unified medical language system
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.
Publications172 found, 100 shown here
- An overview of MetaMap: historical perspective and recent advancesAlan R Aronson
Lister Hill National Center for Biomedical Communications, US National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
J Am Med Inform Assoc 17:229-36. 2010MetaMap is a widely available program providing access to the concepts in the unified medical language system (UMLS) Metathesaurus from biomedical text...
- The Unified Medical Language System (UMLS): integrating biomedical terminologyOlivier Bodenreider
Lister Hill Center for Biomedical Communications, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 32:D267-70. 2004The Unified Medical Language System (http://umlsks.nlm.nih.gov) is a repository of biomedical vocabularies developed by the US National Library of Medicine...
- The interaction of domain knowledge and linguistic structure in natural language processing: interpreting hypernymic propositions in biomedical textThomas C Rindflesch
Lister Hill National Center for Biomedical Communications, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894, USA
J Biomed Inform 36:462-77. 2003..constructions, we exploit underspecified syntactic analysis and structured domain knowledge from the Unified Medical Language System (UMLS)...
- A reference ontology for biomedical informatics: the Foundational Model of AnatomyCornelius Rosse
Departments of Biological Structure, and Medical Education and Biomedical Informatics, Structural Informatics Group, University of Washington, Seattle, WA 98195, USA
J Biomed Inform 36:478-500. 2003....
- Exploring semantic groups through visual approachesOlivier Bodenreider
Department of Health and Human Services, National Institutes of Health, National Library of Medicine, Lister Hill National Center for Biomedical Communications, MS 43, Bldg 38A Rm B1N28U, 8600 Rockville Pike, Bethesda, MD 20894, USA
J Biomed Inform 36:414-32. 2003..several visual approaches for exploring semantic groups, a grouping of semantic types from the Unified Medical Language System (UMLS) semantic network...
- "Understanding" medical school curriculum content using KnowledgeMapJoshua C Denny
Department of Biomedical Informatics, Vanderbilt School of Medicine, Nashville, Tennessee 37232, USA
J Am Med Inform Assoc 10:351-62. 2003..medical curricular documents, using information derived from the National Library of Medicine's Unified Medical Language System (UMLS)...
- Evaluation of emergency medical text processor, a system for cleaning chief complaint text dataDebbie A Travers
Department of Emergency Medicine, School of Medicine, CB 7594, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 7594, USA
Acad Emerg Med 11:1170-6. 2004..g., chest pain). The authors compared the number of standard terms extracted from raw chief complaint (CC) data with that for CC data cleaned with EMT-P and evaluated the accuracy of EMT-P...
- Alignment of the UMLS semantic network with BioTop: methodology and assessmentStefan Schulz
Institute of Medical Biometry and Medical Informatics, University Medical Center Freiburg, Freiburg, Germany
Bioinformatics 25:i69-76. 2009For 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...
- A simple algorithm for identifying negated findings and diseases in discharge summariesW W Chapman
Center for Biomedical Informatics, 8084 Forbes Tower, University of Pittsburgh, Pittsburgh, PA 15213, USA
J Biomed Inform 34:301-10. 2001..We conclude that with little implementation effort a simple regular expression algorithm for determining whether a finding or disease is absent can identify a large portion of the pertinent negatives from discharge summaries...
- Mining biomedical data using MetaMap Transfer (MMtx) and the Unified Medical Language System (UMLS)John D Osborne
Robert H Lurie Cancer Center, Northwestern University, Chicago, IL, USA
Methods Mol Biol 408:153-69. 2007..free text data into common biomedical concepts (drugs, diseases, anatomy, and so on) found in the Unified Medical Language System using MetaMap Transfer (MMTx)...
- Unified Medical Language System term occurrences in clinical notes: a large-scale corpus analysisStephen T Wu
Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA
J Am Med Inform Assoc 19:e149-56. 2012To 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.
- Performance evaluation of Unified Medical Language System®'s synonyms expansion to query PubMedNicolas Griffon
CISMeF, Rouen University Hospital, Cour Leschevin, Porte 21, 3ème étage, 1 rue de Germont, 76031 Rouen Cedex, France
BMC Med Inform Decis Mak 12:12. 2012..retrieval 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.
- Automated encoding of clinical documents based on natural language processingCarol Friedman
Department of Biomedical Informatics, Columbia University, 622 West 168 Street, VC 5, New York, NY 10032, USA
J Am Med Inform Assoc 11:392-402. 2004..The aim of this study was to develop a method based on natural language processing (NLP) that automatically maps an entire clinical document to codes with modifiers and to quantitatively evaluate the method...
- Ontology-guided feature engineering for clinical text classificationVijay N Garla
Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, 300 George Street, Suite 501, New Haven, CT 06520 8009, USA
J Biomed Inform 45:992-8. 2012..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...
- UMLS-based conceptual queries to biomedical information databases: an overview of the project ARIANE. Unified Medical Language SystemM Joubert
LERTIM, Faculte de Medecine, Universite de la Mediterranee, Marseille, France
J Am Med Inform Assoc 5:52-61. 1998..The aim of the project ARIANE is to model and implement seamless, natural, and easy-to-use interfaces with various kinds of heterogeneous biomedical information databases...
