotation Project (CGAP) Clinical Trials Cancer Molecular Analysis Project (CMAP) Molecular Analysis of Cancer (Director's Challenge) Mouse Models of Human Cancer Consortium (MMHCC)

• Cancer Core Infrastructure (caCORE) Cancer Data Standards Repository (caDSR) Cancer Bioinformatics Infrastructure Objects (caBIO) Enterprise Vocabulary Services (EVS)

NCI Center for Bioinformatics

NCI Center for BioinformaticscaBIO

• Model of cancer research domain• Sample caBIO classes

Gene Protein Sequence SNP Chromosome Clone Library

Taxon Agent Pathway Tissue Organ Disease ClinicalTrialProtocol

• Applicable to other biomedical domains• Released as part of caCORE version 1• http://ncicb.nci.nih.gov, follow Infrastructure

• Collection of services and resources that address NCI's needs for controlled vocabulary

• Main vocabulary products• NCI Thesaurus• NCI Metathesaurus• http://ncimeta.nci.nih.gov

• Specialty vocabularies• MMHCC (Mouse Models of Human Cancer Cons.)• CTRM (Core Terminology Reference Model)

NCI Center for BioinformaticsEnterprise Vocabulary Services

NCI Thesaurus

• Reference biomedical vocabulary for the NCI

• Contains all the codes, keywords, and special purpose vocabulary used in the Institute

• Features• NCI-only vocabulary sources• No licensing restrictions

• Description logic-based• Consistency checks• Auto-classification

• Primary purpose is to support coding and retrieval applications

NCI Thesaurus

• Freely available Online access via browser application and API• API extensions provided by caBIO

Flat file format• Terminology and hierarchies only• FTP site will be advertised in our Web site

DAML+OIL (Future)

Concepts

IdentifiersName, Code, ID

Kind (Group)Defined / Primitive tag

Parent ConceptRoles

Properties

Elements of the NCI Thesaurus

Concepts

IdentifiersName, Code, ID

Kind (Group)Defined / Primitive tag

Parent ConceptRoles

Properties

Properties

Preferred NameSynonymsCUI (UMLS)Semantic TypeDefinitionExternal DB ID

OmimLocusIDGenBankSwissProt

CommentsEditor’s NotesDesign Notes

Elements of the NCI Thesaurus

Anatomy

Technique

Protein

PropertiesOr Attributes

Organism

OccupationOr Discipline

NCI

Gene

FindingsAnd Disorders

Equipment

Diagnostic AndPrognostic Factors

Clinical Or ResearchActivityChemicals

And Drugs

Cancer Science

Biological Process

"Kinds" in the NCI Thesaurus

Top Level Concepts in Various Kinds

NCI Kind

Business RulesConceptual EntitiesFundingPatient or Public EducationSocial ConceptsTraining and Education

Anatomy Kind

Anatomic Structures and Systems

Anatomic SitesAnatomic StructureBody Part, Organ, or TissueBody RegionCell StructureEmbryonic StructuresExtracellular StructureMacromolecular StructureMiscellaneous Anatomy TermsOrgan Systems

Top Level Concepts in Various Kinds

Chemicals And Drugs Kind

Drugs and Chemicals

Chemical ModifiersDrug of AbuseFoods and Food ProductsImmunologicsIndustrial ProductsPharmacologic SubstancesPhysiology - Regulatory FactorsReagents

Inorganic ChemicalsOrganic Chemicals

Drugs and Chemicals, Structural Classification

Drugs and Chemicals, Functional Classification

Gene Kind

Genes

Oncogene Oncogene, G-Protein Oncogene, Growth Factor Oncogene, Transcription FactorsProto-OncogeneSusceptibility / Resistance GeneTumor Promoter Induced GeneTumor Supressor Gene

Cancer Gene

Top Level Concepts in Various Kinds

Candidate Disease GeneReporter Gene

Top Level Concepts in Various Kinds

Findings And Disorders Kind

Diseases, Disorders, and Findings

Familial Neoplastic SyndromeLymphoproliferative DisorderMolecular DiseaseNeoplasm Neoplasm by Morphology Neoplasm by Site Neoplasm by Special Category Neoplasm by Disease NECNon-Neoplastic Disease, Syndrome, or ConditionPrecancerous Condition

Findings

Diseases and Disorders

Top Level Concepts in Various Kinds

Biological Process Kind

Biological Processes

Cell ProcessesIntercellular ProcessesMetabolic ProcessesOrganismal ProcessesPathologic ProcessesPhysiologic ProcessesPopulation ProcessesViral Functions and Activities

"Roles" in the NCI Thesaurus

• Semantic relations between concepts are expressed via roles

• We define a small number of roles for the various kinds

Support classification Support specific use cases Reproducible usage by domain experts

• A concept is tagged as "defined" when a specific set of roles is asserted

Anatomy

Roles in the Anatomy Kind

Anatomic Structure is Physical Part of

Anatomic Structure Has Location

Exp Organism Anatomic Structure is Physical Part of

Anatomy

PropertiesOr Attributes

FindingsAnd Disorders

Disease Roles

Disease has Associated Anatomy

Disease has Associated Cell Type

Disease Metastatic to Site

Disease has Modifier

Exp Org Disease has Associated Exp Org Anatomy

Anatomy

Protein

Organism

FindingsAnd Disorders

ChemicalsAnd Drugs

Biological Process

Roles in the Chemicals & Drugs Kind

CD has Target Anatomy

CD FDA Approved for Disease

CD has Target Organism

CD has Source

CD has Target Protein

CD Plays Role in Biological Process

CD is Part of CD

CD has Biochemical Class or Structure

Anatomy

Organism

Gene

FindingsAnd Disorders

Diagnostic AndPrognostic Factors

Biological Process

Gene in Chromosomal Location

Gene Has Function

Gene Found in OrganismGene Associated With

Disease

Gene is Biomarker Type

Roles in the Gene Kind

Anatomy

Protein

OrganismGene

FindingsAnd Disorders

Diagnostic AndPrognostic Factors

Biological Process

Protein Encoded by Gene

Protein Expressed in Tissue

Protein Has Biochemical Function

Protein Has Organism Source

Protein Has Associated Anatomy

Protein Has Chemical Classification

Protein Malfunction Associated with Disease

Protein Has Structural Domain or Motif

Protein Plays Role in Biological Process

Protein is Biomarker Type

Protein is Physical Part Of

Roles in the Protein Kind

Issues

• Increasing number of non-cancer genes

• Hierarchies for multiple organisms Unified, or one subtype per organism?

• Tangled hierarchies

Acknowledgements

NCICB

Frank HartelSherri de CoronadoJames OberthalerGilberto Fragoso

Peter CovitzKen Buetow

Office of Communications

Larry WrightMargaret Haber

Contractors

Kevric, IncApelon, Inc