# Presentation: 167058

## Unified Medical Language System® (UMLS®) 

- NLM Presentation Theater
- MLA 2005
- May 16 & 17, 2005
- Rachel Kleinsorge

**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 is: 

- Metathesaurus

- Semantic Network

- SPECIALIST Lexicon & Lexical Tools

- Categories and relationships

- Concepts

- Lexicon, lexical databases and programs

- The Knowledge Sources
- (delivered as machine readable files)

**Notes:**
The UMLS project produces and distributes three electronic knowledge sources and some associated multi-purpose software tools for use by system developers

A set of multi-purpose tools or “intellectual middleware” for system developers

## 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”
- Complementary to IAIMS

- [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.»

- (Integrated Academic
- Information Management 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

- 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)
- problems in mapping and aggregating within and across databases and systems

## UMLS in Practice

- Intellectual “middleware” = a set of multi-purpose tools for system developers
- 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**

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

## UMLS Uses

- Information retrieval
- Thesaurus construction
- Natural language processing
- Automated indexing
- Electronic patient records

## License Agreements

- Semantic Network, SPECIALIST Lexicon, and Lexical Programs
- terms and conditions of use online
- Metathesaurus
- liscense 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 *

## Addison’s Disease in medical vocabularies

- Synonyms: different terms
- Addisonian syndrome
- Bronzed disease
- Addison melanoderma
- Asthenia pigmentosa
- Primary adrenal deficiency
- Primary adrenal insufficiency
- Primary adrenocortical insufficiency
- Chronic adrenocortical insufficiency
- Contexts: different hierarchies

- symptoms

- clinical
- variants

- eponym

**Notes:**
rare endocrine disorder

occurs when the adrenal glands do not produce enough of the hormone cortisol

sometimes called chronic adrenal insufficiency, or hypocortisolism

Symptoms – pigmentation of the skin, fatigue, weakness, & low blood pressure 

There are many synonyms, or names, for Addison’s Disease in the various terminologies included in the Metathesaurus.  Sometimes the name is eponymous, as in Addisonian syndrome.  Sometimes it refers to the symptoms like Bronzed disease, and so on.  Sometimes there are clinical variants.  And frequently these terms appear in different contexts, with varying degrees of granularity or specificity.  Context means the hierachical arrangements of terms in a vocabulary.  

## Metathesaurus gathers and organizes terms

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

- Adrenal Gland Diseases

- Adrenal gland diseases	MeSH	D000307
- Adrenal disorder	AOD	0000005418
- Disorder of adrenal gland	Read	C15z.
- Diseases of the adrenal glands	SNOMED	DB-70000

- C0001621

**Notes:**
In the UMLS Metathesaurus, all the different names we give to a meaning, or synonyms, are gathered together into a concept.  A preferred name is chosen. The concept is given a Concept Unique Identifier.  Here is an example of some of the different names for Addison’s disease in several vocabularies.  You will notice that while the concept is given the unique identifier of C0001621 in the Metathesaurus, the individual unique identifiers for the names in the vocabularies are retained. So for example, the D MeSH unique identifier for adrenal gland diseases is kept.

## Cluster of synonymous terms

- [...]

## Semantic Network

- Organizes terms into 135 broad subject categories
- Semantic Types (Clinical Drug, Virus)
- Addison’s Disease **Semantic Type: ****Disease or Syndrome**
- Defines 54 Semantic Relationships
- Links between categories (isa, causes, treats)
- Ex: Virus** ****causes **Disease or Syndrome
- Together, types and relations:
- 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 

## Lexical Tools process terms and text

- Organization is accomplished using:
- Normalization
- Semantic pre-processing
- UMLS editors

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

## 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