Genomes and Genes
natural language processing
Summary: Computer processing of a language with rules that reflect and describe current usage rather than prescribed usage.
Publications264 found, 100 shown here
- Mayo clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applicationsGuergana K Savova
Mayo Clinic College of Medicine, Rochester, Minnesota, USA
J Am Med Inform Assoc 17:507-13. 2010We aim to build and evaluate an open-source natural language processing system for information extraction from electronic medical record clinical free-text...
- 2010 i2b2/VA challenge on concepts, assertions, and relations in clinical textOzlem Uzuner
Department of Information Studies, University at Albany, State University of New York, Albany, New York 12222, USA
J Am Med Inform Assoc 18:552-6. 2011The 2010 i2b2/VA Workshop on Natural Language Processing Challenges for Clinical Records presented three tasks: a concept extraction task focused on the extraction of medical concepts from patient reports; an assertion classification ..
- The structural and content aspects of abstracts versus bodies of full text journal articles are differentK Bretonnel Cohen
Department of Pharmacology, Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, USA
BMC Bioinformatics 11:492. 2010..However, until now there has been no comprehensive characterization of how the bodies of full text journal articles differ from the abstracts that until now have been the subject of most biomedical text mining research...
- Evaluating contributions of natural language parsers to protein-protein interaction extractionYusuke Miyao
Department of Computer Science, University of Tokyo, Tokyo, Japan
Bioinformatics 25:394-400. 2009..of the explosive growth of information in text form in biomedical papers, selecting appropriate natural language processing (NLP) tools is still difficult for researchers who are not familiar with recent advances in NLP...
- Portability of an algorithm to identify rheumatoid arthritis in electronic health recordsRobert J Carroll
Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
J Am Med Inform Assoc 19:e162-9. 2012..This study evaluated the portability of a published phenotype algorithm to identify rheumatoid arthritis (RA) patients from EHR records at three institutions with different EHR systems...
- Machine-learned solutions for three stages of clinical information extraction: the state of the art at i2b2 2010Berry de Bruijn
Institute for Information Technology, National Research Council, Ottawa, Ontario, Canada
J Am Med Inform Assoc 18:557-62. 2011..A critical part of that process is rigid benchmark testing of natural language processing methods on realistic clinical narrative...
- Extracting medication information from clinical textOzlem Uzuner
Department of Information Studies, University at Albany, State University of New York, Albany, NY, USA
J Am Med Inform Assoc 17:514-8. 2010The Third i2b2 Workshop on Natural Language Processing Challenges for Clinical Records focused on the identification of medications, their dosages, modes (routes) of administration, frequencies, durations, and reasons for administration ..
- Complex event extraction at PubMed scaleJari Björne
Department of Information Technology, University of Turku, Turku, Finland
Bioinformatics 26:i382-90. 2010..A recent collaborative evaluation demonstrated the potential of event extraction systems, yet there have so far been no studies of the generalization ability of the systems nor the feasibility of large-scale extraction...
- All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learningAntti Airola
Turku Centre for Computer Science TUCS and the Department of IT, University of Turku, Joukahaisenkatu 3 5, 20520 Turku, Finland
BMC Bioinformatics 9:S2. 2008..In contrast to earlier approaches to PPI extraction, the introduced all-paths graph kernel has the capability to make use of full, general dependency graphs representing the sentence structure...
- Inter-species normalization of gene mentions with GNATJörg Hakenberg
Department of Computer Science and Engineering, Arizona State University, Tempe, AZ 85287, USA
Bioinformatics 24:i126-132. 2008....
- 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..as a paradigm for investigating the interaction between domain knowledge and linguistic structure in natural language processing, and could also make a contribution to research on automatic processing of discourse structure...
- What can natural language processing do for clinical decision support?Dina Demner-Fushman
U S National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
J Biomed Inform 42:760-72. 2009..b>natural language processing (NLP) is instrumental in using free-text information to drive CDS, representing clinical knowledge and ..
- Extracting principal diagnosis, co-morbidity and smoking status for asthma research: evaluation of a natural language processing systemQing T Zeng
Decision Systems Group, Brigham and Women s Hospital, Boston, MA, USA
BMC Med Inform Decis Mak 6:30. 2006..The text descriptions in electronic medical records are a rich source of information. We have developed a Health Information Text Extraction (HITEx) tool and used it to extract key findings for a research study on airways disease...
