unified medical language system

Summary

Summary: A research and development program initiated by the NATIONAL LIBRARY OF MEDICINE to build knowledge sources for the purpose of aiding the development of systems that help health professionals retrieve and integrate biomedical information. The knowledge sources can be used to link disparate information systems to overcome retrieval problems caused by differences in terminology and the scattering of relevant information across many databases. The three knowledge sources are the Metathesaurus, the Semantic Network, and the Specialist Lexicon.

Top Publications

  1. Humphreys B, Lindberg D. The UMLS project: making the conceptual connection between users and the information they need. Bull Med Libr Assoc. 1993;81:170-7 pubmed
    ..The goal of the National Library of Medicine's Unified Medical Language System (UMLS) project is to facilitate the development of conceptual connections between users and relevant ..
  2. Berman J. A tool for sharing annotated research data: the "Category 0" UMLS (Unified Medical Language System) vocabularies. BMC Med Inform Decis Mak. 2003;3:6 pubmed
    ..The largest curated listing of biomedical terms is the the National Library of Medicine's Unified Medical Language System (UMLS)...
  3. Fung K, Bodenreider O, Aronson A, Hole W, Srinivasan S. Combining lexical and semantic methods of inter-terminology mapping using the UMLS. Stud Health Technol Inform. 2007;129:605-9 pubmed
    ..The combined method outperformed both methods, achieving coverage of 91%, recall of 43% and precision of 27%. It is also possible to customize the method of combination to optimize performance according to the task at hand. ..
  4. Zhang L, Perl Y, Halper M, Geller J, Hripcsak G. A lexical metaschema for the UMLS semantic network. Artif Intell Med. 2005;33:41-59 pubmed
    ..It compares favorably with the cohesive metaschema derived via the SN's relationship configuration. ..
  5. Stevenson M, Guo Y, Gaizauskas R, Martinez D. Disambiguation of biomedical text using diverse sources of information. BMC Bioinformatics. 2008;9 Suppl 11:S7 pubmed publisher
    ..Disambiguation of biomedical terms benefits from the use of information from a variety of sources. In particular, MeSH terms have proved to be useful and should be used if available. ..
  6. Fan J, Friedman C. Semantic classification of biomedical concepts using distributional similarity. J Am Med Inform Assoc. 2007;14:467-77 pubmed
    ..We developed a distributional similarity approach to classify the Unified Medical Language System (UMLS) concepts...
  7. Liu H, Johnson S, Friedman C. Automatic resolution of ambiguous terms based on machine learning and conceptual relations in the UMLS. J Am Med Inform Assoc. 2002;9:621-36 pubmed
    ..8% and the overall recall was 50.6%. UMLS conceptual relations and MEDLINE abstracts can be used to automatically acquire knowledge needed for resolving ambiguity when mapping free-text to UMLS concepts. ..
  8. Taboada M, Lalín R, Martinez D. An automated approach to mapping external terminologies to the UMLS. IEEE Trans Biomed Eng. 2009;56:1598-605 pubmed publisher
    ..In this study, we propose an automated approach to mapping external terminologies to the Unified Medical Language System (UMLS)...
  9. Thirion B, Robu I, Darmoni S. Optimization of the PubMed Automatic Term Mapping. Stud Health Technol Inform. 2009;150:238-42 pubmed
    ..The proposed query is significantly more precise than the current PubMed query (54.5% vs. 27%). The optimized query proposed would be easy to implement into PubMed. ..

More Information

Publications62

  1. McInnes B, Pedersen T, Pakhomov S. UMLS-Interface and UMLS-Similarity : open source software for measuring paths and semantic similarity. AMIA Annu Symp Proc. 2009;2009:431-5 pubmed
    ..In this paper, we introduce two new open-source frameworks based on the Unified Medical Language System (UMLS). These frameworks consist of the UMLS-Similarity and UMLS-Interface packages...
  2. Leroy G, Rindflesch T. Effects of information and machine learning algorithms on word sense disambiguation with small datasets. Int J Med Inform. 2005;74:573-85 pubmed
    ..A naïve Bayes classifier was trained for 15 words with 100 examples for each. Unified Medical Language System (UMLS) semantic types assigned to concepts found in the sentence and relationships between these ..
