Medical Subject Headings MeSH Unified Medical Language System UMLS

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Medical Subject Headings (MeSH)Unified Medical
Language System(UMLS)

• Evangelos Milios

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What is MeSH?

• Controlled vocabulary thesaurus
• Hierarchical structure
• Concepts at various levels of specificity
• PubMed citations indexed using MeSH
• Help find the most suitable MeSH terms for
  searching PubMed

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Updating MeSH

• Updated manually by subject specialists
• Suggestions from indexers and others
• Staff collect new terms as they appear in
• The scientific literature
• Emerging areas of research
• Recommend addition to MeSH

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MeSH Browser

• Online vocabulary look-up aid
• Stand-alone (not linked to PubMed content)
• Look-up can be restricted with
• Main Headings
• Qualifiers
• Supplementary concepts
• Limited to fields
• Heading mapped to (HM)
• Indexing Information (II)
• Pharmacological action (PA)
• CAS Registry / EC Number (RN)
• Related CAS Registry Number (RR)

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Features of the MeSH Vocabulary

• Descriptors (main headings) characterize content
• Qualifiers Qualifier Hierarchies
• Publication types
• Geographical features
• Entry terms (synonyms, cross-references to
  descriptors)
• Complex concepts
• Coordinated (multiple) descriptors jejunal
  enteritis
• Descriptor with qualifiers Monoamine
  Oxidase/deficiency
• Pre-coordinated (for common concepts) Heart
  Surgery

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Entry terms / See cross-references

• Information related to one term found under a
  different term
• See definition found elsewhere
• See related related headings not in the same
  subcategory of MeSH tree structures
• See related presence of other descriptors
  related to the topic conceptually
• Consider also with anatomical descriptors
• Used for
• Online searching
• Indexing
• Cataloging

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MeSH Tree Structures

• 15 categories (organisms, diseases, drugs, )
• Subcategories
• Within a subcategory, descriptors arranged from
  general to specific (11 hierarchical levels)
• A MeSH descriptor may appear in multiple places
• Each descriptor followed by the number showing
  its tree location

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MeSH and retrieval

• Citations in PubMed are searchable by
• MeSH headings
• Any word in title, abstract, or citation entry
• A combination of the above
• Search strategy
• Begin with text word search
• Look at MeSH terms used in good citations found
• Use them in iterative searches
• Use MeSH to adjust level of specificity

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Availability

• MeSH is available for downloading

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Unified Medical Language System (UMLS)

• Aims to facilitate computer systems that
  understand the meaning of biomedical language
• Three knowledge sources
• Metathesaurus
• Semantic Network
• SPECIALIST Lexicon

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Metathesaurus

• Vocabulary database containing
• Biomedical, health-related concepts
• Their names
• Relationships between them
• Organized by concept of meaning
• Concepts assigned to semantic types in Semantic
  network
• Many terms appear also in the SPECIALIST Lexicon
• Custom subsets must be extracted using
  MetamorphoSys to be used effectively

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Semantic Network

• Categorization of concepts in the Metathesaurus
• 135 Semantic types (Nodes)
• 54 relationships (Links)
• Major groupings of semantic types
• Organisms
• Anatomical structures
• Biologic function
• Chemicals
• Events
• Physical objects
• Concepts or ideas

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Relations

• Isa
• Part of
• Conceptual part of
• Contained in
• Process of
• Property of
• Evaluation of

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Biologic Function Hierarchy
What is the type of the links?
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Affects Hierarchy
What is the type of the links?
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(No Transcript)
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SPECIALIST Lexicon

• General English lexicon with many biomedical
  terms
• Lexical programs or tools to handle variants
• Inflectional variants
• Alphabetic case variants
• Word order variants (e.g. human clones, clones
  of humans)

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Summary

• MeSH
• Browser
• Features
• Tree structures
• MeSH in PubMed retrieval
• UMLS
• Metathesaurus
• Semantic network
• SPECIALIST lexicon