- Optimization of the PubMed Automatic Term MappingBenoit Thirion
CISMeF, Rouen University Hospital and GCSIS, TIBS, LITIS EA 4108, Biomedical Research Institute, 76031 Rouen, France
Stud Health Technol Inform 150:238-42. 2009..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...
- Clinical terminology: why is it so hard?A L Rector
Department of Computer Science, University of Manchester, UK
Methods Inf Med 38:239-52. 1999..This implies that validation of clinical terminologies must include validation in use as implemented in software...
- Characteristics of consumer terminology for health information retrievalQ Zeng
Decision Systems Group, Brigham and Women s Hospital, Harvard Medical School, Boston, MA, USA
Methods Inf Med 41:289-98. 2002..To address this problem, we studied the characteristics of consumer terminology for health information retrieval...
- MKEM: a Multi-level Knowledge Emergence Model for mining undiscovered public knowledgeAli Z Ijaz
Department of Bio and Brain Engineering, KAIST, South Korea
BMC Bioinformatics 11:S3. 2010..With the advancement in biomedical science, it has become imperative to extract and combine information from multiple disjoint researches, studies and articles to infer new hypotheses and expand knowledge...
- An enriched unified medical language system semantic network with a multiple subsumption hierarchyLi Zhang
CS Department, NJIT, University Heights, Newark, NJ 07102, USA
J Am Med Inform Assoc 11:195-206. 2004The 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...
- Quality evaluation of cancer study Common Data Elements using the UMLS Semantic NetworkGuoqian Jiang
Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
J Biomed Inform 44:S78-85. 2011..This approach could provide useful insight about how to build mechanisms of quality assurance in a meta-data repository...
- A cluster-based approach for semantic similarity in the biomedical domainHisham Al-Mubaid
Univ of Houston Clear Lake, Houston, TX 77058, USA
Conf Proc IEEE Eng Med Biol Soc 1:2713-7. 2006..We show, further, that using MeSH ontology produces better semantic correlations with human experts' scores than SNOMED-CT in all of the tested measures...
- Term identification in the biomedical literatureMichael Krauthammer
Department of Biomedical Informatics, Columbia Genome Center, Columbia University, New York, USA
J Biomed Inform 37:512-26. 2004..By assessing previous work in context of the overall term identification process, the review also tries to delineate needs for future work in the field...
- Graph-based word sense disambiguation of biomedical documentsEneko Agirre
IXA NLP Group, University of the Basque Country, Donostia, Basque Country, Spain
Bioinformatics 26:2889-96. 2010..It makes use of knowledge from the Unified Medical Language System (UMLS) Metathesaurus which is represented as a graph...
- Towards the development of a conceptual distance metric for the UMLSJorge E Caviedes
Intel Corporation, 5000 W Chandler Blvd, Chandler, AZ 85226, USA
J Biomed Inform 37:77-85. 2004..this work is to investigate the feasibility of conceptual similarity metrics in the framework of the Unified Medical Language System (UMLS)...
- Consumer health concepts that do not map to the UMLS: where do they fit?Alla Keselman
Lister Hill National Center for Biomedical Communications, National Library of Medicine, National Institute of Health, 8600 Rockville Pike, Bethesda, MD, USA
J Am Med Inform Assoc 15:496-505. 2008..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 ..
- Use of general-purpose negation detection to augment concept indexing of medical documents: a quantitative study using the UMLSP G Mutalik
Department of Diagnostic Raiology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
J Am Med Inform Assoc 8:598-609. 2001....
- Disambiguation in the biomedical domain: the role of ambiguity typeMark Stevenson
Natural Language Processing Group, Department of Computer Science, University of Sheffield, Regent Court, 211 Portobello, Sheffield S14DP, United Kingdom
J Biomed Inform 43:972-81. 2010..such as local collocations, and features derived from domain-specific knowledge sources, the Unified Medical Language System (UMLS) and Medical Subject Headings (MeSH)...
- Automatic processing of multilingual medical terminology: applications to thesaurus enrichment and cross-language information retrievalH Déjean
Xerox Research Centre Europe, 6 Chemin de Maupertuis, F 38240 Meylan, France
Artif Intell Med 33:111-24. 2005..For such applications, multilingual terminology plays a crucial role when working on specialized languages and specific domains...
- UMLS-Interface and UMLS-Similarity : open source software for measuring paths and semantic similarityBridget T McInnes
University of Minnesota, Minneapolis, MN, USA
AMIA Annu Symp Proc 2009:431-5. 2009..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...
- Semantic reclassification of the UMLS conceptsJung Wei Fan
Department of Biomedical Informatics, Columbia University, 622 W 168th St, VC5, New York, NY10032, USA
Bioinformatics 24:1971-3. 2008..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 ..
