National Cancer Institute Enterprise Vocabulary Services & Semantic Interoperability

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National Cancer Institute Enterprise Vocabulary Services & Semantic Interoperability. May 25, 2010 Margaret Haber, Enterprise Vocabulary Services Larry Wright, Enterprise Vocabulary Services. Interoperability. Interoperability:
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National Cancer Institute Enterprise Vocabulary Services & Semantic Interoperability May 25, 2010 Margaret Haber, Enterprise Vocabulary Services Larry Wright, Enterprise Vocabulary Services Interoperability
  • Interoperability: The ability of a system...to use the parts or equipment of another system Source: Merriam-Webster web site
  • Interoperability: The ability of two or more systems or components to exchangeinformation and to use the information that has been exchanged. Source: IEEE Standard Computer Dictionary, 1990
  • Syntacticinteroperability Semanticinteroperability NCI Designfor Interoperability
  • Common API Integration: Part of the syntactic component of interoperability.
  • Vocabularies/Terminologies/Ontologies: Provides semantic interoperability, used to record information in and about systems and data.
  • Data Elements: or Metadata, provides a description of the meaning of recorded information in addition to its value. For example “Patient Temperature” would describe both a meaning and what constitutes a valid value for patient temperature (such as a number range measured in degrees Fahrenheit).
  • Information Models: Describe the structure of the data maintained in a system, such as a grid system.
  • Extending Interoperability Beyond the Enterprise
  • cancer Biomedical Informatics Grid (caBIG)
  • Shared infrastructure, applications and data
  • Permits cancer research community to focus on innovation
  • Shared vocabulary, data elements, data models enable information exchange
  • Interoperable applications developed to common standard
  • Making research data available for mining and integration
  • Several new ARRA initiatives leverage this infrastructure to extend interoperability principles to the broader healthcare community
  • Semantic Infrastructure Futures
  • Evolution, notRevolution
  • Still gathering requirements and defining approaches
  • Aim: support interoperability with a broader range of partners
  • Services-Oriented Architecture (SOA) approach.
  • Technology-independent specifications that enable others to build interoperable components.
  • Design, develop and deploy software components defined as business capabilities rather than monolithic applications.
  • No Controlled Terminology?No Interoperability
  • Systems cannot exchange or use information if they use incompatible codes or tokens to signify meaning
  • Terminology services provide those tokens and codes
  • Proper use of them assures consistent meaning across and among enterprises
  • NCI Enterprise Vocabulary Services (NCIEVS)Goals
  • Mission: The development of services and resources that address the needs of the National Cancer Institute (NCI) for controlled terminology, and to facilitate the standardization of terminology and information systems across the Institute and the larger biomedical community. Goal – Integration by Meaning
  • Clinical, translational, and basic research terminology have overlapping but specialized needs, therefore EVS assists to:
  • Integrate different conceptual frameworks
  • Create terminological and taxonomic conventions across diverse systems
  • Background
  • EVS began in 1996 as an applied research project; Production started in 1999 with the publication of the NCI Metathesaurus (NCIm). NCI Thesaurus (NCIt) followed in 2000, becoming the primary terminology for NCI coding including for metadata and data model semantics.
  • NCI EVS also provides freely available tools for terminology/ontology development and publication. NCIt and NCIm are now joined by several other terminologies published or hosted by NCI.
  • NCI EVS provides the semantic foundation for sharing and re-use of data, services, applications, and other resources at NCI . The caBIG community, other NIH institutes, and many collaborating organizations such as FDA and CDISC also depend on the EVS for terminology needs.
  • High Value Use Cases
  • EVS Used Directly for Drug and Clinical Information Integration
  • Agents, Clinical Trials and Adverse Events
  • CTEP and DCP clinical trials
  • PDQ Cancer Clinical Trials Registry & NCI Drug Dictionary
  • Federal Medication Terminologies (FMT)
  • FDA Structured Product Labeling
  • NCPDP (SCRIPT Standard for e-prescribing)
  • caBIG infrastructure and application use cases
  • Infrastructure providing semantic interoperability
  • caTIES/caTissueCore/caMOD/caNanolab
  • FDA/NCI/CDISC/RCRIM – harmonization/ development - standards
  • EVS Resources
  • NCI Thesaurus (NCIt) – an ontology-like terminology
  • NCI Metathesaurus (NCIm) – mapped vocabularies
  • NCI Term Browser - NCI and external vocabularies maintained and served: MedDRA, HL7, NDF-RT, LOINC, GO, Zebrafish, etc.
