# Presentation: 215457

***The UMLS Semantic Network***
**Alexa T. McCray**
**Center for Clinical Computing**
**Beth Israel Deaconess Medical Center**
**Harvard Medical School**
**mccray@bidmc.harvard.edu**

***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**
**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 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 categorization of all Metathesaurus concepts**
**Early attempts at organizing the suggested types into a network of interrelated types**

## First Released Version of UMLS 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 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

**Portion of the Entity Hierarchy**

## 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)

**Relationships (isa and associative)**

## A Portion of the Current Semantic Network

**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 may or may not hold at the concept level**
**A child semantic type inherits properties from its parents **

## Inheritance at Concept Level

**Inheritance at Concept Level**

- Semantic Network

- 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 of groups should be as small as possible**
**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**
**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**

## Summary

**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 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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