- A system for automated lexical mappingJennifer Y Sun
Newborn Medicine Informatics Program, Children s Hospital, Boston, MA, USA
J Am Med Inform Assoc 13:334-43. 2006..To automate the mapping of disparate databases to standardized medical vocabularies...
- Disambiguation of biomedical text using diverse sources of informationMark Stevenson
Department of Computer Science, University of Sheffield, Regent Court, 211 Portobello, Sheffield S14DP, UK
BMC Bioinformatics 9:S7. 2008..Previous approaches to resolving this problem have made use of various sources of information including linguistic features of the context in which the ambiguous term is used and domain-specific resources, such as UMLS...
- Exploiting MeSH indexing in MEDLINE to generate a data set for word sense disambiguationAntonio J Jimeno-Yepes
National Library of Medicine, Bethesda, MD 20894, USA
BMC Bioinformatics 12:223. 2011..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...
- An automated approach to mapping external terminologies to the UMLSMaria Taboada
Department of Electronics and Computer Science, University of Santiago de Compostela, Santiago de Compostela 15782, Spain
IEEE Trans Biomed Eng 56:1598-605. 2009..In this study, we propose an automated approach to mapping external terminologies to the Unified Medical Language System (UMLS)...
- Amplification of Terminologia anatomica by French language terms using Latin terms matching algorithm: a prototype for other languagePaul Fabry
CRED, Centre Hospitalier Universitaire de Sherbrooke, Quebec, Canada
Int J Med Inform 75:542-52. 2006..On the other hand, Nomina anatomica, the previous standard, has been widely translated. Aim of this work was to append foreign terms to Terminologia by using similarity-matching algorithm between its Latin terms and those from Nomina...
- The UMLS project: making the conceptual connection between users and the information they needB L Humphreys
National Library of Medicine, Bethesda, MD 20894
Bull Med Libr Assoc 81:170-7. 1993..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 ..
- Medical knowledge reengineering--converting major portions of the UMLS into a terminological knowledge baseS Schulz
Freiburg University Hospital, Department of Medical Informatics, Stefan Meier Strasse 26, D 79104 Freiburg, Germany
Int J Med Inform 64:207-21. 2001....
- Combining lexical and semantic methods of inter-terminology mapping using the UMLSKin Wah Fung
National Library of Medicine, Bethesda, Maryland 20894, USA
Stud Health Technol Inform 129:605-9. 2007..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...
- CALBC silver standard corpusDietrich Rebholz-Schuhmann
EMBL Outstation Hinxton, European Bioinformatics Institute, Hinxton, Cambridge CB101SD, UK
J Bioinform Comput Biol 8:163-79. 2010..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...
- The content coverage of clinical classifications. For The Computer-Based Patient Record Institute's Work Group on Codes & StructuresC G Chute
Section of Medical Information Resources, Mayo Foundation, Rochester, MN 55905, USA
J Am Med Inform Assoc 3:224-33. 1996..To address whether existing major coding systems can serve this function, the authors evaluated major clinical classifications for their content coverage...
- Mapping of the WHO-ART terminology on Snomed CT to improve grouping of related adverse drug reactionsIulian Alecu
INSERM U729, Universite Paris Descartes, Faculte de Medecine, Paris, France
Stud Health Technol Inform 124:833-8. 2006..We plan to improve our method in order to retrieve associative relations between WHO-ART terms...
- Failure analysis of MetaMap Transfer (MMTx)Guy Divita
Lister Hill National Center for Biomedical Communications, National Library of Medicine, Bethesda, MD 20894, USA
Stud Health Technol Inform 107:763-7. 2004..Transfer (MMTx), a tool that extracts terms from free text and suggests matches to concepts in the Unified Medical Language System' (UMLS')...
- Implementation and evaluation of a negation tagger in a pipeline-based system for information extract from pathology reportsKevin J Mitchell
Centers for Pathology and Oncology Informatics, University of Pittsburgh, UPMC Shadyside, 5230 Centre Avenue, Pittsburgh, PA 15232, USA
Stud Health Technol Inform 107:663-7. 2004..Further work will focus on refining the Negation Tagger and UMLS Tagger and adding additional processing resources for annotating free-text pathology reports...
- Semantic classification of biomedical concepts using distributional similarityJung Wei Fan
Department of Biomedical Informatics, Columbia University, New York, NY, USA
J Am Med Inform Assoc 14:467-77. 2007..To develop an automated, high-throughput, and reproducible method for reclassifying and validating ontological concepts for natural language processing applications...
- Creation and implications of a phenome-genome networkAtul J Butte
Stanford Medical Informatics, Department of Medicine, Stanford University School of Medicine, 251 Campus Drive, Room X 215, Stanford, California 94305 5479, USA
Nat Biotechnol 24:55-62. 2006..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...
- A lexical metaschema for the UMLS semantic networkLi Zhang
Computer Science Department, New Jersey Institute of Technology, University Heights, Newark, NJ 07102, USA
Artif Intell Med 33:41-59. 2005..A new kind of metaschema, called the lexical metaschema, is derived from a lexical partition of the SN. The lexical metaschema is compared to previously derived metaschemas, e.g., the cohesive metaschema...