- A comprehensive benchmark of kernel methods to extract protein-protein interactions from literatureDomonkos Tikk
Knowledge Management in Bioinformatics, Computer Science Department, Humboldt Universitat zu Berlin, Berlin, Germany
PLoS Comput Biol 6:e1000837. 2010..Nevertheless, our study shows that three kernels are clearly superior to the other methods...
- Electronic Support for Public Health: validated case finding and reporting for notifiable diseases using electronic medical dataRoss Lazarus
Department of Ambulatory Care and Prevention, Harvard Medical School and Harvard Pilgrim Health Care, Boston, MA, USA
J Am Med Inform Assoc 16:18-24. 2009..Source code for this highly interoperable application is freely available under an approved open-source license at http://esphealth.org...
- Building a robust, scalable and standards-driven infrastructure for secondary use of EHR data: the SHARPn projectSusan Rea
Homer Warner Center for Informatics Research, Intermountain Healthcare, Murray, UT 84107, USA
J Biomed Inform 45:763-71. 2012..Based on the demonstration, observed challenges for standardization of EHR data for interoperable secondary use are discussed...
- Recognizing obesity and comorbidities in sparse dataOzlem Uzuner
University at Albany, SUNY, Albany, NY, USA
J Am Med Inform Assoc 16:561-70. 2009..Information on disease-related concepts, such as symptoms and medications, and general medical knowledge help systems infer intuitive judgments on the diseases...
- Literature mining and database annotation of protein phosphorylation using a rule-based systemZ Z Hu
Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, Washington, DC 20057, USA
Bioinformatics 21:2759-65. 2005..While of great value, such information is limited in databases owing to the laborious process of literature-based curation. Computational literature mining holds promise to facilitate database curation...
- 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....
- OrganismTagger: detection, normalization and grounding of organism entities in biomedical documentsNona Naderi
Department of Computer Science and Software Engineering, Concordia University, Montreal, Quebec, Canada
Bioinformatics 27:2721-9. 2011..In addition, such a system must resolve abbreviations and acronyms, assign the scientific name and if possible link the detected mention to the NCBI Taxonomy database for further semantic queries and literature navigation...
- Protein-protein interaction extraction by leveraging multiple kernels and parsersMakoto Miwa
Department of Computer Science, The University of Tokyo, Tokyo, Japan
Int J Med Inform 78:e39-46. 2009..Protein-protein interaction (PPI) extraction is an important and widely researched task in the biomedical natural language processing (BioNLP) field...
- 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..They make outliers immediately apparent, and, thus, serve as a tool for auditing and validating both the semantic network and the semantic groups...
- Active computerized pharmacovigilance using natural language processing, statistics, and electronic health records: a feasibility studyXiaoyan Wang
Department of Biomedical Informatics, Columbia University, 622 West 168 Street, VC5, New York, NY 10032, USA
J Am Med Inform Assoc 16:328-37. 2009..The objective of our work is to demonstrate the feasibility of using natural language processing (NLP), the comprehensive Electronic Health Record (EHR), and association statistics for ..
- Evaluation of text-mining systems for biology: overview of the Second BioCreative community challengeMartin Krallinger
Structural Biology and Biocomputing Programme, Spanish Nacional Cancer Research Centre CNIO, Madrid, Spain
Genome Biol 9:S1. 2008....
- Event extraction with complex event classification using rich featuresMakoto Miwa
Department of Computer Science, University of Tokyo, Hongo 7 3 1, Bunkyo ku, Tokyo, Japan
J Bioinform Comput Biol 8:131-46. 2010Biomedical Natural Language Processing (BioNLP) attempts to capture biomedical phenomena from texts by extracting relations between biomedical entities (i.e. proteins and genes)...
- Evaluating the state-of-the-art in automatic de-identificationOzlem Uzuner
University at Albany, SUNY, Draper 114A, 135 Western Ave, Albany, NY 12222, USA
J Am Med Inform Assoc 14:550-63. 2007..as a part of the i2b2 (Informatics for Integrating Biology to the Bedside) project, authors organized a Natural Language Processing (NLP) challenge on automatically removing private health information (PHI) from medical discharge ..
