The Unified Medical Language System (UMLS) is a
compendium
A compendium (plural: compendia or compendiums) is a comprehensive collection of information and analysis pertaining to a body of knowledge. A compendium may concisely summarize a larger work. In most cases, the body of knowledge will concern a s ...
of many
controlled vocabularies
Control may refer to:
Basic meanings Economics and business
* Control (management), an element of management
* Control, an element of management accounting
* Comptroller (or controller), a senior financial officer in an organization
* Controlling ...
in the
biomedical
Biomedicine (also referred to as Western medicine, mainstream medicine or conventional medicine) sciences (created 1986). It provides a mapping structure among these vocabularies and thus allows one to translate among the various terminology systems; it may also be viewed as a comprehensive
thesaurus
A thesaurus (plural ''thesauri'' or ''thesauruses'') or synonym dictionary is a reference work for finding synonyms and sometimes antonyms of words. They are often used by writers to help find the best word to express an idea:
Synonym diction ...
and
ontology
In metaphysics, ontology is the philosophical study of being, as well as related concepts such as existence, becoming, and reality.
Ontology addresses questions like how entities are grouped into categories and which of these entities exis ...
of biomedical concepts. UMLS further provides facilities for
natural language processing
Natural language processing (NLP) is an interdisciplinary subfield of linguistics, computer science, and artificial intelligence concerned with the interactions between computers and human language, in particular how to program computers to pro ...
. It is intended to be used mainly by developers of systems in
medical informatics
Health informatics is the field of science and engineering that aims at developing methods and technologies for the acquisition, processing, and study of patient data, which can come from different sources and modalities, such as electronic hea ...
.
UMLS consists of Knowledge Sources (databases) and a set of software tools.
The UMLS was designed and is maintained by the
US National Library of Medicine
The United States National Library of Medicine (NLM), operated by the United States federal government, is the world's largest medical library.
Located in Bethesda, Maryland, the NLM is an institute within the National Institutes of Health. Its ...
, is updated quarterly and may be used for free. The project was initiated in 1986 by
Donald A.B. Lindberg
Donald Allen Bror Lindberg (September 21, 1933 – August 17, 2019) was the Director of the United States National Library of Medicine from 1984 until his retirement in 2015. He was known for his work in medical computing, especially the developm ...
,
M.D.
Doctor of Medicine (abbreviated M.D., from the Latin ''Medicinae Doctor'') is a medical degree, the meaning of which varies between different jurisdictions. In the United States, and some other countries, the M.D. denotes a professional degree. T ...
, then Director of the Library of Medicine, and directed by
Betsy Humphreys
Betsy L. Humphreys is an American medical librarian. She was the deputy director of the United States National Library of Medicine, National Library of Medicine from 2005 until her retirement in 2017, serving as Acting Director from 2015 to 2016.
...
.
Purpose and applications
The number of biomedical resources available to researchers is enormous. Often this is a problem due to the large volume of documents retrieved when the medical literature is searched. The purpose of the UMLS is to enhance access to this literature by facilitating the development of computer systems that understand biomedical language. This is achieved by overcoming two significant barriers: "the variety of ways the same concepts are expressed in different machine-readable sources & by different people" and "the distribution of useful information among many disparate databases & systems".
Licensing
Users of the system are required to sign a "UMLS agreement" and file brief annual usage reports. Academic users may use the UMLS free of charge for research purposes. Commercial or production use requires copyright licenses for some of the incorporated source vocabularies.
Knowledge Sources
Metathesaurus
The Metathesaurus forms the base of the UMLS and comprises over 1 million biomedical concepts and 5 million concept names, all of which stem from the over 100 incorporated controlled vocabularies and classification systems. Some examples of the incorporated controlled vocabularies are
CPT,
ICD-10
ICD-10 is the 10th revision of the International Statistical Classification of Diseases and Related Health Problems (ICD), a medical classification list by the World Health Organization (WHO). It contains codes for diseases, signs and symptoms, ...
,
MeSH
A mesh is a barrier made of connected strands of metal, fiber, or other flexible or ductile materials. A mesh is similar to a web or a net in that it has many attached or woven strands.
Types
* A plastic mesh may be extruded, oriented, ex ...
,
SNOMED CT
SNOMED CT or SNOMED Clinical Terms is a systematically organized computer-processable collection of medical terms providing codes, terms, synonyms and definitions used in clinical documentation and reporting. SNOMED CT is considered to be the mo ...