- Effects of information and machine learning algorithms on word sense disambiguation with small datasetsGondy Leroy
School of Information Science, Claremont Graduate University, 130 E Ninth Street, Claremont, CA 91711, USA
Int J Med Inform 74:573-85. 2005..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 ..
- Machine learning and word sense disambiguation in the biomedical domain: design and evaluation issuesHua Xu
Department of Biomedical Informatics, Columbia University, 622 168th St, New York City, New York, USA
BMC Bioinformatics 7:334. 2006..Thus, there is a need to explicitly address the factors and to systematically quantify their effects on performance...
- Assessment of disease named entity recognition on a corpus of annotated sentencesAntonio Jimeno
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
BMC Bioinformatics 9:S3. 2008..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...
- Concept-match medical data scrubbing. How pathology text can be used in researchJules J Berman
Pathology Informatics, Cancer Diagnosis Program, National Cancer Institute, National Institutes of Health, Rockville, MD 20892, USA
Arch Pathol Lab Med 127:680-6. 2003..This article addresses the problem of data scrubbing...
- The Unified Medical Language System: an informatics research collaborationB L Humphreys
National Library of Medicine, Bethesda, MD, USA
J Am Med Inform Assoc 5:1-11. 1998..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 ..
- Consistency across the hierarchies of the UMLS Semantic Network and MetathesaurusJ J Cimino
Department of Medical Informatics, Columbia University, New York, NY, USA
J Biomed Inform 36:450-61. 2003..test a method for automatically detecting inconsistencies between the parent-child is-a relationships in the Metathesaurus and the ancestor-descendant relationships in the Semantic Network of the Unified Medical Language System (UMLS).
- Automatic resolution of ambiguous terms based on machine learning and conceptual relations in the UMLSHongfang Liu
City University of New York, New York, New York 10032, USA
J Am Med Inform Assoc 9:621-36. 2002..However, manual annotation of a corpus is an expensive task. We propose an automatic method that constructs sense-tagged corpora for ambiguous terms in the UMLS using MEDLINE abstracts...
- Towards linking patients and clinical information: detecting UMLS concepts in e-mailPatricia Flatley Brennan
University of Wisconsin Madison, 372 Mechanical Engineering, 1513 University Avenue, Madison, WI 53706, USA
J Biomed Inform 36:334-41. 2003..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)...
- Generating hypotheses by discovering implicit associations in the literature: a case report of a search for new potential therapeutic uses for thalidomideMarc Weeber
Department of Social Pharmacy and Pharmacoepidemiology, Groningen University Institute for Drug Exploration, The Netherlands
J Am Med Inform Assoc 10:252-9. 2003..However, experimental and clinical evaluation is needed to validate these hypotheses and to assess the trade-off between therapeutic benefits and toxicities...
- Resolving abbreviations to their senses in MedlineS Gaudan
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Bioinformatics 21:3658-64. 2005..Resolving an abbreviation in a document consists of retrieving its sense in use. Abbreviation resolution improves accuracy of document retrieval engines and of information extraction systems...
- Using contextual and lexical features to restructure and validate the classification of biomedical conceptsJung Wei Fan
Department of Biomedical Informatics, Columbia University Vanderbilt Clinic, 5th Floor, 622 West 168th Street, New York, NY 10032, USA
BMC Bioinformatics 8:264. 2007..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...
- Auditing the Unified Medical Language System with semantic methodsJ J Cimino
Department of Medical Informatics, Columbia University College of Physicians and Surgeons, New York, NY, USA
J Am Med Inform Assoc 5:41-51. 1998The 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 ..
- Heterogeneous but "standard" coding systems for adverse events: Issues in achieving interoperability between apples and orangesRachel L Richesson
University of South Florida College of Medicine, Tampa, FL, USA
Contemp Clin Trials 29:635-45. 2008..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.
- Perils of providing visual health information overviews for consumers with low health literacy or high stressGondy Leroy
Information Systems and Technology, Claremont Graduate University, Claremont, California 91711, USA
J Am Med Inform Assoc 17:220-3. 2010..The HTO is generated automatically based on the presence of Unified Medical Language System terms. In a controlled setting, we presented health texts and posed 15 questions for each...
- [Standardization of terminology in laboratory medicine I]Soo Young Yoon
Department of Laboratory Medicine, School of Medicine, Korea University, Seoul, Korea
Korean J Lab Med 27:151-5. 2007..During the first year of the study, we developed a standard database of concept names for laboratory terms, which covered the terms used in government health care centers, their branch offices, and primary health care units...
- Disambiguation of ambiguous biomedical terms using examples generated from the UMLS MetathesaurusMark Stevenson
Department of Computer Science, University of Sheffield, Sheffield S1 4DP, UK
J Biomed Inform 43:762-73. 2010..The examples generated using the novel approach produce an improvement in WSD performance when combined with manually labeled examples...