- High accuracy information extraction of medication information from clinical notes: 2009 i2b2 medication extraction challengeJon Patrick
Faculty of Engineering and IT, The University of Sydney, Sydney, Australia
J Am Med Inform Assoc 17:524-7. 2010..Medication information comprises a most valuable source of data in clinical records. This paper describes use of a cascade of machine learners that automatically extract medication information from clinical records...
- Lancet: a high precision medication event extraction system for clinical textZuofeng Li
College of Health Sciences, University of Wisconsin Milwaukee, Wisconsin, USA
J Am Med Inform Assoc 17:563-7. 2010....
- Evaluating natural language processors in the clinical domainC Friedman
Department of Computer Science, Queens College CUNY, New York, USA
Methods Inf Med 37:334-44. 1998Evaluating natural language processing (NLP) systems in the clinical domain is a difficult task which is important for advancement of the field...
- Description of a rule-based system for the i2b2 challenge in natural language processing for clinical dataLois C Childs
Lockheed Martin, Inc, Valley Forge, Philadelphia, PA, USA
J Am Med Inform Assoc 16:571-5. 2009..The authors describe their methodology and discuss the results of applying Lockheed Martin's rule-based natural language processing (NLP) capability, ClinREAD...
- MITRE system for clinical assertion status classificationCheryl Clark
The MITRE Corporation, Bedford, Massachusetts 01730 1420, USA
J Am Med Inform Assoc 18:563-7. 2011..in clinical reports, which was entered in the 2010 i2b2/VA community evaluation 'Challenges in natural language processing for clinical data' for the task of classifying assertions associated with problem concepts extracted ..
- Anaphoric relations in the clinical narrative: corpus creationGuergana K Savova
Children s Hospital Boston Informatics Program and Harvard Medical School, Boston, Massachusetts 02114, USA
J Am Med Inform Assoc 18:459-65. 2011..The creation of a gold standard set from a cross-institutional corpus of clinical notes and high-level characteristics of that gold standard are described...
- Drug side effect extraction from clinical narratives of psychiatry and psychology patientsSunghwan Sohn
Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
J Am Med Inform Assoc 18:i144-9. 2011..To extract physician-asserted drug side effects from electronic medical record clinical narratives...
- Clinical decision support with automated text processing for cervical cancer screeningKavishwar B Wagholikar
Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota 55905, USA
J Am Med Inform Assoc 19:833-9. 2012..To develop a computerized clinical decision support system (CDSS) for cervical cancer screening that can interpret free-text Papanicolaou (Pap) reports...
- Importance of multi-modal approaches to effectively identify cataract cases from electronic health recordsPeggy L Peissig
Biomedical Informatics Research Center, Marshfield Clinic Research Foundation, Marshfield, Wisconsin 54449, USA
J Am Med Inform Assoc 19:225-34. 2012..We describe the construction and validation of an EHR-based algorithm to identify subjects with age-related cataracts...
- Recognizing names in biomedical texts: a machine learning approachGuodong Zhou
Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613
Bioinformatics 20:1178-90. 2004..In order to make organized and structured information available, automatically recognizing biomedical entity names becomes critical and is important for information retrieval, information extraction and automated knowledge acquisition...
- Web 2.0-based crowdsourcing for high-quality gold standard development in clinical natural language processingHaijun Zhai
Division of Biomedical Informatics, Cincinnati Children s Hospital Medical Center, Cincinnati, OH 45229, USA
J Med Internet Res 15:e73. 2013A high-quality gold standard is vital for supervised, machine learning-based, clinical natural language processing (NLP) systems. In clinical NLP projects, expert annotators traditionally create the gold standard...
- Comparison of natural language processing biosurveillance methods for identifying influenza from encounter notesPeter L Elkin
Mount Sinai School of Medicine, New York, New York, USA
Ann Intern Med 156:11-8. 2012..The BioSense system, used at the Centers for Disease Control and Prevention, incorporates chief complaints but not data from the whole encounter note into its surveillance algorithms...
- Degree centrality for semantic abstraction summarization of therapeutic studiesHan Zhang
Department of Medical Informatics, China Medical University, Shenyang, China
J Biomed Inform 44:830-8. 2011..The results showed that recall for system results was 72%, precision was 73%, and F-score was 0.72. The system F-score was considerably higher than that for the baseline (0.47)...
- A study of machine-learning-based approaches to extract clinical entities and their assertions from discharge summariesMin Jiang
Department of Biomedical Informatics, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232, USA
J Am Med Inform Assoc 18:601-6. 2011..This project was part of the 2010 Center of Informatics for Integrating Biology and the Bedside/Veterans Affairs (VA) natural-language-processing challenge...
