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1 The Unified Medical Language System What is it and how to use it?
Olivier Olivier Bodenreider Bodenreider Jan Willis Jan Willis William Hole William Outline

1.1 What is UMLS?
How to use to use the the UMLS? Obtaining Obtaining a license license Remote Remote access access Knowledge Knowledge Source Server (UMLSKS) Source Server (UMLSKS) UMLSKS Application UMLSKS Application programming interface (API) interface (API) Local installation Local installation and customization (MetamorphoSys) Questions What is the UMLS? NOT END- USER Application

1.2 Introduction
Overview through an example The three UMLS Knowledge Sources UMLS Metathesaurus UMLS Semantic UMLS Lexicon Univifed medical language system Started in 1986 National Library of Medicine National Library of Medicine “Long “Long-term R&D project” term R&D project” Complementary to IAIMS

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1.3 Overview through example
1.3.1 Addison’s disease
Addison's disease is a rare endocrine disorder ‫اضطرابات الغدد الصماء‬ Addison's disease occurs when the adrenal glands ‫الغدد الكظريه‬ do not produce enough of the cortisol For this reason, the disease is sometimes Called   chronic adrenal insufficiency, or hypocortisolism

1.3.2 Adrenal insufficiency "Clinical variants"
Primary / Secondary Primary: lesion ‫ الفه‬of adrenal glands themselves Secondary: inadequate Secondary: inadequate ‫غير كافية‬ Acute / Chronic ‫الغده نخامي‬ Isolated / Polyendocrine deficiency syndrome ‫متلزمه نقص‬ secretion ‫ الفراز‬of ACTH ‫ هرمون‬by the

1.3.3 Addison’s disease Symptoms
Fatigue Weakness Low blood pressure Pigmentation of the skin (exposed and non Pigmentation of the ………..

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1.3.4 AD in medical vocabularies
Synonyms: different terms different Addisonian syndrome Bronzed disease ‫برونزي البشره المرض‬ Addison melanoderma Asthenia pigmentosa ‫الوهن الصباغي‬ Primary adrenal deficiency Primary adrenal insufficiency Primary adrenocortical insufficiency Chronic adrenocortical insufficiency Contexts: different hierarchies eponym ‫مسمى على اسم‬ ‫ العراض‬symptoms eponym

Clinical variants

1.4 Organize terms
   Synonymous terms clustered into a concept Preferred term Unique identifier (CUI)

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Organize concepts One graph instead of instead of Multiple trees (Multiple inheritance) B C 7 .

5 Relate to other concepts  Additional hierarchical relationships o link to other trees o make relationships explicit Non-hierarchical relationships Co-occurring concepts Mapping relationships    Relate to other concepts 8 .1.

7 How do they do that? Lexical knowledge Semantic pre-processing UMLS editors 1.6 Categorize concepts High -level categories (semantic types) Assigned by the Metathesaurus editors Independently of the hierarchies in which these concepts are located 1.2 Semantic pre-processing Metadata in the source vocabularies Tentative ‫ مؤقت‬categorization Positive (or negative) evidence for tentative lexical features synonymy relations based on lexical features 9 .1 Lexical knowledge 1.7.7.1.

8 UMLS Summary       Synonymous Terms clustered into concepts Unique identifier Finer granularity Broader scope Additional hierarchical relationships Semantic categorization 10 .1.3 UMLS editors: Additional knowledge 1.7.

.9. DXplain.4 Terminology of knowledge bases (AI/Rheum. WHO ART) primary care (ICPC) 1.9 Biomedical terminologies 1. CPT-4) data exchange terminologies (HL7. CRISP) administrative terminologies (ICD-9-CM.9. QMR) The UMLS serves as a vehicle for the regulatory standards 11 . SPN) 1.1 General vocabularies    Anatomy drugs ( drugs ( RxNorm. LOINC) 1.2 UMLS Knowledge Sources  Metathesaurus o concepts o Inter-concept relationships Semantic Network o Semantic types o Semantic network relationships Lexical resources o SPECIALIST Lexicon SPECIALIST Lexicon o Lexical tools Lexical tools   1.9. Micromedex) SPN) medical devices (UMD. APA) adverse reactions (COSTART.9. First DataBank. CPT CM.3 Specialized vocabularies       nursing dentistry (CDT) oncology (PDQ) psychiatry (DSM.2 Several perspectives     clinical terms (SNOMED CT) Information sciences (MeSH.Micromedex) .

e.10.. Unique identifier UniqueDefinition 1..g.10 Metathesaurus Basic organization 1.g.g.Type of relationship Type of relationship 1. e. Properties are attached to relations. e.1Concepts Synonymous terms are clustered into a concept Properties are attached to concepts.1.2 Inter-concept relationships Concepts are related to other concepts Properties are attached to relations.3Addison’s Disease: Addison’s Disease: Concept 12 .10.10.

1.10.4Metathesaurus Concepts 13 .