- Aggregating UMLS semantic types for reducing conceptual complexityA T McCray
National Library of Medicine, Bethesda, Maryland, 20894, USA
Stud Health Technol Inform 84:216-20. 2001..The Unified Medical Language System (UMLS) currently integrates over 730,000 biomedical concepts from more than fifty biomedical ..
- Auditing concept categorizations in the UMLSHuanying Gu
Department of Health Informatics, University of Medicine and Dentistry of NJ, Newark, NJ 07107, USA
Artif Intell Med 31:29-44. 2004The 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...
- UMLS concept indexing for production databases: a feasibility studyP Nadkarni
Yale University School of Medicine, New Haven, CT 06520 8009, USA
J Am Med Inform Assoc 8:80-91. 2001To 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...
- Partitioning the UMLS semantic networkZong Chen
Computer Science Department, New Jersey Institute of Technology, Newark 07102, USA
IEEE Trans Inf Technol Biomed 6:102-8. 2002The unified medical language system (UMLS) integrates many well-established biomedical terminologies...
- Resources for comparing the speed and performance of medical autocodersJules J Berman
Cancer Diagnosis Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
BMC Med Inform Decis Mak 4:8. 2004..on any operating system); 2) a nomenclature database derived from the unencumbered subset of the publicly available Unified Medical Language System; 3) a large corpus of autocoded output derived from a publicly available medical text.
- A tool for sharing annotated research data: the "Category 0" UMLS (Unified Medical Language System) vocabulariesJules J Berman
Cancer Diagnosis Program, National Cancer Institute, NIH, Rockville, MD, USA
BMC Med Inform Decis Mak 3:6. 2003..The largest curated listing of biomedical terms is the the National Library of Medicine's Unified Medical Language System (UMLS)...
- Corpus-based statistical screening for phrase identificationW Kim
National Library of Medicine, Bethesda, Maryland 20894, USA
J Am Med Inform Assoc 7:499-511. 2000..The authors study the extraction of useful phrases from a natural language database by statistical methods. The aim is to leverage human effort by providing preprocessed phrase lists with a high percentage of useful material...
- Inter-patient distance metrics using SNOMED CT defining relationshipsGenevieve B Melton
Department of Surgery, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
J Biomed Inform 39:697-705. 2006..Ontology and information content principles may be potentially helpful tools for similarity metric development...
- Defining and relating biomedical terms: towards a cross-language morphosemantics-based systemFiammetta Namer
UMR 7118 ATILF and Université Nancy2, CLSH, 23 Boulevard Albert 1er, BP3397, 54015 Nancy Cedex, France
Int J Med Inform 76:226-33. 2007..A validation of the results against a manually annotated file by experts of the domain is presented, followed by a discussion of our method...
- Enrichment of OBO ontologiesMichael Bada
University of Colorado at Denver and Health Sciences Center, Department of Pharmacology, MS 8303, RC 1 South, 12801 East 17th Avenue, L18 6101, P O Box 6511, Aurora, CO 80045, USA
J Biomed Inform 40:300-15. 2007..Furthermore, this methodology programmatically integrates assertions into an ontology such that each assertion is fully consistent with respect to higher (i.e., more general) relevant class and slot levels...
- ADAM: another database of abbreviations in MEDLINEWei Zhou
Department of Psychiatry and Psychiatric Institute, MC912, University of Illinois at Chicago Chicago, IL 60612, USA
Bioinformatics 22:2813-8. 2006..We have created another abbreviation database, ADAM, which covers commonly used abbreviations and their definitions (or long-forms) within MEDLINE titles and abstracts, including both acronym and non-acronym abbreviations...
- Automatic lexeme acquisition for a multilingual medical subword thesaurusKornél Markó
Freiburg University Hospital, Medical Informatics Department, Stefan Meier Strasse 26, D 79104 Freiburg, Germany
Int J Med Inform 76:184-9. 2007..We present a method for the automated acquisition of a multilingual medical lexicon (for Spanish, French and Swedish) to be used within the framework of a medical cross-language text retrieval system...
- Knowledge acquisition for computation of semantic distance between WHO-ART termsJimison Iavindrasana
INSERM U729, Universite Paris Descartes, Faculte de Medecine, Paris, France
Stud Health Technol Inform 124:839-44. 2006..Our knowledge acquisition method can help us to generate new formal definitions of medical terms for our semantic distance terminology services...
- Semantic relation mining of solid compounds in medical corporaDimitrios Kokkinakis
Department of Swedish Language, Språkdata, University of Gothenburg, Sweden
Stud Health Technol Inform 136:217-22. 2008..g. virus diseases vs. virussjukdomar, which makes the problem more challenging, since solid compounds are harder to identify and segment...
- A method for indexing biomedical resources over the internetGuillermo de la Calle
Biomedical Informatics Group, Artificial Intelligence Lab, Facultad de Informatica, Universidad Politecnica de Madrid, Campus de Montegancedo s n, 28660 Boadilla del Monte, Madrid, Spain
Stud Health Technol Inform 136:163-8. 2008....