  • Terminology development, licensing & publication; software and server development & licensing; FTP sites & API development
  • NCI Thesaurus (NCIt)
  • Standard reference terminology/ontology for clinical, biomedical and scientific knowledge used by NCI, caBIG; underpins caCORE/caBIG/caGRID semantics
  • A Federal Standard Terminology
  • Built using description logics
  • Public domain, open content license
  • Used by many public and private partners, nationally and internationally
  • NCI Thesaurus (2)
  • Broad coverage of cancer and other clinical and researchdomains including prevention and treatment trials:
  • Neoplastic and other Diseases
  • Findings and Abnormalities
  • Anatomy, Tissues, Subcellular Structures
  • Agents, Drugs, Chemicals
  • Genes, Gene Products, Biological Processes
  • Animal Models – Mouse, other
  • Research techniques and management, apparatus, clinical and lab, radiology, imagery
  • NCI Thesaurus (3)
  • Published Monthly
  • 89,000 “Concepts” hierarchically organized into domains
  • Concept History
  • Available on-line and by download (OWL, LexGrid XML, flat files)
  • Accessible through the LexEVS API and caGrid terminology node
  • What ‘s in NCIt ? Events & Entities  +89,000 concepts Hierarchical arrangement Preferred Names, Synonyms & Definitions Concept relationships & properties Unique, permanent identifier codes Semantic Diversity eukaryote plants fungus virus bacterium archaeon animal mammal vertebrates amphibian bird fish reptile human medical device embryonic structure laboratory tests anatomical structure anatomical abnormality bodyparts &organs congenital abnormality language clinical drug regulation or law tissue sign or symptoms nucleic acid gene findings geographic area research activity cell s genetic function family group molecular sequence disease or syndrome neoplastic process educational activity Mental process natural phenomenon event experimental model of disease therapeutic or preventative procedure organization behavior health care activity activity laboratory procedure quantitative concept element,ion,isotope Terminology Subsets FDA-NCIMemorandum of Understanding
  • Significance of MOU
  • Avoids expenditure at FDA to replicate existing, available resources at NCI
  • Increased return on investment for NIH/NCI
  • Leverages multiple efforts
  • FDA collaboration with NIH/NCI results in improved trials, drug and related regulatory terminology for cancer and the broader clinical trials community
  • Complementary to the CDISC/NCI collaborations on terminology requirements for CDISC models such as the Study Data Tabulation Model (SDTM)
  • Scope of MOU (2)
  • Under the MOU:
  • NCI leverages terminology-related resources to address FDA needs
  • FDA and NCI coordinate regarding relevant terminology standards and standards development efforts such as those of the HL7 RCRIM technical committee
  • FDA and NCI seek to identify opportunities to employ consistent terminology and terminology practices, for example in support of FHA/ONC initiatives and goals and such as eGOV
  • NCI-FDA Terminology Collaboration
  • 2002- partnership and agreements in several terminology areas.
  • Structured Product Labeling (SPL)
  • Unique Ingredient Identifier (UNII)
  • Regulated Product Submission (RPS)
  • Individual Case Safety Report (ICSR)
  • Center for Devices and Radiological Health (CDRH)
  • FDA PDUFA IV IT Plan: “For terminology standards, the FDA partners with the National Cancer Institute Enterprise Vocabulary Services (EVS). The NCI EVS hosts the FDA terminologies and makes them freely available to the public.”
  • FDA terminology resources are available on the NCI portal website: http://www.cancer.gov/cancertopics/terminologyresources/FDA
  • Example:Structured Product Label FDA Announces the Use of New Electronic Drug Labels to Help Better Inform the Public and Improve Patient Safety In a continuing effort to use modern information technology to help inform the public and health care providers and to further improve patient safety, the Food and Drug Administration (FDA) today began requiring drug manufacturers to submit prescription drug label information to FDA in a new electronic format. This electronic format will allow healthcare providers and the general public to more easily access the product information found in the FDA-approved package inserts ("labels") for all approved medicines in the United States. Pharmaceutical Companies must provide information for electronic labels to FDA using controlled terminology FDA Structured Product Labels
  • FDA needs rapid turnaround terminology for the content of labels but doesn’t want to be in the terminology business.
  • FDA requests terminology in various areas related to product labels, NCI editors work with them, integrate them into NCI Thesaurus, and tag them with subset properties. FDA publishes the lists on their website, and provides links to NCI Thesaurus.