  3. Jimeno Yepes A, McInnes B, Aronson A. Exploiting MeSH indexing in MEDLINE to generate a data set for word sense disambiguation. BMC Bioinformatics. 2011;12:223 pubmed publisher
    ..We present a method that can be used to automatically develop a WSD test collection using the Unified Medical Language System (UMLS) Metathesaurus and the manual MeSH indexing of MEDLINE...
  4. Jiang G, Solbrig H, Chute C. Quality evaluation of cancer study Common Data Elements using the UMLS Semantic Network. J Biomed Inform. 2011;44 Suppl 1:S78-85 pubmed publisher
    ..This approach could provide useful insight about how to build mechanisms of quality assurance in a meta-data repository. ..
  5. Fabry P, Baud R, Burgun A, Lovis C. Amplification of Terminologia anatomica by French language terms using Latin terms matching algorithm: a prototype for other language. Int J Med Inform. 2006;75:542-52 pubmed
    ..We consider this work as a starting point for adding terms to other knowledge sources, such as the foundational model of anatomy or the Unified Medical Language System (UMLS).
  6. Alecu I, Bousquet C, Mougin F, Jaulent M. Mapping of the WHO-ART terminology on Snomed CT to improve grouping of related adverse drug reactions. Stud Health Technol Inform. 2006;124:833-8 pubmed
    ..We plan to improve our method in order to retrieve associative relations between WHO-ART terms. ..
  7. Chute C, Cohn S, Campbell K, Oliver D, Campbell J. The content coverage of clinical classifications. For The Computer-Based Patient Record Institute's Work Group on Codes & Structures. J Am Med Inform Assoc. 1996;3:224-33 pubmed
    ..ICD-10 does not perform better than ICD-9-CM. The major clinical classifications in use today incompletely cover the clinical content of patient records; thus analytic conclusions that depend on these systems may be suspect. ..
  8. Zhang L, Perl Y, Halper M, Geller J, Cimino J. An enriched unified medical language system semantic network with a multiple subsumption hierarchy. J Am Med Inform Assoc. 2004;11:195-206 pubmed
    The Unified Medical Language System's (UMLS's) Semantic Network's (SN's) two-tree structure is restrictive because it does not allow a semantic type to be a specialization of several other semantic types...
  9. Jimeno A, Jimenez Ruiz E, Lee V, Gaudan S, Berlanga R, Rebholz Schuhmann D. Assessment of disease named entity recognition on a corpus of annotated sentences. BMC Bioinformatics. 2008;9 Suppl 3:S3 pubmed publisher
    ..Library of Medicine (NLM) is the state of the art solution for the annotation of concepts from UMLS (Unified Medical Language System) in the literature. Nonetheless, its performance has not yet been assessed on an annotated corpus...
  10. Fan J, Friedman C. Semantic reclassification of the UMLS concepts. Bioinformatics. 2008;24:1971-3 pubmed publisher
    ..To benefit applications using the semantic classification of the Unified Medical Language System (UMLS) concepts, we automatically reclassified the concepts based on their lexical and contextual ..
  11. Ijaz A, Song M, Lee D. MKEM: a Multi-level Knowledge Emergence Model for mining undiscovered public knowledge. BMC Bioinformatics. 2010;11 Suppl 2:S3 pubmed publisher
    ..using Natural Language Processing techniques such as Link Grammar and Ontologies such as Unified Medical Language System (UMLS) MetaMap...
  12. Stevenson M, Guo Y. Disambiguation in the biomedical domain: the role of ambiguity type. J Biomed Inform. 2010;43:972-81 pubmed publisher
    ..such as local collocations, and features derived from domain-specific knowledge sources, the Unified Medical Language System (UMLS) and Medical Subject Headings (MeSH)...
  13. Griffon N, Chebil W, Rollin L, Kerdelhué G, Thirion B, Gehanno J, et al. Performance evaluation of Unified Medical Language System®'s synonyms expansion to query PubMed. BMC Med Inform Decis Mak. 2012;12:12 pubmed publisher
    ..tools, primarily non-indexed citations, the authors propose a method: expanding users' queries using Unified Medical Language System' (UMLS) synonyms i.e. all the terms gathered under one unique Concept Unique Identifier...