- Aligning lay and specialized passages in comparable medical corporaLouise Deleger
INSERM UMRS 872 Eq 20, Paris, France
Stud Health Technol Inform 136:89-94. 2008..This is encouraging evidence for the target task of finding equivalent expressions between these two varieties of language...
- Enhanced information retrieval from narrative German-language clinical text documents using automated document classificationStephan Spat
Institute of Medical Technologies and Health Management, Joanneum Research Forschungsgesellschaft mbH, Graz, Austria
Stud Health Technol Inform 136:473-8. 2008..The system has been designed as a J2EE Web-application. First findings are based on a sample of 18,000 unstructured, clinical text documents written in German...
- Enhancing knowledge representations by ontological relationsKerstin Denecke
Research Center L3S, University of Hannover, Germany
Stud Health Technol Inform 136:791-6. 2008..First results show that these relations can enhance and ameliorate the automatically generated semantic structures...
- Automatic acquisition of synonyms from French UMLS for enhanced search of EHRsNatalia Grabar
Centre de Recherche des Cordeliers Université Paris Descartes, INSERM, U872, Paris, France
Stud Health Technol Inform 136:809-14. 2008..Applied to series of synonym terms from the French subset of the UMLS, the method shows 99% precision. The overlap between thus inferred terms and the existing sparse resources of synonyms is very low...
- Comparing and consolidating two heuristic metaschemasYan Chen
New Jersey Institute of Technology, Newark, NJ 07102, USA
J Biomed Inform 41:293-317. 2008....
- Efficient bibliographic searches on allergology using PubMedJ M Sáez Gómez
Department of Social and Health Sciences University of Murcia Medical School Spain
Allergol Immunopathol (Madr) 35:264-75. 2007..Although it can be used as an unique Data Base, as a matter of fact is the addition of several subgroups (among them MEDLINE) that can be searched simultaneously...
- Mining knowledge from corpora: an application to retrieval and indexingLina F Soualmia
LIM and Bio EA 3969, SMBH Léonard de Vinci, Paris XIII University, Bobigny, France
Stud Health Technol Inform 136:467-72. 2008..The present work aims at discovering new associations between medical concepts to be exploited as input in retrieval and indexing...
- User-centered semantic harmonization: a case studyChunhua Weng
Department of Biomedical Informatics, University of Pittsburgh, UPMC Shadyside Cancer Pavilion Suit 301, 5150 Centre Avenue, Pittsburgh, PA 15232, USA
J Biomed Inform 40:353-64. 2007....
- Classification of cancer stage from free-text histology reportsIan McCowan
CSIRO eHealth Research Centre, Brisbane, Australia
Conf Proc IEEE Eng Med Biol Soc 1:5153-6. 2006..The article presents initial experiments quantifying system performance for T and N staging on a corpus of histology reports from more than 700 lung cancer patients...
- Automatic concept extraction from spoken medical reportsAndré Happe
Intermede, La Basse Revachais, 35580 Guignen, France
Int J Med Inform 70:255-63. 2003..The objective of this project is to investigate methods whereby a combination of speech recognition and automated indexing methods substitute for current transcription and indexing practices...
- MediClass: A system for detecting and classifying encounter-based clinical events in any electronic medical recordBrian Hazlehurst
Center for Health Research, 3800 N Interstate Ave, Portland, OR 97227, USA
J Am Med Inform Assoc 12:517-29. 2005..MediClass could aid both clinical operations and health services research through enhancing care quality assessment, disease surveillance, and adverse event detection...
- Research on structural issues of the UMLS--past, present, and futureYehoshua Perl
J Biomed Inform 36:409-13. 2003
- Assessing the consistency of a biomedical terminology through lexical knowledgeOlivier Bodenreider
US National Library of Medicine, 8600 Rockville Pike, MS 43, Bethesda, MD 20894, USA
Int J Med Inform 67:85-95. 2002..We investigate the use of adjectival modification as a way of assessing the systematic use of linguistic phenomena to represent similar lexical or semantic features in the constituent terms of a vocabulary...
- A comparative study on concept representation between the UMLS and the clinical terms in Korean medical recordsSeung Bin Han
Department of Biomedical Engineering, College of Medicine, Seoul National University, 28 Yongon dong Jongno gu, Seoul 110 799, Korea
Stud Health Technol Inform 107:616-20. 2004The Unified Medical Language System (UMLS) is a rich source of knowledge in the biomedical domain...
- Automating terminological networks to link heterogeneous biomedical databasesXiaoyan Wang
Department of Biomedical Informatics, College of Physicians and Surgeons, Columbia University, 622 W 168th Street VC5, New York, NY 10032, USA
Stud Health Technol Inform 107:555-9. 2004..Taken together, our conclusion may suggest the combined manual and automated terminology networks could offer recall and precision in an incremental manner..
- MeSH and specialized terminologies: coverage in the field of molecular biologyVincent Mary
Laboratory of Medical Informatics, Faculty of Medicine, University of Rennes, Rennes, France
Stud Health Technol Inform 107:530-4. 2004..In this article we assess the contribution of specialized terminologies in the field of molecular biology compared to MeSH...
