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Pdf name UMLS_tutorial.pdf "this doc is a copy and past from original one Tutorial T20 September 8, 2004 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 1 The Unified Medical Language System What is it and how to use it? 1

What IsUMLS

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Page 1: What IsUMLS

Pdf name UMLS_tutorial.pdf

"this doc is a copy and past from original one

Tutorial T20

September 8, 2004

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

1 The Unified Medical Language System What is it and how to use it?

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1.3 Overview through example

1.3.1 Addison’s disease

Addison's disease is a rare endocrine disorder الصماء الغدد اضطرابات

Addison's disease occurs when the adrenal glands الكظريه الغدد

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 االفه of adrenal glands themselves

Secondary: inadequate Secondary: inadequate كافية هرمون of ACTH االفراز secretion غيرby the Acute / Chronic نخامي الغده

Isolated / Polyendocrine

deficiency syndrome نقص متالزمه

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

Contexts: different hierarchies

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

Addisonian syndrome eponym اسم على مسمى

Bronzed disease المرض البشره برونزيsymptoms االعراض

Addison melanodermaAsthenia pigmentosa الصباغي الوهنPrimary adrenal deficiency

Clinical variantsPrimary adrenal insufficiency

Primary adrenocortical insufficiencyChronic adrenocortical insufficiency

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eponym

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Organize concepts

One graph instead of instead of

Multiple trees

(Multiple inheritance)

B

C

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1.5 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

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1.6 Categorize concepts High -level categories (semantic types) Assigned by the Metathesaurus editors Independently of the hierarchies in which these concepts are located

1.7 How do they do that? Lexical knowledge

Semantic pre-processing

UMLS editors

1.7.1 Lexical knowledge

1.7.2 Semantic pre-processing Metadata in the source vocabularies

Tentative مؤقت categorization

Positive (or negative) evidence for tentative lexical features synonymy relations based on lexical features

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1.7.3 UMLS editors: Additional knowledge

1.8 UMLS Summary

Synonymous Terms clustered into concepts Unique identifier Finer granularity Broader scope Additional hierarchical relationships Semantic categorization

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Metathesaurus

o conceptso Inter-concept relationships

Semantic Network o Semantic types o Semantic network relationships

Lexical resources o SPECIALIST Lexicon SPECIALIST Lexicono Lexical tools Lexical tools

1.9 Biomedical terminologies

1.9.1 General vocabularies Anatomy drugs ( drugs ( RxNorm, First DataBank,Micromedex) , Micromedex) SPN) medical devices (UMD, SPN)

1.9.2 Several perspectives clinical terms (SNOMED CT) Information sciences (MeSH, CRISP) administrative terminologies (ICD-9-CM, CPT CM, CPT-4) data exchange terminologies (HL7, LOINC)

1.9.3 Specialized vocabularies nursing dentistry (CDT) oncology (PDQ) psychiatry (DSM, APA) adverse reactions (COSTART, WHO ART) primary care (ICPC)

1.9.4 Terminology of knowledge bases (AI/Rheum, DXplain, , QMR)

The UMLS serves as a vehicle for the regulatory standards

2 UMLS Knowledge Sources

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1.10Metathesaurus Basic organization

1.10.1 Concepts Synonymous terms are clustered into a conceptProperties are attached to concepts, e.g., Unique identifier UniqueDefinition

1.10.2 Inter-concept relationshipsConcepts are related to other conceptsProperties are attached to relations, e.g., Properties are attached to relations, e.g.Type of relationship Type of relationship

1.10.3 Addison’s Disease: Addison’s Disease: Concept

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1.10.4 Metathesaurus Concepts

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1.10.5 Cluster of synonymous terms of synonymous terms

1.10.6

1.10.7

1.10.8

1.10.9

1.10.10

1.10.11

1.10.12

1.10.13

1.10.14

1.10.15

1.11Metathesaurus RELATIONSHIP Symbolic relations: Symbolic relations: ~9 M pairs of concepts Statistical relations ~7 M pairs of concepts co-occurring concepts Mapping relations: Mapping relations: 100,000 pairs of concepts Categorization: Relationships between concepts: and semantic types from the Semantic

Network

1.11.1 Symbolic relations Relations:- 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

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1.11.1.1 Symbolic relations type

Hierarchal

Parent / Child PAR/CHD

Broader / Narrower than RB/RN

Derived from hierarchies

Siblings (children of parents)

SIB

Associative

Other RO

Various flavors of near Various flavors of near-synonymy

Similar RL

Source asserted synonymy SY

Possible synonymy

RQ

1.11.1.2 Symbolic relations attributes Hierarchical

o isa -a ( is a kind-of) o part of

Associative o location-of o caused byo treats

Cross -references (mapping)

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1.11.1.3

1.12 Semantic Network

1.12.1 Semantic typesTree structure 2 major hierarchies 2 major hierarchies

Entity o Physical Object o Conceptual Entity

Event o Activity o Phenomenon or Process

1.12.2 Semantic 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)

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Associative (non--isa) relationships

Semantic serve as high level categories Semantic assigned to Metathesaurus concepts, 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 levelRelationships can inherit semantics Relationships can inherit semantics

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1.13 Lexical resources

1.13.1 SPECIALIST Lexicon Content

o English lexicon o Many words from the biomedical

200,000+ lexical items Word properties Word properties

o morphology o orthography o syntax

the lexical tools Used by the lexical tools

1.13.1.1 Morphology Inflection

o noun nucleus ,nucleio verb cauterize, cauterizes, cauterized, cauterizingo adjective red, redder, reddest

Derivation o verb noun cauterize --- cauterization o adjective noun red -- redness

1.13.1.2 Orthography Spelling variants Spelling variants

o oe/e oesophagus - esophaguso ae/e anaemia - anemiao ise/ize cauterise - cauterizeo genitive mark Addison's disease

Addison disease Addisons disease

1.13.1.3 Syntax Complementation

o verbs intransitive I'll treat. transitive He treated the patient. ditransitive He treated the patient with a drug.

o nouns prepositional phrase Valve of coronary sinus

Position for adjectives

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1.13.2 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, search engines

1.13.2.1 Normalization

e.g. and steps Hodgkin’s diseases, NOS

Remove genitive Hodgkin diseases, NOS Remove stop words Hodgkin diseasesLowercase hodgkin diseases,Strip punctuation hodgkin diseasesUninflect hodgkin diseaseSort words disease hodgkin

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

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1.13.2.2 Indexes Word index Word

o word to Metathesaurus strings o one word index per language

Normalized word index Normalized word indexo normalized word to Metathesaurus stringso English only

Normalized string index o normalized term to Metathesaurus stringso English only English only

1.13.2.3 Lexical Variant Generation program (lvg) Tool for specialists (linguists) Performs atomic lexical transformations

o generating inflectional variants o lowercase lowercaseo …

Performs sequences of atomic transformations o a specialized sequence of transformations provides the normalized form of a term

(the norm program)

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Obtaining a license Remote access

o Knowledge Knowledge Source Server (UMLSKS) o UMLSKS Application UMLSKS Application programming interface (API)

Local installation and customization ( MetamorphoSys)

1.14Obtaining a license

3 How to use the UMLS?

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1.15Remote access UMLS Knowledge Source Server:

http://umlsks.nlm.nih.gov Web search interface Application programming interface (API)

1.15.1 UMLS Knowledge Source Server: Web search interface

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1.16

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1.17

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1.17.1

1.17.2 Knowledge Source Server :Application Programming Interface

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1.17.3 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

…………………….i didn’t complete implementation issues

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