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The Unified Medical Language System What Is It and How to Use It? Korea Advanced Institute of Science and Technology December 4, 2007 The Unified Medical Language System What is it and how to use it? Olivier Bodenreider, MD, PhD Lister Hill National Center for Biomedical Communications Bethesda, Maryland - USA OutlineOutline PartPart I:I: WhatWhat isis thethe UMLS?UMLS? z Introduction z Overview through an example z The three UMLS Knowledge Sources UMLS Metathesaurus UMLS Semantic Network SPECIALIST Lexicon and lexical tools PartPart II:II: HowHow toto useuse thethe UMLS?UMLS? z A UMLS-based algorithm 2 Part I What is the UMLS? (1) Introduction WhatWhat doesdoes UMLSUMLS standstand for?for? UUnifiednified MMedicaledical LLanguageanguage SSystemystem UMLS® Unified Medical Language System® UMLS Metathesaurus® 4 MotivationMotivation StartedStarted inin 19861986 NationalNational LibraryLibrary ofof MedicineMedicine ““LongLong--termterm R&DR&D projectproject”” (Integrated Academic ComplementaryComplementary toto IAIMSIAIMS Information Management Systems) «[…] the UMLS project is an effort to overcome two significant barriers to effective retrieval of machine-readable information. • The first is the variety of ways the same concepts are expressed in different machine-readable sources and by different people. • The second is the distribution of useful information among many disparate databases and systems.» 5 TheThe UMLSUMLS inin practicepractice DatabaseDatabase z Series of relational files InterfacesInterfaces z Web interface: Knowledge Source Server (UMLSKS) z Application programming interfaces (Java and XML-based) ApplicationsApplications z lvg (lexical programs) z MetamorphoSys (installation and customization) z RRF browser (browsing subsets) The UMLS is not an end-user application 6 Part I What is the UMLS? (2) Overview through an example AddisonAddison’’ss diseasedisease Addison's disease is a rare endocrine disorder Addison's disease occurs when the adrenal glands do not produce enough of the hormone cortisol For this reason, the disease is sometimes called chronic adrenal insufficiency, or hypocortisolism 8 AdrenalAdrenal insufficiencyinsufficiency ClinicalClinical variantsvariants Primary / Secondary z Primary: lesion of the adrenal glands themselves ACTH z Secondary: inadequate secretion of ACTH by the pituitary gland Acute / Chronic Isolated / Polyendocrine deficiency syndrome 9 AddisonAddison’’ss disease:disease: SymptomsSymptoms FatigueFatigue WeaknessWeakness LowLow bloodblood pressurepressure PigmentationPigmentation ofof thethe skinskin (exposed(exposed andand nonnon-- exposedexposed partsparts ofof thethe body)body) …… 10 ADAD inin medicalmedical vocabulariesvocabularies Synonyms:Synonyms: differentdifferent termsterms z Addisonian syndrome eponym z Bronzed disease z Melasma addisonii symptoms z Asthenia pigmentosa z Primary adrenal deficiency z Primary adrenal insufficiency clinical z Primary adrenocortical insufficiency variants z Chronic adrenocortical insufficiency Contexts:Contexts: differentdifferent hierarchieshierarchies 11 OrganizeOrganize termsterms SynonymousSynonymous termsterms clusteredclustered intointo aa conceptconcept PreferredPreferred termterm UniqueUnique identifieridentifier (CUI)(CUI) Addison Disease MeSH D000224 Primary hypoadrenalism MedDRA 10036696 Primary adrenocortical insufficiency ICD-10 E27.1 Addison's disease (disorder) SNOMED CT 363732003 C0001403 Addison's disease 12 MeSH Disease Endocrine system diseases Adrenal gland diseases Adrenal Insufficiency Addison Disease MedDRA Endocrine disorders Adrenal gland disorders Adrenal cortical hypofunctions Addison’’s Disease SNOMED International Disease/Diagnoses Diseases of the endocrine system Diseases of the adrenal glands Addison’’s Disease SNOMED CT (native) Disorder of endocrine system Disorder of adrenal gland Hypoadrenalism Disorder of Adrenal hypofunction adrenal cortex Adrenal cortical hypofunction Addison’’s Disease SNOMED CT (UMLS view) Disorder of endocrine system Disorder of adrenal gland Adrenal gland Disorder of hypofunction adrenal cortex Adrenal cortical hypofunction Addison’’s Disease NCI Thesaurus Endocrine Disorder Non-neoplastic endocrine disorder Adrenal gland disorder Non-neoplastic adrenal gland disorder Adrenal gland insufficiencyinsufficiency Adrenal cortical insufficiency Addison’’s Disease ICD-10 Endocrine, nutritional and metabolic diseases Disorders of other endocrine glands Other disorders of adrenal gland Primary adrenocortical insuffinsufficiencyiciency OrganizeOrganize conceptsconcepts Inter-concept A C B relationships: hierarchies from the source B D E H E F H D E vocabularies G H Redundancy: multiple paths One graph instead of A multiple trees B C (multiple inheritance) D E F G H 20 organize