# Presentation: 678620

## Unified Medical Language System® (UMLS®) 

- NLM Presentation Theater
- MLA 2006
- Rachel Kleinsorge
- Jan Willis

**Notes:**
Welcome to the UMLS Basics class
Certified for 6 CE credit hours by the Medical Library Association

The National Library of Medicine (NLM), part of the National Institutes of Health (NIH) in Bethesda, Maryland, is the world's largest medical library.

NLM produces the MEDLINE database, searchable through PubMed, a freely accessible Web search engine for biomedical literature and MEDLINEplus, a source of high quality consumer health information. Other NLM databases provide information on such specialized subjects as toxicology, environmental health, and molecular biology. 

## What does UMLS stand for?

- Unified
- Medical
- Language
- System

- UMLS®
- Unified Medical Language System®

**Notes:**
What do the letters UMLS stand for?  They stand for Unified Medical Language System.  

What is the UMLS?  The UMLS was initiated in 1986 as a long-term research & development project of the National Library of Medicine to reduce system development problems caused by differences in medical terminologies.  

## The UMLS consists of

- Metathesaurus

- Semantic Network

- SPECIALIST
- Lexicon & Tools

- 135 broad categories and 54 relationships between categories

- 1 million+
- biomedical concepts from over 130 sources

- lexical information and programs for language processing

**3 Knowledge Sources**
- used separately or together

**Notes:**
knowledge sources = data files and associated tools.
Users may use any one or all 3 knowledge sources. 
independently, or in conjunction with each other.

## UMLS  3 Knowledge Sources

- Metathesaurus
- Over 100 source vocabularies
- Over 1 million concepts
- Inter-concept relationships
- Semantic Network
- 135 Semantic types (broad categories)
- 54 Semantic relations (between categories)
- Lexical resources
- SPECIALIST Lexicon
- Lexical tools (programs and databases)

**Notes:**
There are  3 components, or Knowledge Sources that comprise the UMLS.  

The Metathesaurus contains                       concepts and                   names or strings, and                               inter-concept relationships. 

The Semantic Network with 
135 Semantic Types, which are broad subject categories, like Disease or Syndrom or Clinical Drug
and 54 relationships that can be made between the semantic types, such as Clinical Drug treats Disease or Syndrome.  

The 3rd component consists of lexical resources including the SPECIALIST Lexicon and lexical tools.

There are three UMLS knowledge sources:

The first knowledge source is the Metathesaurus.  As the main component of the UMLS, the Metathesaurus is a relational database containing 65 plus biomedical vocabularies and classification systems organized by concept in a simple, explicit format. The Metathesaurus preserves the names, meanings, hierarchical contexts, attributes, and inter-term relationships present in its source vocabularies; adds certain basic information to each concept; and establishes new relationships between terms from different source vocabularies. 

The SPECIALIST Lexicon is an English language lexicon containing many biomedical terms.  The lexicon provides basic word usage for terms found in the Metathesaurus thus enabling the use of natural language processing.   The lexical tools provided with the UMLS include a set of lexical programs, indexes, and databases that generate a range of variations for English lexical items that is useful for recognizing lexical variations in biomedical terminologies and texts. 

The Semantic Network encodes biomedical “common sense” by representing sensible relationships among semantic types or broad categories of biomedical entities.  All concepts in the Metathesaurus are assigned semantic types.  For example, the concept “diabetes” is assigned the semantic type of “disease or syndrome”. 

## History of the UMLS

- Started at National Library of Medicine, 1986
- “Long-term R&D project”

- [Lindberg & al., *Methods*, 1993]
- [Humphreys & al., *JAMIA*, 1998]

- «[...] 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.»

**Notes:**
The UMLS dates from 1986, when then newly appointed NLM Director, Dr. Donald A.B. Lindberg, testified to Congress at the Library’s budget appropriations asking for some additional seed money.  The first 4 years were spent 

## UMLS Objectives

- Intellectual “middleware”
- A set of multi-purpose tools for system developers
- Knowledge Sources used to overcome:
- disparities in language format
- 		Ex: atrial fibrillation, auricular fibrillation, af
- disparities in granularity and perspective
- Ex: Contusions, hematoma, bruise
- Ex:  Instruct patient to promptly report nosebleeds and excessive bruising (NIC), Epistaxis (MeSH)

**Notes:**
Ask Bill/Kin Wah

In terms of most specific to most general
Contusions, 	hematoma, 	bruise 
(most specific)			(most general)

## UMLS in Practice

- Databases: 3 separate sets of relational files
- Tools:
**MetamorphoSys (installation and customization)**
**Web interface Knowledge Source Server (UMLSKS)**
**Application programming interfaces**
**lvg (lexical programs)**
**RRF Subset Browser**
- Distributed on DVD; downloaded from UMLSKS

- The UMLS is *not* an end-user application

## UMLS Uses

- Information retrieval
- Thesaurus construction
- Natural language processing
- Automated indexing
- Electronic health records (EHR)
- Distribution mechanism for HIPAA, CHI, PHIN regulatory standards

