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The UMLS Semantic Network
Alexa T. McCrayCenter for Clinical Computing
Beth Israel Deaconess Medical CenterHarvard Medical School
mccray@bidmc.harvard.edu
The Future of the UMLS Semantic Network National Library of Medicine, April 7, 2005
UMLS ProjectUMLS Project
• Begun in 1986
- Well before the advent of the World Wide Web
• Goal
- To provide intelligent access to biomedical resources in multiple, disparate databases• Language of those resources of primary interest
• Methodology
- Consultation with broad medical informatics constituency
- Development of Knowledge Sources
Initial EffortsInitial 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 Early Development of the UMLS Semantic Network (1988-1989)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 categorization of all Metathesaurus
concepts
• Early attempts at organizing the suggested types into a network of interrelated types
First Released Version of UMLS First Released Version of UMLS Semantic Network (1990)Semantic Network (1990)
• 131 semantic types
- Each Metathesaurus concept assigned one or more semantic types, according to definitions of the types and a set of guidelines
• 35 relationships
- Relationships developed by top-down and bottom-up approaches and included definitions• Those deemed to be important for information retrieval
• Review of (implicit) relationships in MeSH and in MEDLINE citation records
Current Semantic NetworkCurrent Semantic Network
•135 semantic types
-2 major hierarchies• Entity
- Physical Object
- Conceptual Entity
• Event- Activity
- Phenomenon or Process
•54 relationships
Sample Semantic Type DefinitionSample Semantic Type Definition
UI: T190STY: Anatomical AbnormalityABR: anabSTN: A1.2.2DEF: 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 orcongenital abnormality. Neoplasms are not included here. These are given thetype 'Neoplastic Process'. If an anatomical abnormality has a pathologicmanifestation, then it will additionally be given the type 'Disease orSyndrome', 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 DefinitionSample Relationship Definition
UI: T151RL: affectsABR: AFRIN: affected_byRTN: R3.1DEF: Produces a direct effect on. Implied here is the altering or influencing ofan 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] …
BodySystem
Body Spaceor Junction
Body Locationor Region
Entity
Physical Object Conceptual Entity
Substance Idea orConcept
FunctionalConcept
SpatialConcept
BodySubstance
EmbryonicStructure
Fully FormedAnatomicalStructure
Body Part, Organ orOrgan Component
Tissue Cell CellComponent
Gene orGenome
AnatomicalStructure
CongenitalAbnormality
AcquiredAbnormality
AnatomicalAbnormality
Portion of the Entity HierarchyPortion of the Entity Hierarchy
RelationshipsRelationships•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
RelationshipsRelationships
•Relationship between a pair of semantic types is a possible link between the concepts assigned to those semantic types
-Relationship may or may not hold at the concept level
•A child semantic type inherits properties from its parents
Inheritance at Concept LevelInheritance at Concept LevelSemantic Network
Metathesaurus
AdrenalCortex
AdrenalCortical
hypofunction
Disease or SyndromeBody Part, Organ,
or Organ Component
Pathologic Functionisa
Biologic Function
isa
Fully FormedAnatomical
Structure
isa
location of
location of
Grouping SemanticTypesGrouping 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)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 PrinciplesGrouping Principles
•Completeness
-Groups must cover the full domain
•Parsimony
-Number of groups should be as small as possible
•Naturalness
-Groups must be acceptable to a domain expert
Grouping Principles (cont.)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
GroupingsGroupings (2001 Data) (2001 Data)
Some Relationships between Semantic GroupsSome Relationships between Semantic Groups
Distribution of Concepts in Distribution of Concepts in the UMLS (2001 Data)the UMLS (2001 Data)
Distribution of Concepts in Distribution of Concepts in PDQ (2001 Data)PDQ (2001 Data)
Research Applications of the Research Applications of the Semantic NetworkSemantic Network
• Natural language processing
• Information extraction and retrieval
• Ontological research
• Subsetting the domain
- E.g. extract all Metathesaurus concepts with a particular set of semantic types
• Conceptualizing the domain
- E.g., one resource oriented heavily to chemicals, another oriented to diseases
SummarySummary
•UMLS Semantic Network
-Provides overall conceptual structure to the UMLS by• 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 ReferencesSome 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.)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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