,
DSM-IV
The ''Diagnostic and Statistical Manual of Mental Disorders'' (DSM; latest edition: DSM-5-TR, published in March 2022) is a publication by the American Psychiatric Association (APA) for the classification of mental disorders using a common langua ...
,
LOINC
Logical Observation Identifiers Names and Codes (LOINC) is a database and universal standard for identifying medical laboratory observations. First developed in 1994, it was created and is maintained by the Regenstrief Institute, a US nonprofit me ...
,
WHO Adverse Drug Reaction Terminology
Who or WHO may refer to:
* Who (pronoun), an interrogative or relative pronoun
* Who?, one of the Five Ws in journalism
* World Health Organization
Arts and entertainment Fictional characters
* Who, a creature in the Dr. Seuss book ''Horton Hear ...
,
UK Clinical Terms
The United Kingdom of Great Britain and Northern Ireland, commonly known as the United Kingdom (UK) or Britain, is a country in Europe, off the north-western coast of the European mainland, continental mainland. It comprises England, Scotlan ...
,
RxNorm
RxNorm is US-specific terminology in medicine that contains all medications available on the US market. It can also be used in personal health records applications. RxNorm is part of Unified Medical Language System (UMLS) terminology and is mainta ...
,
Gene Ontology
The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and g ...
, and
OMIM
Online Mendelian Inheritance in Man (OMIM) is a continuously updated catalog of human genes and genetic disorders and traits, with a particular focus on the gene-phenotype relationship. , approximately 9,000 of the over 25,000 entries in OMIM r ...
(se
full list.
The Metathesaurus is organized by concept, and each concept has specific attributes defining its meaning and is linked to the corresponding concept names in the various source vocabularies. Numerous relationships between the concepts are represented, for instance hierarchical ones such as "
isa" for subclasses and "is part of" for subunits, and associative ones such as "is caused by" or "in the literature often occurs close to" (the latter being derived from
Medline
MEDLINE (Medical Literature Analysis and Retrieval System Online, or MEDLARS Online) is a bibliographic database of life sciences and biomedical information. It includes bibliographic information for articles from academic journals covering medic ...
).
The scope of the Metathesaurus is determined by the scope of the source vocabularies. If different vocabularies use different names for the same concept, or if they use the same name for different concepts, then this will be faithfully represented in the Metathesaurus. All hierarchical information from the source vocabularies is retained in the Metathesaurus. Metathesaurus concepts can also link to resources outside of the database, for instance gene sequence databases.
Semantic Network
Each concept in the Metathesaurus is assigned one or more ''semantic types'' (categories), which are linked with one another through ''semantic relationships''.
The
semantic network
A semantic network, or frame network is a knowledge base that represents semantic relations between concepts in a network. This is often used as a form of knowledge representation. It is a directed or undirected graph consisting of vertices, ...
is a catalog of these semantic types and relationships. This is a rather broad classification; there are 127 semantic types and 54 relationships in total.
The major semantic types are organisms, anatomical structures, biologic function, chemicals, events, physical objects, and concepts or ideas.
The links among semantic types define the structure of the network and show important relationships between the
groupings and concepts. The primary link between semantic types is the "
isa" link, establishing a
hierarchy
A hierarchy (from Greek: , from , 'president of sacred rites') is an arrangement of items (objects, names, values, categories, etc.) that are represented as being "above", "below", or "at the same level as" one another. Hierarchy is an important ...
of types.
The network also has 5 major categories of non-hierarchical (or associative) relationships, which constitute the remaining 53 relationship types. These are "physically related to", "spatially related to", "temporally related to", "functionally related to" and "conceptually related to".
The information about a semantic type includes an identifier, definition, examples, hierarchical information about the encompassing semantic type(s), and
associative
In mathematics, the associative property is a property of some binary operations, which means that rearranging the parentheses in an expression will not change the result. In propositional logic, associativity is a valid rule of replacement f ...
relationships. Associative relationships within the Semantic Network are very weak. They capture at most some-some relationships, i.e. they capture the fact that some instance of the first type may be connected by the salient relationship to some instance of the second type. Phrased differently, they capture the fact that a corresponding relational assertion is meaningful (though it need not be true in all cases).
An example of an associative relationship is "''may-cause''", applied to the terms (smoking, lung cancer) would yield: smoking "''may-cause''" lung cancer.
