Presentation on theme: "Enterprise Vocabulary Services National Cancer Institute"— Presentation transcript:
1Enterprise Vocabulary Services National Cancer Institute HL7 RCRIM Vocabulary Update: Standards Available or in Development Through NCI Enterprise Vocabulary Services (EVS)3/27/2017Margaret HaberCo-DirectorEnterprise Vocabulary ServicesNational Cancer Institute
2NCI EVS: Goals & Services Meet the controlled terminology needs of NCI and its partners.Promote semantic integration of clinical, translational and basic research, administrative, and public information systems.ServicesControlled TerminologiesNCI Thesaurus: logic-based, rapid-response reference terminology.NCI Metathesaurus: cross-link meanings from 60+ terminologies.Standalone terminologies: MedDRA, LOINC, SNOMED, GO, etc.Partnerships & ToolsDevelop term sets & standards: FedMed, CDISC, HL7, CHI/FHA,…Sharable tools: Share ours, help develop open-source tools.
3NCI Thesaurus (NCIt) Reference terminology for NCI and its partners. Semantic reference for caCORE/caBIG metadata and models.A Federal standard terminology used in NCI, NIH, other systems.Richly structured content for people and computers>58,000 concepts with >200,000 synonyms and codes.>37,000 text definitions.>200,000 “role” relationships semantically connect concepts.Description logic classifier uses roles to check concept hierarchies.Directly incorporates terms and codes from closely integrated partners, e.g., FDA, CDISC, caDSR.
4NCI Thesaurus (2)Broad coverage of cancer and other clinical and research related subject areas.Neoplastic and other diseases, findings and abnormalities.Anatomy, tissues, subcellular structures.Agents, drugs, chemicals.Genes, gene products, biological processes.Clinical & research procedures, tools, trials, management, etc.Animal models – mouse, other.Rapid updates & freely available.Published monthly, with pre-release available during test cycle.Available via Web browsers, program APIs, downloadable files in OWL, Ontylog XML, and flat file formats.Public domain, open content license.
8Mapping Terminologies: NCI Metathesaurus Access to and cross-links between 60+ terminologies.1,200,000 concepts, 2,700,000 terms and phrases, with definitions.Extensive synonymy, e.g. 7,000 neoplasm concepts provide over 40,000 synonym terms from many sources.Based on NLM’s UMLS Metathesaurus, dropping less useful sources and adding special purpose terminologies.Integrates access to key terminologies: NCI Thesaurus, the ICD’s, MedDRA, SNOMED, MeSH (NLM Medical Subject Headings), HCPCS (procedures), LOINC (lab values), drugs (VA NDF, AOD, RxNORM, Multum, etc.), science (GO, HUGO, OMIM, JAX, KEGG, NCBI), etc.Frequent updates, freely availablePublish minor releases monthly, major releases 2-3 times a year.Mostly open content, with some source licence restrictions.Available via public browsers, APIs, and flat file formats.
10NCI EVS: Semantic Base of caCORE Bioinformatics Infrastructure & caBIG cancer Bioinformatics Infrastructure Objects (caBIO)UML Object ModelsApplications & APIscancer Data Standards Repository (caDSR)ISO metadata repositoryCommon Data Elements (CDEs)for forms etc.Enterprise Vocabulary Services (EVS)Core semanticsAPIsBrowsersbiomedical objectscommon data elementscontrolled vocabulary
11NCI EVS: Extending Interoperability Developing collaborations beyond NCI.Federal: FDA, VA, CDC, other NIH Institutes.Major standards organizations: HL7, CDISC, W3C.Cancer Centers and Cooperative Groups: caBIG, caGRID.Research collaborators such as the Microarray Gene Expression Data Society (MGED).Some areas of collaboration.FDA (drugs, devices, and clinical trials).VA (drugs, clinical trials semantics, terminology operations).CDC (cancer incidence and prevention, terminology operations).Cancer Centers & caBIG (clinical trials, experimental organisms, micro-nutrients, open terminology servers).CDISC/HL7 RCRIM (clinical research and health care data standards).
