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The UMLS Semantic Network

The document discusses the UMLS Semantic Network, which provides an overall conceptual structure for the UMLS by linking semantic types to concepts in the Metathesaurus and providing relationships between types. It describes the initial development of the network in the late 1980s/early 1990s and its current status with over 100 semantic types and 50 relationships. Examples of semantic type and relationship definitions are provided.

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32 views32 pages

The UMLS Semantic Network

The document discusses the UMLS Semantic Network, which provides an overall conceptual structure for the UMLS by linking semantic types to concepts in the Metathesaurus and providing relationships between types. It describes the initial development of the network in the late 1980s/early 1990s and its current status with over 100 semantic types and 50 relationships. Examples of semantic type and relationship definitions are provided.

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laij8883890
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© Attribution Non-Commercial (BY-NC)
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The UMLS Semantic Network

Alexa T. McCray
Center for Clinical Computing
Beth Israel Deaconess Medical Center
Harvard Medical School
[email protected]

The Future of the UMLS Semantic Network


National Library of Medicine, April 7, 2005
UMLS Project
• Begun in 1986
- Well before the advent of the World Wide Web
• GoalTo provide intelligent access to biomedical resources
- in multiple, disparate databases
• Language of those resources of primary interest
• Methodology
- constituency
Consultation with broad medical informatics

- Development of Knowledge Sources


Initial Efforts
• First versions of knowledge sources available to
researchers in early 1990’s
- Metathesaurus (1990)
• Interrelate existing vocabularies, thesauri
- Semantic Network (1990)
• Assignment of semantic types to Metathesaurus concepts
- Information Sources Map (1991)
• Characterization of existing databases, including query
syntax and MeSH indexing
- SPECIALIST Lexicon (1994)
• Syntactic, morphologic, orthographic information about
biomedical and general English terminology
Early Development of the UMLS
Semantic Network (1988-1989)
• UMLS collaborators asked to submit lists of
useful semantic types and potential
relationships between them
- Active participation by BWH, Yale, Pittsburgh
• Purpose
- Consistent
concepts
categorization of all Metathesaurus

• Early attempts at organizing the suggested


types into a network of interrelated types
First Released Version of UMLS
Semantic Network (1990)
• 131Each
semantic types
- semantic types, according to definitions of the types
Metathesaurus concept assigned one or more

and a set of guidelines


• 35 Relationships
relationships
- up approaches and included definitions
developed by top-down and bottom-

• Those deemed to be important for information retrieval


• Review of (implicit) relationships in MeSH and in
MEDLINE citation records
Current Semantic Network

• 135 semantic types


- 2 major hierarchies
•Entity
- Physical Object
- Conceptual Entity
• Event
- Activity
- Phenomenon or Process
• 54 relationships
Sample Semantic Type Definition

UI: T190
STY: Anatomical Abnormality
ABR: anab
STN: A1.2.2
DEF: An abnormal structure, or one that is abnormal in size or location.
UN: Use this type if the abnormality in question can be either an acquired or
congenital abnormality. Neoplasms are not included here. These are given the
type 'Neoplastic Process'. If an anatomical abnormality has a pathologic
manifestation, then it will additionally be given the type 'Disease or
Syndrome', e.g., "Diabetic Cataract" will be double-typed for this reason.
HL: {isa} Anatomical Structure;
{inverse_isa} Congenital Abnormality;
{inverse_isa} Acquired Abnormality
Sample Relationship Definition
UI: T151
RL: affects
ABR: AF
RIN: affected_by
RTN: R3.1
DEF: Produces a direct effect on. Implied here is the altering or influencing of
an existing condition, state, situation, or entity. This includes has a role in,
alters, influences, predisposes, catalyzes, stimulates, regulates, depresses,
impedes, enhances, contributes to, leads to, and modifies.
HL: {isa} functionally_related_to;
{inverse_isa} interacts_with;
{inverse_isa} disrupts;
{inverse_isa} prevents …
STL: [Anatomical Abnormality|Organism];
[Anatomical Abnormality|Physiologic Function] …
Portion of the Entity Hierarchy
Entity