- Semantic annotation for concept-based cross-language medical information retrievalMartin Volk
Eurospider Information Technology AG, Schaffhauserstrasse 18, CH 8006, Zurich, Switzerland
Int J Med Inform 67:97-112. 2002..Our approach is based on using the Unified Medical Language System (UMLS) as the primary source of semantic data...
- OQAFMA Querying agent for the Foundational Model of Anatomy: a prototype for providing flexible and efficient access to large semantic networksPeter Mork
Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
J Biomed Inform 36:501-17. 2003..access to one such large semantic network, the Foundational Model of Anatomy, and suggests that OQAFMA could be an efficient query interface to other large biomedical knowledge bases, such as the Unified Medical Language System.
- Designing metaschemas for the UMLS enriched semantic networkLi Zhang
Computer Science Department NJIT, Newark, NJ 07102, USA
J Biomed Inform 36:433-49. 2003..These two metaschemas and their underlying partitions are compared. Both metaschemas serve as compact representations of the ESN, allowing for convenient viewing of its hierarchy and easier comprehension...
- An evaluation of the usefulness of two terminology models for integrating nursing diagnosis concepts into SNOMED Clinical TermsS Bakken
Department of Medical Informatics, School of Nursing, Columbia University, 630 West 168th Street, Mailbox 6, New York, NY, USA
Int J Med Inform 68:71-7. 2002..We evaluated the usefulness of two models for integrating nursing diagnosis concepts into SNOMED Clinical Terms (CT)...
- Identification of key concepts in biomedical literature using a modified Markov heuristicW H Majoros
The Institute for Genomic Research, Rockville, MD 20850, USA
Bioinformatics 19:402-7. 2003..Furthermore, the use of statistically salient noun phrases as surrogates for curated terminology is not without difficulties, due to the lack of high-quality part-of-speech taggers specific to medical nomenclature...
- The cohesive metaschema: a higher-level abstraction of the UMLS Semantic NetworkYehoshua Perl
Computer Science Department, New Jersey Institute of Technology, Newark, NJ 07102, USA
J Biomed Inform 35:194-212. 2002The Unified Medical Language System (UMLS) joins together a group of established medical terminologies in a unified knowledge representation framework...
- An expert study evaluating the UMLS lexical metaschemaLi Zhang
Computer Science Department, New Jersey Institute of Technology, University Heights, Newark, NJ 07102, USA
Artif Intell Med 34:219-33. 2005..In this paper, a statistical analysis methodology is presented to evaluate the lexical metaschema based on a study involving a group of established UMLS experts...
- Vocabulary Support for Consumer Health InformaticsQing Zeng; Fiscal Year: 2010..Consider the following examples from the Unified Medical Language System (UMLS), the most comprehensive source of medical vocabularies...
- Continued Development and Evaluation of caTIESRebecca S Crowley; Fiscal Year: 2013..Documents are automatically coded against a controlled terminology such as the Unified Medical Language System (UMLS), SNOMED-CT, or NCI Metathesaurus...
- Integrating Microarray and Proteomic Data by Ontology-based AnnotationAtul J Butte; Fiscal Year: 2011..develop tools that comprehensively map contextual annotations to the largest biomedical ontology, the Unified Medical Language System (UMLS), built and supported by the National Library of Medicine, validate, and disseminate the ..
- Sematic Relatedness for Active Medication Safety and Outcomes SurveillanceSerguei V S Pakhomov; Fiscal Year: 2010..this proposal seeks to develop methods that leverage the medical knowledge contained within Unified Medical Language System (UMLS) and corpora of clinical text...
- Increasing Clinical Trial Enrollment: A Semi-Automated Patient Centered ApproachIMRE SOLTI; Fiscal Year: 2012..The PI will develop the tool around the National Library of Medicine's Unified Medical Language System knowledgebase. He will use Java for programming...
- Efficient Discovery of Medical AssociationsPing Chen; Fiscal Year: 2013..will develop an automatic semantic network building component to extract knowledge directly from the Unified Medical Language System, a large medical knowledge base developed by NIH...
- OAMiner: Integrative Knowledge Anchored Hypothesis DiscoveryMETIN NAFI GURCAN; Fiscal Year: 2010..repositories;2) publically available ontologies included in the National Library of Medicine's Unified Medical Language System (UMLS);3) one or more databases containing phenotypic and functional (e.g...
- Testing Evaluation Metrics for Interface TerminologiesSAMUEL ROSENBLOOM; Fiscal Year: 2007..interface terminologies takes on particular urgency with the recent licensing of SNOMED CT into the Unified Medical Language System and its subsequent recommendation as a national terminology standard...
- UNIVERSITY OF PITTSBURGH IAIMS PHASE IIJEFFREY ROMOFF; Fiscal Year: 1992..The University has participated in the NLM's Unified Medical Language System initiative and is one of eight sites with an NLM sponsored training program for medical informatics...
