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The NCI Thesaurus: A Controlled Vocabulary Of NCI Functions. Gilberto Fragoso Center for Bioinformatics National Cancer Institute National Institutes of Health (U.S.). Overview. Center for Bioinformatics (NCICB) Mission Supported NCI Activities http://ncicb.nci.nih.gov - PowerPoint PPT Presentation
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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
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