  • Examples
  • Route of Administration
  • Unit of Presentation (Potency)
  • Dosage Form
  • Package Type
  • FDA SPL Web page: http://www.fda.gov/oc/datacouncil/spl.html
  • SPL in NCIt
  • For solid oral dosage form appearance
  • SPL Color – BLUE C48333
  • SPL Shape - ROUND C48348
  • For drug interactions
  • Contributing Factor - General - FOOD OR FOOD PRODUCT C1949
  • Type of Drug Interaction Consequence - PHARMACOKINETIC EFFECT C54386
  • Pharmacokinetic Effect Consequence - INCREASED DRUG LEVEL C54355
  • Limitation of Use – CONTRAINDICATION C50646
  • Sex – FEMALE C16576
  • Race - ASIAN C41259
  • Other
  • SPL DEA Schedule - CII C48675
  • Concept details from Browser Concept details from Browser (2) CDISC Terminology
  • Clinical Data Interchange Standards Consortium (CDISC) is an international, non-profit organization that develops and supports global data standards for medical research.
  • FDA points to CDISC as key provider of clinical & preclinical standards: “The foundation for the standardized clinical content is the Clinical Data Interchange Standards Consortium (CDISC) Study Data Tabulation Model (SDTM).” FDA PDUFA IV IT Plan
  • EVS is partnered with CDISC to support and publish SDTM and other CDISC terminology including SEND (animal studies), Glossary, CDASH
  • CDISC terminology also published on NCI portal website: http://www.cancer.gov/cancertopics/terminologyresources/CDISC
  • Federal Register / Volume 71, No. 237 /Monday, December 11, 2006 The Food and Drug Administration is proposing to amend the regulations governing the format in which clinical study data and bioequivalence data are required to be submitted for new drug applications (NDAs), biological license applications (BLAs), and abbreviated new drug applications (ANDAs). The proposal would revise our regulations to require that data submitted for NDAs, BLAs, and ANDAs, and their supplements and amendments be provided in an electronic format that FDA can process, review, and archive. The proposal would also require the use of standardized data structure, terminology, and code sets contained in current FDA guidance (the Study Data Tabulation Model (SDTM) developed by the Clinical Data Interchange Standards Consortium) to allow for more efficient and comprehensive data review. NCIthesaurushttp://ncit.nci.nih.gov Search Box Choices, choices... Version information Term search Search on term - mg - 5 results Code Search Search on Code - 1 result 6 sources Concept Code:A unique, permanent identifier mammal? spy? chemistry measure-ment? chocolate sauce? skin lesion? Concept Code Terms Term Source Additional Source Data Concept Code:A unique, permanent identifier (2) Concept Code Terms Additional Source Data Term Source Unambiguous Meaning Semantic Type:Quantitative Concept Code: C42539 Definition: A unit of amount of substance, one of the seven base units of the International System of Units (Systeme International d'Unites, SI). It is the amount of substance that contains as many elementary units as there are atoms in 0.012 kg of carbon-12. When the mole is used, the elementary entities must be specified and may be atoms, molecules, ions, electrons, other particles, or specified groups of such particles. Semantic Type: Mammal Code: C14876 Definition: A small, furry creature of the family Talpidae that lives underground and feeds on small invertebrates. The mole has tiny covered eyes that are believed to be able to distinguish night from day, and not much else. Semantic Type: Neoplastic Process Code: C7570 Definition: A neoplasm composed of melanocytes that usually appears as a dark spot on the skin. mole Semantic Type: Occupation or Discipline Definition: [No use case for this term yet, but welcome CIA inquiries]. Semantic Type: Food or Food Product Definition: [Nouse case for this term yet, but welcome inquiries accompanied by samples]. Concept Relationships & Associations Subset Associations: How concepts are "bundled" NCIt: Example Concept (1 of 2) Preferred Name: Gastric Mucosa-Associated Lymphoid Tissue Lymphoma Code:C5266 Semantic Type: Neoplastic Process Parent Concepts: Extranodal Marginal Zone B-Cell