Physical Object Conceptual Entity

Anatomical Substance Idea or


Structure Concept

Anatomical Embryonic Fully Formed Body Functional Spatial


Abnormality Structure Anatomical Substance Concept Concept
Structure

Congenital Acquired Body Body Space Body Location


Abnormality Abnormality System or Junction or Region

Body Part, Organ or Tissue Cell Cell Gene or


Organ Component Component Genome
Relationships
• Hierarchical (isa)
- Among types
•
Animal isa Organism
• Enzyme isa Biologically Active Substance
- Among relationships
•
treats isa affects

• Non-hierarchical (associative)
- Sign or Symptom diagnoses Pathologic Function
- Pharmacologic Substance treats Pathologic Function
Relationships (isa and associative)
A Portion of the Current Semantic Network
Relationships
• Relationship between a pair of semantic
types is a possible link between the
concepts assigned to those semantic types
- Relationship
concept level
may or may not hold at the

• Afrom
child semantic type inherits properties
its parents
Inheritance at Concept Level
Semantic Network

Fully Formed Biologic Function


Anatomical
location of
Structure isa
Pathologic Function
isa Body Part, Organ, isa
or Organ Component Disease or Syndrome

Adrenal
Adrenal
Cortical
Cortex hypofunction

location of
Metathesaurus
Grouping SemanticTypes
• Complexity of domain makes it difficult to
- Navigate and display the knowledge
- Reason with the objects in the domain
- Comprehend the conceptual space
• Semantic Network reduces the conceptual
complexity of the UMLS, but
- For some purposes, smaller and coarser-
grained groupings are needed
Semantic Type Groupings (2001)

• Clustered the larger set of semantic types


into a small number of general groups
• Total of 15 groupings
• Effected an almost complete partitioning
of the UMLS Metathesaurus
Grouping Principles

• Completeness
- Groups must cover the full domain
• Parsimony
- Number
possible
of groups should be as small as

• Naturalness
- Groups must be acceptable to a domain expert
Grouping Principles (cont.)

• Utility
- Groups must be useful for some purpose
• Semantic validity
- Groups must be semantically coherent
- Relationships shared by members of group
• Exclusivity
- Groups fully partition the domain
Groupings (2001 Data)
Some Relationships between Semantic Groups
Distribution of Concepts in
the UMLS (2001 Data)
Distribution of Concepts in
PDQ (2001 Data)
Research Applications of the
Semantic Network
• Natural language processing
• Information extraction and retrieval
• Ontological research
• Subsetting the domain
- particular set of semantic types
E.g. extract all Metathesaurus concepts with a

• Conceptualizing the domain


- another oriented to diseases
E.g., one resource oriented heavily to chemicals,
Summary
• UMLS Semantic Network
- UMLS by
Provides overall conceptual structure to the

• Linking semantic types to Metathesaurus


concepts
• Providing a set of relationships to interrelate the
types and (by inference) the concepts
• Allowing users to extract all concepts with a
particular type
- Used in a number of research applications
- Variety of enhancements possible
Some References
• McCray AT, Hole WT. The scope and structure of the
first version of the UMLS Semantic Network. Proc
Annu Symp Comput Appl Med Care, 1990; 126‑130.
• McCray AT. The UMLS Semantic Network. Proc
Annu Symp Comput Appl Med Care. 1989; 503-7.
• McCray AT. Representing biomedical knowledge in the
UMLS Semantic Network. High‑Performance Medical
Libraries: Advances in Information Management for
the Virtual Era. Westport: Meckler Publishing, 1993;
45‑55.
Some References (cont.)
• McCray AT, Nelson SJ. The representation of meaning
in the UMLS. Methods Inf Med. 1995; 34(1‑2):193‑201.
• McCray AT, Burgun A, Bodenreider O. Aggregating
UMLS semantic types for reducing conceptual
complexity. MEDINFO. 2001; 216-220.
• McCray AT. An upper level ontology for the
biomedical domain. Comp Funct Genom 2003; 4:80-4.
• Bodenreider O, McCray AT. Exploring semantic
groups through visual approaches. Journal of
Biomedical Informatics 2003;36(6):414-432.

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