- Software Leveraging a Standards-Based Web Service Framework for Decision SupportDavid Lobach; Fiscal Year: 2006..information model based on the Health Level 7 Reference Information Model and concepts from the NLM Unified Medical Language System; (2) executable knowledge modules that capture medical knowledge in a simple, expandable, and ..
- LINGUISTIC ANALYSIS OF VARIANT EXPRESSIONS IN MEDLINEAmy Warner; Fiscal Year: 1993..It specifically relates to the Unified Medical Language System (UMLS) effort to identify, extract and relate variant medical expressions in machine-readable bio-..
- SYSTEMATIC COMBINATION OF ANATOMY AND NOMENCLATUREJonathan Silverstein; Fiscal Year: 2004..and Veterinary Medicine (SNOMED, a data table relating terms to codes), which is a component of the Unified Medical Language System (UMLS, a relational database)...
- Increasing Clinical Trial Enrollment: A Semi-Automated Patient Centered ApproachIMRE SOLTI; Fiscal Year: 2009..The PI will develop the tool around the National Library of Medicine's Unified Medical Language System knowledgebase. He will use Java for programming...
- UMLS ENHANCED DYNAMIC AGENTS TO MANAGE MEDICAL KNOWLEDGEHsinchun Chen; Fiscal Year: 2003..NSF-funded Illinois Digital Library Initiative (DLI) project with existing components found in the Unified Medical Language System (UMLS) developed by NLM...
- BIOMEDICAL SCIENCE INFORMATION RETRIEVAL AND MANAGEMENTKENNETH BACLAWSKI; Fiscal Year: 1999..The proposed search engine will use the Unified Medical Language System as its basis...
- VOCABULARY MANAGEMENT FOR CLINICAL RESEARCH DATABASESCynthia Brandt; Fiscal Year: 2005....
- DELIVERY OF THE CGN INFORMATION RESOURCE DATABASEPrakash Nadkarni; Fiscal Year: 2006..Informatics assistance will be provided to the individual nodes to assist the task of data exchange, and when necessary, to assist the design of local data collection systems. ..
- DESIGN AND IMPLEMENTATION OF PHARMACOGENETIC DATABASEPrakash Nadkarni; Fiscal Year: 2002..Informatics assistance will be provided to the individual nodes to assist the task of data exchange, and when necessary, to assist the design of local data collection systems. ..
- ROBUST QUERY OF HETEROGENEOUS CLINICAL DATABASESPrakash Nadkarni; Fiscal Year: 2002..In particular, research will be performed on utilization of newer database technologies, such as new indexing methods, as well as parallel database implementations. ..
- Taxonomies Supporting Orientation, Navigation and Auditing of TerminologiesYehoshua Perl; Fiscal Year: 2010..We will demonstrate the utility of our taxonomy-based methodologies by defining various complexity measures with respect to the underlying terminology networks and by tracking terminology evolution. ..
- Enhancing Clinical Effectiveness Research with Natural Language Processing of EMRBRIAN L HAZLEHURST; Fiscal Year: 2010..We will demonstrate the utility of this infrastructure by conducting CER studies investigating the effectiveness of interventions in asthma and smoking, across the 6 participating health systems. ..
- LATENT SEMANTIC INDEXING IN SUPPORT OF DATA RETRIEVALCHRISTOPHER CHUTE; Fiscal Year: 2001..We commit these activities to remain compliant with emerging standards for medical concept representation arising from the Canon efforts and the standardization processes at ANSI-HISPP, CEN TC251 and the CPRI initiatives. ..
- Partitioning to Support Auditing and Extending the UMLSYehoshua Perl; Fiscal Year: 2009....
- Automating Assessment of Asthma Care QualityBrian Hazlehurst; Fiscal Year: 2008..Finally, we will evaluate the association between ACQ measures of recommended asthma care and actual clinical outcomes using extensive longitudinal patient data available at the KPNW study site. [unreadable] [unreadable] [unreadable]..
- Spatial Information Management Resources for Human BrainDOUGLAS BOWDEN; Fiscal Year: 2007..The nomenclature, NeuroNames, is fully integrated with the Unified Medical Language System of the National Library of Medicine...
- Custom Computer Support: Home Care of CABG PatientsPatricia Brennan; Fiscal Year: 2007..Key outcome variables include patient and nurse satisfaction with care, patient self-management, 30-day readmission rate and nurse workload. [unreadable] [unreadable]..
- SPATIAL-SYMBOLIC BRAIN INFORMATION MANAGEMENT SYSTEMDOUGLAS BOWDEN; Fiscal Year: 2001..base that is accessible through the standard terminology of the National Library of Medicine's Unified Medical Language System. Clinicians and neuroscientists any place in the country will be able to access the system via the ..
- Development and Evaluation of Terminology ServicesCHRISTOPHER CHUTE; Fiscal Year: 2004....
- Intelligent Data Storage ResourceCHRISTOPHER CHUTE; Fiscal Year: 2005..Centralizing such access to a secure data warehouse ensures our continued commitment to patient confidentiality and compliance with federal and state regulations. ..