concepts Disease Endocrine system diseases Adrenal gland diseases Adrenal gland Adrenal cortex hypofunction diseases SNOMED CT SNOMED Intl Adrenal cortical hypofunction MeSH MedDRA Addison’’s Disease UMLS view Disease Endocrine / nutritional / metabolic disorder Endocrine system diseases Non-neoplastic Disorders of other endocrine disorder endocrine glands Adrenal gland diseases Non-neoplastic adrenal gland disorder Adrenal gland Adrenal cortex Other disorders of hypofunction diseases adrenal gland Adrenal cortical hypofunction Addison’’s Disease UMLS view Disease Endocrine / nutritional / metabolic disorder Immune system diseases Endocrine system diseases Non-neoplastic Disorders of other endocrine disorder endocrine glands Adrenal gland diseases Non-neoplastic adrenal gland disorder Autoimmune diseases Adrenal gland Adrenal cortex Other disorders of hypofunction diseases adrenal gland Adrenal cortical hypofunction Addison’’s Disease Tuberculous Addison’’s disease Addison's disease due to autoimmunity RelateRelate toto otherother conceptsconcepts AdditionalAdditional hierarchicalhierarchical relationshipsrelationships z link to other trees z make relationships explicit NonNon--hierarchicalhierarchical relationshipsrelationships CoCo--occurringoccurring conceptsconcepts MappingMapping relationshipsrelationships 24 CategorizeCategorize conceptsconcepts High-level categories Disease or Syndrome (semantic types) Assigned by the Diseases Metathesaurus editors Independently of the Endocrine Diseases hierarchies in which these concepts are located Adrenal Gland Diseases Adrenal Gland Hypofunction Addison’s Disease 25 HowHow dodo theythey dodo that?that? LexicalLexical knowledgeknowledge SemanticSemantic prepre--processingprocessing UMLSUMLS editorseditors 26 LexicalLexical knowledgeknowledge Adrenal gland diseases Adrenal disorder Disorder of adrenal gland Diseases of the adrenal glands C0001621 27 SemanticSemantic prepre--processingprocessing MetadataMetadata inin thethe sourcesource vocabulariesvocabularies TentativeTentative categorizationcategorization PositivePositive (or(or negative)negative) evidenceevidence forfor tentativetentative synonymysynonymy relationsrelations basedbased onon lexicallexical featuresfeatures 28 AdditionalAdditional knowledge:knowledge: UMLSUMLS editorseditors Adrenal gland diseases Adrenal gland Adrenal cortex Other disorders of hypofunction diseases adrenal gland Adrenal cortical hypofunction Addison’’s Disease 29 UMLSUMLS SummarySummary SynonymousSynonymous termsterms clusteredclustered intointo conceptsconcepts UniqueUnique identifieridentifier FinerFiner granularitygranularity BroaderBroader scopescope AdditionalAdditional hierarchicalhierarchical relationshipsrelationships SemanticSemantic categorizationcategorization 30 Part I What is the UMLS? (3) UMLS Metathesaurus UnifiedUnified MedicalMedical LanguageLanguage SystemSystem SPECIALISTSPECIALIST LexiconLexicon z 360,000 lexical items Lexical z Part of speech and variant information resources MetathesaurusMetathesaurus z 6M names from over 100 terminologies Terminological z 1.5M concepts resources z 8M relations SemanticSemantic NetworkNetwork Ontological resources z 135 high-level categories z 7000 relations among them 32 MetathesaurusMetathesaurus BasicBasic organizationorganization ConceptsConcepts z Synonymous terms are clustered into a concept z Properties are attached to concepts, e.g., Unique identifier Definition RelationsRelations z Concepts are related to other concepts z Properties are attached to relations, e.g., Type of relationship Source 33 SourceSource VocabulariesVocabularies (2007AC) 141141 sourcesource vocabulariesvocabularies z 17 languages BroadBroad coveragecoverage ofof biomedicinebiomedicine z 6.1M names z 1.5M concepts z 8M relations CommonCommon presentationpresentation 34 BiomedicalBiomedical terminologiesterminologies GeneralGeneral vocabulariesvocabularies z anatomy (UWDA, Neuronames) z drugs (RxNorm, First DataBank, Micromedex) z medical devices (UMD, SPNSPN)) SeveralSeveral perspectivesperspectives z clinical terms (SNOMED CT) z information sciences (MeSH, CRISP) z administrative terminologies (ICD-9-CM, CPT-4) z data exchange terminologies (HL7, LOINC) 35 BiomedicalBiomedical terminologiesterminologies (cont(cont’’d)d) SpecializedSpecialized vocabulariesvocabularies z nursing (NIC, NOC, NANDA, Omaha, PCDS) z dentistry (CDT) z oncology (PDQ) z psychiatry (DSM, APA) z adverse reactions (COSTART, WHO ART) z primary care (ICPC) TerminologyTerminology ofof knowledgeknowledge basesbases ((AI/Rheum, DXplain, QMR)) The UMLS serves as a vehicle for the regulatory standards (HIPAA, CHI) 36 IntegratingIntegrating subdomainssubdomains ClinicalClinical repositoriesrepositories GeneticGenetic knowledgeknowledge
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