12Some Current Projects and Collaborations CDISC terminology hosting, production and publication: SDTM and beyondOther NIH IC’s such as NHLBI and NIH “Roadmap” grant projectsFDA required and regulatory terminology includingSPL (Structured Product Label)ICSR (Individual Case Safety Report)CDRH device and safety related terminology such as for MedWatch reportingUNII’s (> 1,500 Unique Ingredient Identifiers)Regulated Product Submission terminology in early development
13FDA Standards Hosted in NCIt (NCI Thesaurus) For SPL:Limitation of UsePharmacokinetic Effect Consequences(Product) ColorDEA ScheduleDrug Route of AdministrationMedical Product Intent of UsePackage TypePharmaceutical Dosage Form(Product) Potency(Product) ShapeType of Drug Interaction Consequence
14FDA Standards Hosted in NCIt (2) For the ICSR:Adverse Event OutcomeLocation of Event OccurrenceOccupationOperator of Medical DeviceDevice UsageReport SourceType of EventType of Follow-UpReason for Non-EvaluationType of ManufacturerType of Remedial ActionType of Report
15FDA Standards Hosted in NCIt (3) Terminology for the Centers for Device and Radiological Health (CDRH): transformation of current CDRH terminology lists of codes into targeted taxonomies, in order to create a foundation for asserted knowledge on medical device associated events includingPatient ConditionsMedical Device Components or AccessoriesMedical Device Failures or MalfunctionsRegulated Product Submission Terminology for use by CDER, CBER, CDRH in early development
16FDA Subsets in NCIt: FDA_Subsets: Patient_Problem_Codes_FDA_CDRH Medical_Device_Component_Or_Accessory_Terminology_FDA _CDRHMedical_Device_Problem_Codes_FDA_CDRHLimitation_Of_Use_Structured_Product_Labeling_TerminologyPharmacokinetic_Effect_Consequences_Structured_Product_Labeling_TerminologyStructured_Product_Labeling_Color_TerminologyStructured_Product_Labeling_DEA_Schedule_TerminologyStructured_Product_Labeling_Drug_Route_of_Administration_TerminologyStructured_Product_Labeling_Medical_Product_Intent_Of_Use_TerminologyStructured_Product_Labeling_Package_Type_TerminologyStructured_Product_Labeling_Pharmaceutical_Dosage_Form_TerminologyStructured_Product_Labeling_Potency_TerminologyStructured_Product_Labeling_ShapeStructured_Product_Labeling_TerminologyStructured_Product_Labeling_Type_Of_Drug_Interaction_Consequence_Terminology
17FDA subsets in NCIt (2)Type_of_Event_ICSR_TerminologyType_Of_FollowUp_ICSR_TerminologyType_Of_Manufacturer_ICSR_TerminologyType_Of_Remedial_Action_ICSR_TerminologyType_Of_Report_ICSR_TerminologyType_of_Reportable_Event_ICSR_TerminologyType_Of_Reporter_ICSR_TerminologyAdverse_Event_Outcome_ICSR_TerminologyReason_For_Non-Evaluation_ICSR_TerminologyReport_Source_ICSR_TerminologyOccupation_ICSR_TerminologyOperator_of_Medical_Device_ICSR_TerminologyLocation_Of_Event_Occurrence_ICSR_TerminologyDevice_Usage_ICSR_TerminologyIndividual_Case_Safety_Report_TerminologyCurrent total of more than 5,000 standardized electronic FDA tagged concepts in NCI Thesaurus representing well over 10,000 FDA terms and codes.
18Using the NCIt Report Writer The Report writer is a desktop application that retrieves concept data from the production version of the NCIt.The application file, named ReportWriter.zip, is available from the anonymous FTP site: ftp://ftp1.nci.nih.gov/pub/cacore/EVS/fda/The application will retrieve all concepts in any Subset such as CDISCConcepts in every Subset will be identified by the Concept_in_Subset associationA complete list of the available Subsets from the terminology server will be retrievedFrom this list the user will choose the desired SubsetThe application will retrieve all the concepts in the selected Subset and output them as a flat file or XML file
19NCI EVS Partnerships: CDISC Clinical Data Interchange Standards Consortium (CDISC)1997- Global organization for clinical data standards & exchange.Creates open, platform-independent, global standards with participation of private and public organizations.2004- CDISC Controlled Terminology Team began defining terminology standards underlying Study Data Tabulation Model (SDTM).CDISC Terminology Team a close NCI EVS partner.Joint effort to specify and develop broadly based clinical trials standard terminology, based on CDISC models.NCI Thesaurus adopted as CDISC terminology development and publication environment.CDISC is also developing metadata in the NCI Data Standards Repository, using EVS terminology as foundation.Open CDISC standards, developed in collaboration with FDA, NIH, HL7 and others, can provide the basis for a controlled terminology set shared across the clinical trials community.
20SDTM Package 1 Terminology 1. Action Taken with Study Treatment2. AE Severity / Intensity3. Age Span4. Age Units5. Country6. Dictionary Name7. Domain Abbreviation8. Ethnicity9. Formulation (Dose)10. Inclusion/Exclusion Category11. Non -Completion Reason12. Not Done13. No / Yes Responses14. Outcome of Event15. Route of Administration16. Sex17. Sex of Participants18. Size19. System Organ Class20. Relation to Reference Period21. Trial Blinding Schema22. Trial Type of Control23. Trial Diagnosis Group24. Trial Indication Type25. Toxicity Grade26. Trial Phase27. Trial Summary Parameters28. Type of Trial29. Vital Signs Tests30. Vital Signs Units
21SDTM Package 2 Terminology 8 additional SDTM domains including Findings – EG, PE, VS, SC; Interventions – CM, EX, SU; and Events – AE’sECG Test ResultsPhysical ExaminationVital SignsSubject CharacteristicsConcomitant MedicationsExposuresSubstance UseAdverse Events
22NCI EVS: Open Products & Services EVS Web site:Web terminology servers:NCI Thesaurus & Standalone:NCI Metathesaurus:API:Software developed by EVS is free & open source:NCI Thesaurus is open content: ftp://ftp1.nci.nih.gov/pub/cacore/EVS/ThesaurusTermsofUse.htmNCI Metathesaurus is mostly open content: See Each Source’s License at
23Contact: Margaret W. Haber Co-Director NCI Enterprise Vocabulary Services NCI Office of the Director