Lymphoma of Mucosa-Associated Lymphoid Tissue Gastric Non-Hodgkin's Lymphoma Synonyms & Gastric MALT Lymphoma Abbreviations: Gastric MALToma (subset) MALT Lymphoma of the Stomach MALToma of the Stomach Primary Gastric MALT Lymphoma Primary Gastric B-Cell MALT Lymphoma Primary MALT Lymphoma of the Stomach Definition: A low grade, indolent B-cell lymphoma, usually associated with Helicobacter Pylori infection. Morphologically it is characterized by a dense mucosal atypical lymphocytic (centrocyte-like cell) infiltrate with often prominent lymphoepithelial lesions and plasmacytic differentiation. Approximately 40% of gastric MALT lymphomas carry the t(11;18)(q21;q21). Such cases are resistant to Helicobacter Pylori therapy. NCIt: Role Relationships (Gastric MALT Lymphoma) Role Relationships (subset) for Gastric Mucosa-Associated Lymphoid Tissue Lymphoma: Molecular abnormalities: Disease_May_Have_Cytogenetic_Abnormality: Trisomy 3 Disease_May_Have_Cytogenetic_Abnormality: Trisomy 18 Role group 1: Disease_May_Have_Cytogenetic_Abnormality: t(11;18)(q21;q21) Disease_May_Have_Molecular_Abnormality: AP12-MLT Fusion Protein Expression Histogenesis: Disease_Has_Normal_Cell_Origin: Post-Germinal Center Marginal Zone B-Lymphocyte Pathology: Disease_Has_Abnormal_Cell: Centrocyte-Like Cell Disease_May_Have_Abnormal_Cell: Neoplastic Monocytoid B-Lymphocyte Disease_May_Have_Abnormal_Cell: Neoplastic Plasma Cell Disease_May_Have_Finding: Lymphoepithelial Lesion Anatomy: Disease_Has_Primary_Anatomic_Site: Stomach Disease_Has_Normal_Tissue_Origin: Gut Associated Lymphoid Tissue Clinical information: Disease_Has_Finding: Primary Lesion Disease_May_Have_Finding: Indolent Clinical Course Disease_May_Have_Associated_Disease: Hepatitis C NCIt: 200,000 Role Relationships NCI Metathesaurus
  • Purpose: Integrating biomedical and scientific data from some 76 national and international sources into one database.
  • Approximately 3.6 million terms integrated into 1.4 million concepts
  • Provides a mapped overlap and partial inter-relation of current versions of NCI and partner required vocabularies, for ex. the ICD’s, MedDRA, SNOMED, MeSH (NLM Medical Subject Headings), HCPCS (procedures), LOINC (lab values), drug terminologies (VA NDF-RT, AOD, RxNORM, Multum, NCI Thesaurus drugs, etc.)
  • Used as online dictionary and thesaurus, for mapping and document indexing.
  • Minor releases monthly, major releases at least twice a year.
  • NCI Metathesaurushttps://ncim.nci.nih.gov 3,600,000 terms 76 Sources 1,400,000 concepts NCImetathesaurus Choose your source 11 Sources NCITerm Browserhttp://nciterms.nci.nih.gov Sources EVS Products & Services Are Open
  • NCI Thesaurus is Open Content http://evs.nci.nih.gov/terminologies
  • NCI Metathesaurus is Mostly Open Source (See Each Source’s License)http://ncim.nci.nih.gov/ncimbrowser/pages/source_help_info.jsf
  • NCI EVS Servers Are Freely Accessible
  • On the Web: http://nciterms.nci.nih.gov http://ncimeta.nci.nih.gov
  • Via API: https://cabig.nci.nih.gov/tools/LexEVS_API
  • On caGrid: https://cabig.nci.nih.gov/workspaces/Architecture/caGrid
  • All Software Developed by NCI EVS is Public Open Source and Free for the Asking: http://ncicb.nci.nih.gov/download/#ETools
  • Methods of Data Retrieval
  • NCI ftp site: http://evs.nci.nih.gov/ftp1/FDA
  • NCI partner web sites (CDISC, FDA, etc.)
  • Request a report from NCI staff: http://ncit.nci.nih.gov/ncitbrowser/pages/contact_us
  • NCIt Browser by subset :
  • http://ncit.nci.nih.gov/pages/subset.jsf
  • Cancer.gov:
  • http://www.cancer.gov/cancertopics/terminologyresources
  • NCIt ftp sitehttp://evs.nci.nih.gov/ftp1 You can download the entire NCIt in various formats Shared Content Standards NICHD NHLBI NINDS NLM NIH “Roadmap” caBIG UNIIs ICSR SPL RPS CDRH Admin Procedures Other SDTM CDASH SEND ADaM Glossary SHARE Therapeutic Area Standards Consolidated Content Services FedMed SNOMED CT® UCUM Contact Information Lawrence W Wright Acting Director Semantic Infrastructure NCI [email protected] Margaret Haber Associate Director Enterprise Vocabulary Services NCI [email protected]
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