- Using machine learning for concept extraction on clinical documents from multiple data sourcesManabu Torii
Lab of Text Intelligence in Biomedicine, Georgetown University Medical Center, Washington, DC 20007, USA
J Am Med Inform Assoc 18:580-7. 2011..It is a critical component in automated text processing. We investigate the performance of machine learning taggers for clinical concept extraction, particularly the portability of taggers across documents from multiple data sources...
- Desiderata for ontologies to be used in semantic annotation of biomedical documentsMichael Bada
Department of Pharmacology, University of Colorado Denver, MS 8303, RC 1 South, 12801 East 17th Avenue, L18 6400, P O Box 6511, Aurora, CO 80045, USA
J Biomed Inform 44:94-101. 2011....
- Building a semantically annotated corpus of clinical textsAngus Roberts
Department of Computer Science, University of Sheffield, Regent Court, 211 Portobello, Sheffield S1 4DP, UK
J Biomed Inform 42:950-66. 2009..The detailed presentation of our corpus construction and annotation methodology will be of value to others seeking to build high-quality semantically annotated corpora in biomedical domains...
- AskHERMES: An online question answering system for complex clinical questionsYonggang Cao
Department of Health Sciences, University of Wisconsin Milwaukee, 2400 E Hartford Avenue, Milwaukee, WI 53211, USA
J Biomed Inform 44:277-88. 2011..We have built a clinical question answering system named AskHERMES to perform robust semantic analysis on complex clinical questions and output question-focused extractive summaries as answers...
- Comparative analysis of five protein-protein interaction corporaSampo Pyysalo
Turku Centre for Computer Science TUCS, Department of IT, University of Turku, Joukahaisenkatu 3 5, 20520 Turku, Finland
BMC Bioinformatics 9:S6. 2008Growing interest in the application of natural language processing methods to biomedical text has led to an increasing number of corpora and methods targeting protein-protein interaction (PPI) extraction...
- An Overview of BioCreative II.5Florian Leitner
Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, Madrid, Spain
IEEE/ACM Trans Comput Biol Bioinform 7:385-99. 2010..42 and AUC iP/R was 0.29. Ensemble systems improved performance for the interacting protein task...
- ABNER: an open source tool for automatically tagging genes, proteins and other entity names in textBurr Settles
Department of Computer Sciences and Department of Biostatistics and Medical Informatics, University of Wisconsin Madison Madison, WI 52706, USA
Bioinformatics 21:3191-2. 2005..It also includes a Java application programming interface allowing users to incorporate ABNER into their own systems and train models on new corpora...
- MedEx: a medication information extraction system for clinical narrativesHua Xu
Department of Biomedical Informatics, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232, USA
J Am Med Inform Assoc 17:19-24. 2010..We describe a new natural language processing system (MedEx), which extracts medication information from clinical notes...
- Evaluation of a generalizable approach to clinical information retrieval using the automated retrieval console (ARC)Leonard W D'Avolio
Massachusetts Veterans Epidemiology Research and Information Center Cooperative Studies Coordinating Center, VA Boston Healthcare System, Jamaica Plain, Massachusetts 02130, USA
J Am Med Inform Assoc 17:375-82. 2010..set, the automated retrieval console (ARC) iteratively calculated performance of combinations of natural language processing-derived features and supervised classification algorithms...
- Automated identification of postoperative complications within an electronic medical record using natural language processingHarvey J Murff
Tennessee Valley Healthcare System, Veterans Affairs Medical Center, Nashville, TN, USA
JAMA 306:848-55. 2011..Currently most automated methods to identify patient safety occurrences rely on administrative data codes; however, free-text searches of electronic medical records could represent an additional surveillance approach...
- Agreement between patient-reported symptoms and their documentation in the medical recordSerguei V Pakhomov
Department of Pharmaceutical Care and Health Systems, University of Minnesota, 308 Harvard St, SE, 7 125F Weaver Densford Hall, Minneapolis, MN 55401, USA
Am J Manag Care 14:530-9. 2008..To determine the agreement between patient-reported symptoms of chest pain, dyspnea, and cough and the documentation of these symptoms by physicians in the electronic medical record...