**Notes:**
20 year R&D project; NLM funds research, and UMLS is a subject of much research
in order of use, as reported by users and discussed in the  informatics/research and literature (see MEDLINE)
Annual licensee reporting requirement 
IR systems use term mapping of user queries. For example, in MEDLINE/PubMed, when a user searches heart attack, the system uses UMLS to map to the preferred term “myocardial infarction” enabling the system to pull up relevant articles  
Thesaurus construction: use Meta to create 
NLP systems use UMLS KS and lexical tools to abstract away from minor variations in words and terms, identify biomedical concepts in full text, and determine the likely relationships among these concepts. 
Automated indexing systems use NLP tools and techniques to assign subject headings to documents. 
Creation of EHRs can be enhanced by availability of vocs already mapped to one another within the UMLS.  By incorporating the UMLS into an electronic patient record system programmers can include automatic mapping among the various vocabularies and classifications that will be needed within an electronic patient record. 
Health data standards; NLM role in supporting developing and maintenance of standards, includes the commitment to distribute standards via the UMLS

## License Agreements

- Semantic Network, SPECIALIST Lexicon & Lexical Tools
- terms and conditions of use online
- Metathesaurus
- license agreement process
- some restrictions
- 2. No charges, usage fees or royalties will be paid to NLM.
- 5. Within 30 days of the end of any calendar year ... provide NLM with a brief report
- 11.c. required to include ... identifiers from ... the original source vocabularies
- 12. For material ... from some sources additional restrictions ... may apply.

## What is the UMLS?

*Overview through an example *

## Metathesaurus: clusters terms by meaning

- Synonymous terms clustered into a concept
- Preferred term is chosen
- Unique identifier (CUI) is assigned

- Addison’s disease

- Addison’s disease	Metathesaurus      	PN
- Addison’s disease                	SNOMED CT        	PT	363732003
- Addison’s Disease                	MedlinePlus      	PT   	T1233
- Addison Disease                  	MeSH		PT	D000224
- Bronzed disease	SNOMED Intl 1998     SY           DB-70620  Deficiency; corticorenal,     	ICPC2-ICD10	PT	MTHU021575
-     primary                                  	    Thesaurus
- Primary Adrenal Insufficiency    	MeSH		EN	D000224
- Primary hypoadreanlism    	MedDRA		LT	10036696
- syndrome, Addison

- C0001403

**Notes:**
In the Meta, all the different names given to a meaning in the various sources are gathered together into a concept. 
A preferred name is chosen:  from a ranking of sources, one name “wins” to be displayed in an application, to allow us to discuss a concept on some common ground.
Every concept is given a Concept Unique Identifier:  the name that never changes, the name with no meaning.
Here are just of the 17 different names for Addison’s disease in the Metathesaurus from 24 sources.
In addition to the additional terms, or synonyms, all other information from the source is included.  

## Cluster of synonymous terms

- [...]

## Semantic Network

- 135 Semantic Types
- Broad subject categories (Clinical Drug, Virus)
- Ex:  Addison’s Disease
**Semantic Type: Disease or Syndrome**
- 54 Semantic Relationships
- Links between categories (isa, causes, treats)
- Ex: Virus** causes** Disease or Syndrome
- Together
- Form the structure of the semantic network
- Broadly categorize the biomedical domain

**Notes:**
Semantic Types
Broad, or high level categories
Provide a consistent categorization of all concepts in the Metathesaurus
Every concept in the M is assigned at least one; some two-three

Semantic Relationships
Defines the useful relationships that may exist between these categories

Types + Relationships = Network
Represents the biomedical domain
Provides a structure for the Metathesaurus
Reduces the complexity of the UMLS by grouping concepts 

## A portion of the Semantic Network

## SPECIALIST Lexicon

- General English lexicon of common words, biomedical terms
- Used by SPECIALIST Natural Language Processing System
- Lexical records contain encoded information:
- syntactic (how words are put together),
- morphological (inflection, derivation, and compounding), and
- orthographic (spelling) information
- Lexical tools process terms
- Used in Metathesaurus production

- Adrenal gland diseases
- Adrenal disorder
- Disorder of adrenal gland
- Diseases of the adrenal glands
- C0001621

## SPECIALIST Lexicon

- {base=disease entry=E0023270    cat=noun    variants=_[reg](http://umlsks.nlm.nih.gov/kss/servlet/Turbine/action/DoLexInflVarSearch/template/lexicon%2CLexInflVarScreen.vm;jsessionid=E139E7469ACCF004BEA0118405909263.kss3?base=disease&release=2005AA&eui=E0023270&cat=noun&variant=reg)_    variants=_[uncount](http://umlsks.nlm.nih.gov/kss/servlet/Turbine/action/DoLexInflVarSearch/template/lexicon%2CLexInflVarScreen.vm;jsessionid=E139E7469ACCF004BEA0118405909263.kss3?base=disease&release=2005AA&eui=E0023270&cat=noun&variant=uncount)_    compl=pphr(of,np|bone|)    compl=pphr(of,np|breast|)    compl=pphr(of,np|liver|)    compl=pphr(of,np|ovary|)}

## Summary

- Metathesaurus:
- clusters terms into concepts – assigns unique identifier
- Semantic Network:
- defines relationships between concepts, organizes concepts into categories
- Lexicon and Lexical Tools:
- process terms for entry into the Metathesaurus