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Medical terminologies

Medical terminologies: UMLS
UMLS®
name Unified Medical Language System
summary A controlled vocabulary; "Metathesaurus and semantic network with lexical applications".

UMLS is a compendium of a large number of national and international vocabularies and classifications (over 100) and provides a mapping structure between them.
clinical focus  
developed by the National Library of Medicine, USA
introduced The UMLS R&D project was initiated in 1986
current version Current UMLS Release - 2006AA (March 2006)
background / derivation The Unified Medical Language System research and development program was intitiated by Donald A. B. Lindberg, M.D., Director of the US National Library of Medicine (NLM) in 1986.
features
The UMLS is made up of three main knowledge components:
  • The Metathesaurus® of medical concepts (taken from established vocabularies such as SNOMED, ICD-9-CM, and MeSH) and inter-concept relationships whose primary purpose is to map between coding systems and therefore provide information exchange between different clinical databases and systems.
  • The Semantic Network, which specifies categories to which medical concepts defined in the Metathesaurus can belong and the semantic relationships that can be assigned between these concepts and their attributes. 135 semantic types and 54 semantic network relationships exist [Tilley and Willis, 2004].
  • The SPECIALIST Lexicon which"contains syntactic, morphological, and orthographic information for biomedical and common words in the English language. The Lexicon and its associated lexical resources are used to generate the indexes to the Metathesaurus and also have wide applicability in natural language processing applications in the biomedical domain." [NLM]. The SPECIALIST Lexicon includes over 200,000 lexical items [Tilley and Willis, 2004].

  • UMLS supports conversion of terms from one controlled medical vocabulary to another. "The UMLS approach assumes continuing diversity in the formats and vocabularies of different information sources and in the language employed by different elements of the biomedical community. It is not an attempt to build a single standard biomedical vocabulary." [Humphreys and Schuyler, 1993].
  • standards  
    in use " The NLM ... uses UMLS components to enhance retrieval from a number of its information services, including the MEDLINE database available via PubMed, the ClinicalTrials.gov database of ongoing clinical trials sponsored by the National Institutes of Health and other organizations, and the NLM Gateway, which provides a single point of entry to a number of different NLM databases. The Library also relies heavily on the UMLS resources in its natural language processing and digital library research programs." [NLM]
    access Available free of charge under a licence agreement. The UMLS Knowledge Sources and related lexical programs are accessible via the UMLS Web-based Knowledge Source Server (UMLSKS) and "are designed primarily for use by system developers". They can also be used "as reference tools for database builders, librarians and other information professionals" [NLM].

    tools  bullet  UMLS Knowlege Source Server (restricted to registered users) "The UMLSKS is a set of web based interaction tools and a programmer interface to allow users and developers access to the biomedical terminologies found within the UMLS."  bullet  MetaMap Transfer (MMTx) - maps text to concepts in the UMLS Metathesaurus or discovers Metathesaurus concepts in text  bullet  Mycroft terminology browser from Apelon - includes UMLS® Metathesaurus®. ONLY for use within the United States.  bullet  Apelon Distributed Terminology System (DTS) "for managing, integrating, deploying and extending standard terminologies" (licence required).  bullet  Metamorphosys - the UMLS install and customization program which allows a user to create customized Metathesaurus subsets
    references

    Tilley CB, Willis J. Unified Medical Language System basics (PDF course presentation). National Library of Medicine, 1 November 2004.

    []   [NLM]

    Very comprehensive and detailed 1 day course on UMLS. Includes 307 slides (6.36MB).

    " Course Outline: What is the UMLS?; The UMLS and Controlled Vocabularies; How to use the UMLS?; Obtaining a license; Remote access; Knowledge Source Server (UMLSKS); UMLSKS Application programming interface (API); Local installation and customization (MetamorphoSys); UMLS and HIPAA, Applications, What’s new, and Questions. "

    Lindberg DA, Humphreys BL, McCray AT. The Unified Medical Language System. Methods Inf Med 1993 Aug;32(4):281-91.

    [PubMed]
    []

    " In 1986, the National Library of Medicine began a long-term research and development project to build the Unified Medical Language System (UMLS). The purpose of the UMLS is to improve the ability of computer programs to "understand" the biomedical meaning in user inquiries and to use this understanding to retrieve and integrate relevant machine-readable information for users. Underlying the UMLS effort is the assumption that timely access to accurate and up-to-date information will improve decision making and ultimately the quality of patient care and research. The development of the UMLS is a distributed national experiment with a strong element of international collaboration. The general strategy is to develop UMLS components through a series of successive approximations of the capabilities ultimately desired. Three experimental Knowledge Sources, the Metathesaurus, the Semantic Network, and the Information Sources Map have been developed and are distributed annually to interested researchers, many of whom have tested and evaluated them in a range of applications. The UMLS project and current developments in high-speed, high-capacity international networks are converging in ways that have great potential for enhancing access to biomedical information. "
    Schuyler PL, Hole WT, Tuttle MS, Sherertz DD. The UMLS Metathesaurus: representing different views of biomedical concepts. Bull Med Libr Assoc. 1993 Apr;81(2):217-22.