10.10.10.10.7 1.11 1.Pair of “atom” identifiers Pair of “atom” identifiers Type Attribute (if any) List of sources (for type and attribute) Semantics of the relationship: Defined by its type [and attribute] Source transparency: The information is recorded at the “atom” level 14 .11 Metathesaurus RELATIONSHIP  Symbolic relations: Symbolic relations: ~9 M pairs of concepts  Statistical relations ~7 M pairs of concepts  co-occurring concepts  Mapping relations: Mapping relations: 100.15 1.1 Symbolic relations Relations:.11.6 1.8 1.10.10.1.10.10.14 1.10.13 1.10.5Cluster of synonymous terms of synonymous terms 1.10.9 1.12 1.000 pairs of concepts  Categorization: Relationships between concepts: and semantic types from the Semantic Network 1.10 1.

2  Symbolic relations attributes  Hierarchical o isa -a ( is a kind-of) o part of Associative o location-of o caused by o treats 15 .1.1 Symbolic relations type Hierarchal Parent / Child PAR /CH D RB/ RN Broader / Narrower than Derived from hierarchies Siblings (children of parents) SIB Associative Other Various flavors of near Various flavors of near-synonymy Similar Source asserted synonymy Possible synonymy RL SY RO RQ 1.1.11.1.11.

 Cross -references (mapping) 16 .

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12.1.1.11.12 1.1 Semantic Network Semantic types Tree structure 2 major hierarchies 2 major hierarchies  Entity o Physical Object o Conceptual Entity  Event o Activity o Phenomenon or Process 1.12.2Semantic network relationships  hierarchical (isa = is a kind of ) o among types  Animal isa Organism  Enzyme isa Biologically Active Substance o among relations  treats isa affects non-hierarchical o Sign or Symptom Sign diagnoses Pathologic Function o Pharmacologic Substance treats Pathologic Function  Biologic Function” hierarchy (isa) 18 .3 1.

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concepts.Associative (non--isa) relationships Semantic serve as high level categories Semantic assigned to Metathesaurus concepts. independently of their position in a hierarchy A relationship between 2 Semantic Types (ST) is a possible link between 2 concepts that have been assigned to STs The relationship may or may not hold at the concept level Other relationships may apply at the concept level Relationships can inherit semantics Relationships can inherit semantics 20 .

1.  transitive He treated the patient. cauterized.13.esophagus o ae/e anaemia .13.cauterize o genitive mark Addison's disease Addison disease Addisons disease 1. cauterizes.  ditransitive He treated the patient with a drug.3  Syntax Complementation o verbs  intransitive I'll treat.13.1.anemia o ise/ize cauterise .1  Lexical resources SPECIALIST Lexicon Content o English lexicon o Many words from the biomedical 200.nuclei o verb cauterize. cauterizing o adjective red. reddest Derivation o verb  noun cauterize --.  o nouns  prepositional phrase Valve of coronary sinus 21 .13.2  Orthography Spelling variants Spelling variants o oe/e oesophagus .redness 1.1. redder.1.13 1.1  Morphology  Inflection o noun nucleus .cauterization o adjective  noun red -.000+ lexical items Word properties Word properties o morphology o orthography o syntax the lexical tools Used by the lexical tools    1.

 Position for adjectives 22 .

hodgkin diseases hodgkin disease disease hodgkin e.13. NOS Hodgkin diseases hodgkin diseases. and steps Remove genitive Remove stop words Lowercase Strip punctuation Uninflect Sort words       Normalization Applications     Model for lexical resemblance Help find lexical variants for a term o Terms that normalize the same usually share the same LUI Help find candidates to synonymy among terms Help to map input terms to UMLS concepts 23 .1.2. search engines   1.1 Normalization Hodgkin’s diseases.13.2   Lexical tools Lexical tools Tomanage lexical variation in biomedical terminologies Major tools o Normalization o Indexes o Lexical Variant Generation program (lvg) Based on the SPECIALIST Lexicon engines Used by noun phrase extractors. NOS Hodgkin diseases.g.

13.2  Indexes Word index Word o word to Metathesaurus strings o one word index per language Normalized word index Normalized word index o normalized word to Metathesaurus strings o English only Normalized string index o normalized term to Metathesaurus strings o English only English only   1.3   Lexical Variant Generation program (lvg) Tool for specialists (linguists) Performs atomic lexical transformations o generating inflectional variants o lowercase lowercase o … Performs sequences of atomic transformations o a specialized sequence of transformations provides the normalized form of a term (the norm program)  24 .1.13.2.2.

3   How to use the UMLS? Obtaining a license Remote access o Knowledge Knowledge Source Server (UMLSKS) o UMLSKS Application UMLSKS Application programming interface (API) Local installation and customization ( MetamorphoSys)  1.14 Obtaining a license 25 .

nlm.15.1.15 Remote access  UMLS Knowledge Source Server: http://umlsks.nih.gov  Web search interface  Application programming interface (API) 1.1UMLS Knowledge Source Server: Web search interface 26 .

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17.17.2 Knowledge Source Server :Application Programming Interface 35 .1.1 1.

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3    Local installation and ( MetamorphoSys) Tool distributed with the UMLS Multi-platform Java software The UMLS installation and customization wizard o Installs Knowledge Sources to local o Subsets and customizes a local Metathesaurus …………………….1.i didn’t complete implementation issues 37 .17.

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