  14. Humphreys B, Lindberg D, Schoolman H, Barnett G. The Unified Medical Language System: an informatics research collaboration. J Am Med Inform Assoc. 1998;5:1-11 pubmed
    ..National Library of Medicine (NLM) assembled a large multidisciplinary, multisite team to work on the Unified Medical Language System (UMLS), a collaborative research project aimed at reducing fundamental barriers to the application of ..
  15. Joubert M, Fieschi M, Robert J, Volot F, Fieschi D. UMLS-based conceptual queries to biomedical information databases: an overview of the project ARIANE. Unified Medical Language System. J Am Med Inform Assoc. 1998;5:52-61 pubmed
    ..A conceptual model of some of the Unified Medical Language System (UMLS) knowledge sources has been developed to help end users to query information databases...
  16. Rector A. Clinical terminology: why is it so hard?. Methods Inf Med. 1999;38:239-52 pubmed
    ..This implies that validation of clinical terminologies must include validation in use as implemented in software. ..
  17. McCray A, Burgun A, Bodenreider O. Aggregating UMLS semantic types for reducing conceptual complexity. Stud Health Technol Inform. 2001;84:216-20 pubmed
    ..The Unified Medical Language System (UMLS) currently integrates over 730,000 biomedical concepts from more than fifty biomedical ..
  18. Denny J, Smithers J, Miller R, Spickard A. "Understanding" medical school curriculum content using KnowledgeMap. J Am Med Inform Assoc. 2003;10:351-62 pubmed
    ..medical curricular documents, using information derived from the National Library of Medicine's Unified Medical Language System (UMLS)...
  19. Brennan P, Aronson A. Towards linking patients and clinical information: detecting UMLS concepts in e-mail. J Biomed Inform. 2003;36:334-41 pubmed
    ..at the National Library of Medicine (NLM) to the challenge of detecting relevant concepts from the Unified Medical Language System (UMLS) within the free text of lay people's electronic messages (e-mail)...
  20. Gu H, Perl Y, Elhanan G, Min H, Zhang L, Peng Y. Auditing concept categorizations in the UMLS. Artif Intell Med. 2004;31:29-44 pubmed
    The Unified Medical Language System (UMLS) integrates about 880,000 concepts from 100 biomedical terminologies. Each concept is categorized to at least one semantic type of the Semantic Network...
  21. Stevenson M, Guo Y. Disambiguation of ambiguous biomedical terms using examples generated from the UMLS Metathesaurus. J Biomed Inform. 2010;43:762-73 pubmed publisher
    ..The examples generated using the novel approach produce an improvement in WSD performance when combined with manually labeled examples. ..
  22. Kim W, Wilbur W. Corpus-based statistical screening for phrase identification. J Am Med Inform Assoc. 2000;7:499-511 pubmed
    ..The Unified Medical Language System (UMLS) incorporates a large list of humanly acceptable phrases in the medical field as a part of its ..
  23. Mutalik P, Deshpande A, Nadkarni P. Use of general-purpose negation detection to augment concept indexing of medical documents: a quantitative study using the UMLS. J Am Med Inform Assoc. 2001;8:598-609 pubmed
    ..5 percent of all negations. Negation of most concepts in medical narrative can be reliably detected by a simple strategy. The reliability of detection depends on several factors, the most important being the accuracy of concept matching. ..
  24. Richesson R, Fung K, Krischer J. Heterogeneous but "standard" coding systems for adverse events: Issues in achieving interoperability between apples and oranges. Contemp Clin Trials. 2008;29:635-45 pubmed publisher
    ..This paper describes the structural features of each coding system, their content and relationship to the Unified Medical Language System (UMLS), and unsettled issues for future interoperability of these standards.
  25. Osborne J, Lin S, Zhu L, Kibbe W. Mining biomedical data using MetaMap Transfer (MMtx) and the Unified Medical Language System (UMLS). Methods Mol Biol. 2007;408:153-69 pubmed
    ..free text data into common biomedical concepts (drugs, diseases, anatomy, and so on) found in the Unified Medical Language System using MetaMap Transfer (MMTx)...
  26. Berman J. Concept-match medical data scrubbing. How pathology text can be used in research. Arch Pathol Lab Med. 2003;127:680-6 pubmed
    ..the sense of the original sentences, while it blocked terms that did not match terms found in the Unified Medical Language System (UMLS)...