    [PubMed]
    []

    " The UMLS Metathesaurus is a compilation of names, relationships, and associated information from a variety of biomedical naming systems representing different views of biomedical practice or research. The Metathesaurus is organized by meaning, and the fundamental unit in the Metathesaurus is the concept. Differing names for a biomedical meaning are linked in a single Metathesaurus concept. Extensive additional information describing semantic characteristics, occurrence in machine-readable information sources, and how concepts co-occur in these sources is also provided, enabling a greater comprehension of the concept in its various contexts. The Metathesaurus is not a standardized vocabulary; it is a tool for maximizing the usefulness of existing vocabularies. It serves as a knowledge source for developers of biomedical information applications and as a powerful resource for biomedical information specialists. "

    Humphreys, BL and PL Schuyler, The Unified Medical Language System: Moving beyond the vocabulary of bibliographic retrieval. In: Broering NC, ed. High- Performance Medical Libraries: advanced information management for the virtual era. Westport (CT): Meckler;1993. p. 31-44.

    []   []

    " The National Library of Medicine's (NLM) Medical Subject Headings (MeSH) is an extensive biomedical thesaurus used to index, catalog, and retrieve citations to the biomedical literature. It is one of a number of source vocabular ies for the Unified Medical Language System (UMLS), a major NLM research and development program designed to help users to retrieve and integrate information from a variety of disparate information sources. The information sources of interest include bibl iographic databases, patient records systems, factual databanks, and knowledge bases. The UMLS project has produced three new Knowledge Sources: a Metathesaurus of concepts and terms from vocabularies and classifications used in different types of biomedi cal information sources: a Semantic Network of sensible relationships among the broad semantic types or categories to which all Metathesaurus concepts are assigned; and an information Sources Map that describes the scope, content, and access conditions fo r publicly available biomedical information sources. The UMLS Knowledge Sources are intended for use by system developers and can be accessed by a variety of interface programs to interpret user inquiries, identify sources of information relevant to these queries, and retrieve the relevant information. A number of specific projects are underway to assess the usefulness of the current versions of the UMLS Knowledge Sources and to provide feedback that can guide their future development. "

    Fung KW, Hole WT, Nelson SJ et al. Integrating SNOMED CT into the UMLS: an exploration of different views of synonymy and quality of editing. J Am Med Inform Assoc. 2005 Jul-Aug;12(4):486-94.

    [PubMed]   []

    " OBJECTIVE: The integration of SNOMED CT into the Unified Medical Language System (UMLS) involved the alignment of two views of synonymy that were different because the two vocabulary systems have different intended purposes and editing principles. The UMLS is organized according to one view of synonymy, but its structure also represents all the individual views of synonymy present in its source vocabularies. Despite progress in knowledge-based automation of development and maintenance of vocabularies, manual curation is still the main method of determining synonymy. The aim of this study was to investigate the quality of human judgment of synonymy. DESIGN: Sixty pairs of potentially controversial SNOMED CT synonyms were reviewed by 11 domain vocabulary experts (six UMLS editors and five noneditors), and scores were assigned according to the degree of synonymy. MEASUREMENTS: The synonymy scores of each subject were compared to the gold standard (the overall mean synonymy score of all subjects) to assess accuracy. Agreement between UMLS editors and noneditors was measured by comparing the mean synonymy scores of editors to noneditors. RESULTS: Average accuracy was 71% for UMLS editors and 75% for noneditors (difference not statistically significant). Mean scores of editors and noneditors showed significant positive correlation (Spearman's rank correlation coefficient 0.654, two-tailed p < 0.01) with a concurrence rate of 75% and an interrater agreement kappa of 0.43. CONCLUSION: The accuracy in the judgment of synonymy was comparable for UMLS editors and nonediting domain experts. There was reasonable agreement between the two groups. "

    contact

    National Library of Medicine
    8600 Rockville Pike
    Bethesda, MD 20894
    USA

     bullet  Contact NLM

    links  bullet  UMLS (NLM)  bullet  UMLS Metathesaurus  bullet  UMLS Semantic Network  bullet  SPECIALIST lexicon  bullet  License Agreement for use of the UMLS® Metathesaurus®  bullet   "A Dummy's Guide to UMLS" (Powerpoint slides) a partial overview of the UMLS semantic net and Metathesaurus by Jeremy Rogers of Manchester University  bullet  UMLS introduction by Enrico Coiera (taken from Guide to Health Informatics, Arnold, 2003) (AHIC)

    acknowledgements
     
    page history
    Entry on OpenClinical: 09 August 2005
    Last main update: 29 August 2005 (08 May 2006)

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