Medical Informatics Laboratory Department of Biomedical engineering College of Medicine , Seoul National Univ. Eunsil Yoon U.S. National Library of Medicine National Institutes of Health UMLS (The Unified Medical Language System) 2012.11.29 Reviewed by Eunsil Yoon
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Medical Informatics LaboratoryDepartment of Biomedical engineeringCollege of Medicine , Seoul National Univ.
Eunsil Yoon
U.S. National Library of MedicineNational Institutes of Health
UMLS(The Unified Medical Language System)
2012.11.29 Reviewed by Eunsil Yoon
Medical Informatics LaboratoryDepartment of Biomedical engineeringCollege of Medicine , Seoul National Univ.
Eunsil Yoon
Contents
• Introduction
– What is the UMLS?
– UMLS is Use
– www.nlm.nih.gov/research/umls
• The Three UMLS Tools (Knowledge Sources)
– Metathesaurus
– Semantic network
– SPECIALIST Lexicon
• UMLS in JAMIA papers
Medical Informatics LaboratoryDepartment of Biomedical engineeringCollege of Medicine , Seoul National Univ.
Eunsil Yoon
What is the UMLS?
• Started in 1986 (NLM; National Library of Medicine)
• NLM is a member of the IHTSDO(owner of SNOMED CT)
Medical Informatics LaboratoryDepartment of Biomedical engineeringCollege of Medicine , Seoul National Univ.
Eunsil Yoon
What is the UMLS?
• Unified Medical Language System® (UMLS®)
• A set of files and software that brings together many health
and biomedical vocabularies and standards to enable inter-
operability between computer systems.
• You can use the UMLS to enhance or develop applications,
such as electronic health records, classification tools, dic-
tionaries and language translators.
The UMLS is not an end-user application
Medical Informatics LaboratoryDepartment of Biomedical engineeringCollege of Medicine , Seoul National Univ.
Eunsil Yoon
NLM Mainpage
Medical Informatics LaboratoryDepartment of Biomedical engineeringCollege of Medicine , Seoul National Univ.
Eunsil Yoon
NLM > UMLS
Medical Informatics LaboratoryDepartment of Biomedical engineeringCollege of Medicine , Seoul National Univ.
Eunsil Yoon
NLM > UMLS > UTS
Medical Informatics LaboratoryDepartment of Biomedical engineeringCollege of Medicine , Seoul National Univ.
Eunsil Yoon
NLM > UMLS > UTS > Metathesaurus browser
Medical Informatics LaboratoryDepartment of Biomedical engineeringCollege of Medicine , Seoul National Univ.
Eunsil Yoon
Metathesaurus Browser > Synonyms
Synonyms (246)(Acute nasopharyngitis or rhinitis) or (common cold)(Acute nasopharyngitis or rhinitis) or (common cold)
(disorder)ARNAS IBILBIDE GARAIETAKO ZOLDURA/ HOTZALDI
Medical Informatics LaboratoryDepartment of Biomedical engineeringCollege of Medicine , Seoul National Univ.
Eunsil Yoon
FindingIdea orConcept
Physical ObjectConceptual entity
Occupation orDiscipline
LanguageIntellectual
ProductOrganismAttribute
GroupGroup
AttributeOrganization
Regulationor Law
ClassificationClinical
AttributeSign or
SymptomLaboratory or
Test ResultAmino AcidSequence
BiomedicalOccupation or
Discipline
NucleotideSequence
CarbohydrateSequence
Patient orDisabled
Group
PopulationGroup
Professional orOccupational
GroupFamily GroupAge Group
SpatialConcept
QuantitativeConcept
QualitativeConcept
Temporal Concept
FunctionalConcept
Body SystemMolecular Sequence
GeographicArea
Body Space orJunction
Body Locationor Region
CarbohydrateSequence
Amino AcidSequence
NucleotideSequence
Semantic Network Conceptual Ob-ject Entity
Medical Informatics LaboratoryDepartment of Biomedical engineeringCollege of Medicine , Seoul National Univ.
Eunsil Yoon
Event
Behavior
PhenomenonOr ProcessActivity
IndividualBehavior
EducationalActivity
SocialBehavior
Daily orRecreational
Activity
Injury orPoisoning
NaturalPhenomenon
of Process
Human-causedPhenomenon of
Process
MachineActivity
OccupationalActivity
Environmental Effect of
HumanResearchActivity
Health CareActivity
Governmentalor Regulatory
Activity
BiologicFunction
MolecularBiology
ResearchTechnique
Therapeutic orPreventiveProcedure
LaboratoryProcedure
DiagnosticProcedure
PathologicFunction
PhysiologicFunction
Cell orMolecular
DysFunction
OrganismFunction
Organ orTissue
Function
MolecularFunction
CellFunction
ExperimentalModel ofDisease
Diseaseor
Syndrome
Mental orBehavioral
Dysfunction
NeoplasticProcess
MentalProcess
GeneticFunction
Semantic Network - Event
Medical Informatics LaboratoryDepartment of Biomedical engineeringCollege of Medicine , Seoul National Univ.