  27. Fan J, Xu H, Friedman C. Using contextual and lexical features to restructure and validate the classification of biomedical concepts. BMC Bioinformatics. 2007;8:264 pubmed
    ..syntactic features obtained from a large domain corpus to reclassify and validate concepts of the Unified Medical Language System (UMLS), a comprehensive resource of biomedical terminology...
  28. Huang Y, Lowe H, Klein D, Cucina R. Improved identification of noun phrases in clinical radiology reports using a high-performance statistical natural language parser augmented with the UMLS specialist lexicon. J Am Med Inform Assoc. 2005;12:275-85 pubmed
  29. Gaudan S, Kirsch H, Rebholz Schuhmann D. Resolving abbreviations to their senses in Medline. Bioinformatics. 2005;21:3658-64 pubmed
    ..9% for a recall of 98.2% (98.5% accuracy). This performance is superior in comparison with previously reported research work. The abbreviation resolution module is available at http://www.ebi.ac.uk/Rebholz/software.html. ..
  30. Cimino J, Min H, Perl Y. Consistency across the hierarchies of the UMLS Semantic Network and Metathesaurus. J Biomed Inform. 2003;36:450-61 pubmed
    ..in the Metathesaurus and the ancestor-descendant relationships in the Semantic Network of the Unified Medical Language System (UMLS)...
  31. Friedman C, Shagina L, Lussier Y, Hripcsak G. Automated encoding of clinical documents based on natural language processing. J Am Med Inform Assoc. 2004;11:392-402 pubmed
    ..Recall and precision applied to Unified Medical Language System (UMLS) coding were evaluated in two separate studies...
  32. Agirre E, Soroa A, Stevenson M. Graph-based word sense disambiguation of biomedical documents. Bioinformatics. 2010;26:2889-96 pubmed publisher
    ..It makes use of knowledge from the Unified Medical Language System (UMLS) Metathesaurus which is represented as a graph...
  33. Cimino J. Auditing the Unified Medical Language System with semantic methods. J Am Med Inform Assoc. 1998;5:41-51 pubmed
    The National Library of Medicine's (NLM) Unified Medical Language System (UMLS) includes a Metathesaurus (Meta), which is a compilation of medical terms drawn from over 30 controlled vocabularies, and a Semantic Net, which contains the ..
  34. Rindflesch T, Fiszman M. The interaction of domain knowledge and linguistic structure in natural language processing: interpreting hypernymic propositions in biomedical text. J Biomed Inform. 2003;36:462-77 pubmed
    ..constructions, we exploit underspecified syntactic analysis and structured domain knowledge from the Unified Medical Language System (UMLS)...
  35. Aronson A, Lang F. An overview of MetaMap: historical perspective and recent advances. J Am Med Inform Assoc. 2010;17:229-36 pubmed publisher
    MetaMap is a widely available program providing access to the concepts in the unified medical language system (UMLS) Metathesaurus from biomedical text...
  36. Déjean H, Gaussier E, Renders J, Sadat F. Automatic processing of multilingual medical terminology: applications to thesaurus enrichment and cross-language information retrieval. Artif Intell Med. 2005;33:111-24 pubmed
  37. Wu S, Liu H, Li D, Tao C, Musen M, Chute C, et al. Unified Medical Language System term occurrences in clinical notes: a large-scale corpus analysis. J Am Med Inform Assoc. 2012;19:e149-56 pubmed
    To characterise empirical instances of Unified Medical Language System (UMLS) Metathesaurus term strings in a large clinical corpus, and to illustrate what types of term characteristics are generalisable across data sources...
  38. Yoon S, Yoon J, Min W, Lim H, Song J, Chae S, et al. [Standardization of terminology in laboratory medicine I]. Korean J Lab Med. 2007;27:151-5 pubmed
    ..Short names and a mapping table for EDI codes and Unified Medical Language System (UMLS) were added...
  39. Sun J, Sun Y. A system for automated lexical mapping. J Am Med Inform Assoc. 2006;13:334-43 pubmed
    ..lexical mapping can map terms from various databases to standard vocabularies such as the UMLS (Unified Medical Language System) and LOINC (Logical Observation Identifier Names and Codes)...
