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UMLS BASICS. The Unified Medical Language System ( UMLS ). Facilitate the development of computer systems that behave as if they "understand" the meaning of the language of biomedicine and health. There are three UMLS Knowledge Sources: The Metathesaurus The Semantic Network

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the unified medical language system umls
The Unified Medical Language System (UMLS)
  • Facilitate the development of computer systems that behave as if they "understand" the meaning of the language of biomedicine and health.
  • There are three UMLS Knowledge Sources:
  • The Metathesaurus
  • The Semantic Network
  • The SPECIALIST Lexicon & Lexical Tools
the metathesaurus
The Metathesaurus
  • large, multi-purpose, and multi-lingual vocabulary database 
  • contains information about biomedical and health related concepts, their various names, and the relationships among them.
  • built from the electronic versions of many different classifications, code sets, and lists of controlled terms used in patient care, health services billing, public health statistics, indexing and cataloging biomedical literature, and/or basic, clinical, and health services research.
slide5

Contains over five million terms, or names

  • names are organized into concepts and assigned a unique identifier
  • data is stored in a series of relational tables and files
  • Installed using MetamorphoSys
  • It is not a vocabulary.
the semantic network
The Semantic Network
  • consists of semantic types and semantic relationships.
  • Semantic types are broad subject categories, like Disease or Syndrome or Clinical Drug.
  • Semantic relationships are the relationships that exist between semantic types.
  • The Semantic Network is used in applications to help interpret meaning.
specialist lexicon and lexical tools
SPECIALIST Lexicon and Lexical Tools
  • English lexicon containing many words from the biomedical domain.
  • consists of a set of lexical entries
  • Each entry represents a word (lexical item)
  • describes the morphologic, orthographic and syntactic properties of a word.
  • collection of java programs that process natural language words and terms
  • Together the SPECIALIST Lexicon and lexical tools allow users to develop Natural Language Processing programs.
metathesaurus
Metathesaurus
  • Over 100 vocabularies, code sets, and thesauri, or "source vocabularies" are brought together to create the Metathesaurus
  • Terms are assigned a CUI
  • 62 % of vocabularies are in English
  • Terms from 17 other languages.
source vocabularies
Source Vocabularies
  • different types of biomedical vocabularies
  • different ways to categorize them
  • Some vocabularies fall into more than one category
  • Major categories include:
  • Diagnosis
    • Logical Observation Identifier Names and Codes (LOINC)
  • Procedures & Supplies
    • Current Procedural Terminology (CPT)
  • Diseases
    • International Classification of Diseases and Related Health Problems (ICD-10)
  • Comprehensive Vocabularies/Thesauri
    • Systematized Nomenclature of Medicine-Clinical Terms (SNOMED CT)
unique identifiers in the metathesaurus
Unique Identifiers in the Metathesaurus
  • When a concept is added to the Metathesaurus it receives a unique identifier and is placed in the Metathesaurus structure. This structure has four levels of specification:
  • Concept Unique Identifiers (CUI)
  • Lexical (term) Unique Identifiers (LUI) 
  • String Unique Identifiers (SUI)
  • Atom Unique Identifiers (AUI)
semantic network
Semantic Network
  • Semantic types (high level categories)
  • Semantic relationships (relationships between semantic types
  • Used to categorize any medical vocabulary.
  • 133 semantic types.
  • Every concept is assigned atleastone semantic type.
  • Semantic types are listed in the Metathesaurus file MRSTY.RRF.
  • Semantic types and relationships help with interpreting the meaning that has been assigned to the Metathesaurus concept.
identifiers in semantic network
Identifiers in semantic network
  • The information associated with each semantic type includes:
  • A unique identifier
  • A tree number indicating its position in the `isa' hierarchy
  • A definition
  • Its immediate parent and children
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The information associated with eachrelationship includes:

  • A unique identifier
  • The semantic type
  • A tree number
  • A definition
  • Examples
  • The set of semantic types that can plausibly be linked by this relationship.
semantic types
Semantic Types
  • Examples of the semantic types:
  • Organisms
  • Anatomical structures
  • Biologic function
  • Chemicals
  • Events
  • Physical objects
  • Concepts or ideas
  • Semantic types are arranged in a hierarchy which is organized into two main categories, Entity and Event.
  • Entity example : amphibian, carbohydrate
  • Event example: social behavior, mental process
the semantic relationship
The semantic relationship
  •  the primary link between most semantic types is the ‘isa’ relationship
  • Some examples of the 'isa' relationship:
  • Animal isa Entity
  • Carbohydrate isa Chemical
  • Human isa Mammal
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There are five major, non-hierarchical relationships:

  • Physically related to
  • Spatially related to
  • Temporally related to
  • Functionally related to
  • Conceptually related to
lexicon
Lexicon
  • There is one lexical entry for each spelling or set of spelling variants in a particular part of speech. Each lexical record contains information on:
  • Base form of the term
  • The part of speech
  • A unique identifier
  • Rules for spelling variants
lexical tools
Lexical tools
  • The lexical tools are a set of computer programs designed to aid in natural language processing
  • The three primary programs are:
  • A lexical variant generator (LVG)
  • A normalized string generator (Norm)
  • A word Index generator (Wordind)
reference
Reference
  • http://www.nlm.nih.gov/research/umls/new_users/online_learning/OVR_001.htm