SPECIALIST Lexicon
The SPECIALIST Lexicon contains information about common English vocabulary, biomedical terms, terms found in
MEDLINE
MEDLINE (Medical Literature Analysis and Retrieval System Online, or MEDLARS Online) is a bibliographic database of life sciences and biomedical information. It includes bibliographic information for articles from academic journals covering medic ...
and terms found in the UMLS Metathesaurus. Each entry contains
syntactic
In linguistics, syntax () is the study of how words and morphemes combine to form larger units such as phrases and sentences. Central concerns of syntax include word order, grammatical relations, hierarchical sentence structure (constituency), ...
(how words are put together to create meaning),
morphological (form and structure) and
orthographic (spelling) information. A set of
Java
Java (; id, Jawa, ; jv, ꦗꦮ; su, ) is one of the Greater Sunda Islands in Indonesia. It is bordered by the Indian Ocean to the south and the Java Sea to the north. With a population of 151.6 million people, Java is the world's List ...
programs use the lexicon to work through the variations in biomedical texts by relating words by their parts of speech, which can be helpful in
web
Web most often refers to:
* Spider web, a silken structure created by the animal
* World Wide Web or the Web, an Internet-based hypertext system
Web, WEB, or the Web may also refer to:
Computing
* WEB, a literate programming system created by ...
searches or searches through an
electronic medical record
An electronic health record (EHR) is the systematized collection of patient and population electronically stored health information in a digital format. These records can be shared across different health care settings. Records are shared throu ...
.
Entries may be one-word or multiple-word terms. Records contain four parts: base form (i.e. "run" for "running"); parts of speech (of which Specialist recognizes eleven); a unique identifier; and any available spelling variants.
For example, a
query for "anesthetic" would return the following:
The SPECIALIST lexicon is available in two formats. The "unit record" format can be seen above, and comprises ''slots'' and ''fillers''. A ''slot'' is the element (i.e. "base=" or "spelling variant=") and the ''fillers'' are the values attributable to that slot for that entry. The "
relational table" format is not yet
normalized and contain a great deal of redundant data in the files.
Inconsistencies and other errors
Given the size and complexity of the UMLS and its permissive policy on integrating terms, errors are inevitable.
Errors include ambiguity and redundancy, hierarchical relationship cycles (a concept is both an ancestor and descendant to another), missing ancestors (semantic types of parent and child concepts are unrelated), and semantic inversion (the child/parent relationship with the semantic types is not consistent with the concepts).
These errors are discovered and resolved by auditing the UMLS. Manual audits can be very time-consuming and costly. Researchers have attempted to address the issue through a number of ways. Automated tools can be used to search for these errors.
For structural inconsistencies (such as loops), a trivial solution based on the order would work. However, the same wouldn't apply when the inconsistency is at the term or concept level (context-specific meaning of a term).
This requires an informed search strategy to be used (
knowledge representation
Knowledge representation and reasoning (KRR, KR&R, KR²) is the field of artificial intelligence (AI) dedicated to representing information about the world in a form that a computer system can use to solve complex tasks such as diagnosing a medic ...
).
Supporting software tools
In addition to the knowledge sources, the
National Library of Medicine
The United States National Library of Medicine (NLM), operated by the United States federal government, is the world's largest medical library.
Located in Bethesda, Maryland, the NLM is an institute within the National Institutes of Health. Its ...
also provides supporting tools.
Third party software
UMLS-Similarity an open source software package that implements many measures of semantic similarity and relatedness.
UMLS-Similarity web interface a web interface to UMLS-Similarity
See also
*
Medical classification
A medical classification is used to transform descriptions of medical diagnoses or procedures into standardized statistical code in a process known as clinical coding. Diagnosis classifications list diagnosis codes, which are used to track diseases ...
References
Further reading
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*
*
*
External links
*
UMLS Summary description with links to factsheets and documentation for Metathesaurus, Semantic Network, SPECIALIST Lexicon and MetamorphoSys
UMLS Overview and Tutorial by Rachel Kleinsorge, Jan Willis, Allen Browne, Alan Aronson
A Perl module to query a UMLS mysql installation* {{MeSH name, Unified+Medical+Language+System, 3=Unified Medical Language System
UMLS.me- extracts UMLS medical concepts and codes from free text in the browser, by Alexander Scarlat MD.
Knowledge representation and reasoning
Knowledge representation and reasoning (KRR, KR&R, KR²) is the field of artificial intelligence (AI) dedicated to representing information about the world in a form that a computer system can use to solve complex tasks such as Computer-aided diag ...
Nursing classification