  40. Schulz S, Hahn U. Medical knowledge reengineering--converting major portions of the UMLS into a terminological knowledge base. Int J Med Inform. 2001;64:207-21 pubmed
  41. Keselman A, Smith C, Divita G, Kim H, Browne A, Leroy G, et al. Consumer health concepts that do not map to the UMLS: where do they fit?. J Am Med Inform Assoc. 2008;15:496-505 pubmed publisher
    ..study has two objectives: first, to identify and characterize consumer health terms not found in the Unified Medical Language System (UMLS) Metathesaurus (2007 AB); second, to describe the procedure for creating new concepts in the ..
  42. Rosse C, Mejino J. A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J Biomed Inform. 2003;36:478-500 pubmed
  43. Bodenreider O, McCray A. Exploring semantic groups through visual approaches. J Biomed Inform. 2003;36:414-32 pubmed
    ..several visual approaches for exploring semantic groups, a grouping of semantic types from the Unified Medical Language System (UMLS) semantic network...
  44. Rebholz Schuhmann D, Jimeno Yepes A, van Mulligen E, Kang N, Kors J, Milward D, et al. CALBC silver standard corpus. J Bioinform Comput Biol. 2010;8:163-79 pubmed
    ..We expect that we can improve corpus building activities both in terms of the numbers of named entity classes being covered, as well as the size of the corpus in terms of annotated documents. ..
  45. Nadkarni P, Chen R, Brandt C. UMLS concept indexing for production databases: a feasibility study. J Am Med Inform Assoc. 2001;8:80-91 pubmed
    To explore the feasibility of using the National Library of Medicine's Unified Medical Language System (UMLS) Metathesaurus as the basis for a computational strategy to identify concepts in medical narrative text preparatory to indexing...
  46. Butte A, Kohane I. Creation and implications of a phenome-genome network. Nat Biotechnol. 2006;24:55-62 pubmed
    ..the annotations of gene expression data sets in the Gene Expression Omnibus is represented using the Unified Medical Language System, a compendium of biomedical vocabularies with nearly 1-million concepts...
  47. Al Mubaid H, Nguyen H. A cluster-based approach for semantic similarity in the biomedical domain. Conf Proc IEEE Eng Med Biol Soc. 2006;1:2713-7 pubmed
    ..We show, further, that using MeSH ontology produces better semantic correlations with human experts' scores than SNOMED-CT in all of the tested measures. ..
  48. Bodenreider O. The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res. 2004;32:D267-70 pubmed
    The Unified Medical Language System (http://umlsks.nlm.nih.gov) is a repository of biomedical vocabularies developed by the US National Library of Medicine...
  49. Garla V, Brandt C. Ontology-guided feature engineering for clinical text classification. J Biomed Inform. 2012;45:992-8 pubmed publisher
    ..novel feature engineering techniques that leverage the biomedical domain knowledge encoded in the Unified Medical Language System (UMLS) to improve machine-learning based clinical text classification...
  50. Travers D, Haas S. Evaluation of emergency medical text processor, a system for cleaning chief complaint text data. Acad Emerg Med. 2004;11:1170-6 pubmed
    ..of all entries (tokens) and all unique entries (types) that matched a standard term from the Unified Medical Language System (UMLS)...
  51. Schulz S, Beisswanger E, van den Hoek L, Bodenreider O, van Mulligen E. Alignment of the UMLS semantic network with BioTop: methodology and assessment. Bioinformatics. 2009;25:i69-76 pubmed publisher
    For many years, the Unified Medical Language System (UMLS) semantic network (SN) has been used as an upper-level semantic framework for the categorization of terms from terminological resources in biomedicine...
  52. Chen Z, Perl Y, Halper M, Geller J, Gu H. Partitioning the UMLS semantic network. IEEE Trans Inf Technol Biomed. 2002;6:102-8 pubmed
    The unified medical language system (UMLS) integrates many well-established biomedical terminologies...
  53. Xu H, Markatou M, Dimova R, Liu H, Friedman C. Machine learning and word sense disambiguation in the biomedical domain: design and evaluation issues. BMC Bioinformatics. 2006;7:334 pubmed
    ..This should lead to an improved understanding of the generalizablility and the limitations of the methodology. ..