Eunsil Yoon
The Semantic Network - Relationships
• 54 Semantic Relationships
• The primary link between most semantic
types is the ‘isa’ relationship.
• Animal isa Entity
• Carbohydrate isa Chemical
• Human isa Mammal
[ Relation Label ]
isa
part_of
result_of
co-occurs_with
evaluation_of
location_of
Medical Informatics LaboratoryDepartment of Biomedical engineeringCollege of Medicine , Seoul National Univ.
Eunsil Yoon
The Semantic Network - Relationships
Medical Informatics LaboratoryDepartment of Biomedical engineeringCollege of Medicine , Seoul National Univ.
Eunsil Yoon
SPECIALIST Lexicon
• A lexicon is necessarily a core component of any natural language process-
ing system
• Coverage includes both commonly occurring English words and biomedical
vocabulary discovered in the NLM Test Collection and the UMLS Metathe-
saurus.
• The lexicon entry for each word or term records the syntactic, morphologi-
cal, and graphemic information.
– Syntactic information includes syntactic category(part of speech), and complementation pat-
terns for verbs, adjectives and nouns, as well as positional and modification types for adjec-
tives and adverbs.
– Inflectional morphology is indicated for those syntactic categories which inflect, and spelling
variation is recorded for each lexical item known to exhibit such variation.
Medical Informatics LaboratoryDepartment of Biomedical engineeringCollege of Medicine , Seoul National Univ.
Eunsil Yoon
SPECIALIST NLP Tools
Medical Informatics LaboratoryDepartment of Biomedical engineeringCollege of Medicine , Seoul National Univ.
Eunsil Yoon
관련연구
[1] Wu S.T., Liu.H et al (2012). Unified Medical Language System term occurrences in clinical notes: a large-scale corpus analysis. Journal of the American Medical Informatics Association : JAMIA, 19(e1), e149–e156.
Medical Informatics LaboratoryDepartment of Biomedical engineeringCollege of Medicine , Seoul National Univ.
Eunsil Yoon
[1] UMLS term occurrences in clinical notes
• Objective
– To characterise empirical instances of Unified Medical Language Sys-
tem (UMLS) Metathesaurus term strings in a large clinical corpus, and
to illustrate what types of term characteristics are generalisable across
data sources.
• Data Sources
– The data source for the corpus analysis of clinical text was Mayo Clinic
clinical notes between 1 January 2001 and 31 December 2010, re-
trieved from the Mayo’s Enterprise Data Trust (EDT).
– 51,945,627EA documents
– 296,167 unique terms
– 2,319,010,575 case-insensitive exact term match
Medical Informatics LaboratoryDepartment of Biomedical engineeringCollege of Medicine , Seoul National Univ.
Eunsil Yoon
[1] UMLS term occurrences in clinical notes
• Figure 1 shows histograms for the number of words in the UMLS and in the subset that is empirically found in Mayo Clinic data.
• Corpus Analysis – Word Statistics
Medical Informatics LaboratoryDepartment of Biomedical engineeringCollege of Medicine , Seoul National Univ.
Eunsil Yoon
[1] UMLS term occurrences in clinical notes
• Corpus Analysis - Term Frequency
Medical Informatics LaboratoryDepartment of Biomedical engineeringCollege of Medicine , Seoul National Univ.
Eunsil Yoon
[1] UMLS term occurrences in clinical notes
• Corpus Analysis – Source Terminology
Medical Informatics LaboratoryDepartment of Biomedical engineeringCollege of Medicine , Seoul National Univ.
Eunsil Yoon
[1] UMLS term occurrences in clinical notes
• Corpus Analysis – syntactic categories
Medical Informatics LaboratoryDepartment of Biomedical engineeringCollege of Medicine , Seoul National Univ.
Eunsil Yoon
[1] UMLS term occurrences in clinical notes
• Cross-Institutional analysis
① Special characters
② Maximum number of words
③ Maximum number of characters
④ Language
⑤ Source terminology
⑥ Semantic group
⑦ Empirical occurrence filter
⑧ Term frequency
• SNOMED-CT• Consumer Health Vocabulary• National Cancer Institute(NCI) Thesaurus• Medical Subject Headings (MSH)• Read Codes• Medical Dictionary for Regulatory Activities Terminology (Med-
DRA)• SNOMED International• MEDCIN• UMLS Metathesaurus• National Drug Filed Reference Terminology(NDF-RT)• The original SNOMED• Online Mendelian Inheritance in Man (OMIM)• Logical Observation Identifiers Names and Codes (LOINC)• Computer Retrieval of Information on Scientific Projects