- Mayo clinic NLP system for patient smoking status identificationGuergana K Savova
Biomedical Informatics Research, Mayo Clinic, 200 First Street SW, Rochester, MN 55902, USA
J Am Med Inform Assoc 15:25-8. 2008This article describes our system entry for the 2006 I2B2 contest "Challenges in Natural Language Processing for Clinical Data" for the task of identifying the smoking status of patients...
- A recent advance in the automatic indexing of the biomedical literatureAurélie Névéol
National Institutes of Health, US National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA
J Biomed Inform 42:814-23. 2009..b>Natural Language Processing, statistical, and machine learning methods of producing automatic MeSH main heading/subheading pair ..
- Natural language processing in aid of FlyBase curatorsNikiforos Karamanis
Computer Laboratory, University of Cambridge, William Gates Building, Cambridge, CB3 0FD, UK
BMC Bioinformatics 9:193. 2008Despite increasing interest in applying Natural Language Processing (NLP) to biomedical text, whether this technology can facilitate tasks such as database curation remains unclear.
- Medication information extraction with linguistic pattern matching and semantic rulesIrena Spasic
Cardiff School of Computer Science and Informatics, Cardiff University, Cardiff, UK
J Am Med Inform Assoc 17:532-5. 2010This study presents a system developed for the 2009 i2b2 Challenge in Natural Language Processing for Clinical Data, whose aim was to automatically extract certain information about medications used by a patient from his/her medical ..
- Cascaded classifiers for confidence-based chemical named entity recognitionPeter Corbett
Unilever Centre for Molecular Science Informatics, Chemical Laboratory, University of Cambridge, CB21EW UK
BMC Bioinformatics 9:S4. 2008..Chemical named entities represent an important facet of biomedical text...
- Evaluation of linguistic features useful in extraction of interactions from PubMed; application to annotating known, high-throughput and predicted interactions in I2DYun Niu
Ontario Cancer Institute, UHN, 101 College Street, Toronto, Ontario M5G1L7, Canada
Bioinformatics 26:111-9. 2010..More accurate PPI detection will also improve the ability to extract experimental data related to PPIs and provide multiple evidence for each interaction...
- A new measure for functional similarity of gene products based on Gene OntologyAndreas Schlicker
Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrucken, Germany
BMC Bioinformatics 7:302. 2006..These annotations provide a basis for new methods that compare gene products regarding their molecular function and biological role...
- Biomedical negation scope detection with conditional random fieldsShashank Agarwal
Medical Informatics, University of Wisconsin Milwaukee, Milwaukee, Wisconsin, USA
J Am Med Inform Assoc 17:696-701. 2010..Text mining applications benefit from the detection of negation and its scope. However, due to the complexity of language, identifying the scope of negation in a sentence is not a trivial task...
- GOstat: find statistically overrepresented Gene Ontologies within a group of genesTim Beissbarth
Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3050, Australia
Bioinformatics 20:1464-5. 2004..This program automatically obtains the GO annotations from a database and generates statistics of which annotations are overrepresented in the analyzed list of genes. This results in a list of GO terms sorted by their specificity...
- Automatic detection of acute bacterial pneumonia from chest X-ray reportsM Fiszman
The University of Utah, Salt Lake City, Utah, USA
J Am Med Inform Assoc 7:593-604. 2000To evaluate the performance of a natural language processing system in extracting pneumonia-related concepts from chest x-ray reports.
- Constructing biological networks through combined literature mining and microarray analysis: a LMMA approachShao Li
Bioinformatics Division, TNLIST and Department of Automation, Tsinghua University, Beijing 100084, China
Bioinformatics 22:2143-50. 2006..This work focuses on integrating both the literatures and microarray gene-expression data, and a combined literature mining and microarray analysis (LMMA) approach is developed to construct gene networks of a specific biological system...
- Automated detection of adverse events using natural language processing of discharge summariesGenevieve B Melton
Department of Biomedical Informatics, Columbia University, 622 West 168th Street, Vanderbilt Clinic, 5th Floor, New York, NY 10032, USA
J Am Med Inform Assoc 12:448-57. 2005To determine whether natural language processing (NLP) can effectively detect adverse events defined in the New York Patient Occurrence Reporting and Tracking System (NYPORTS) using discharge summaries.
- Development and evaluation of an open source software tool for deidentification of pathology reportsBruce A Beckwith
Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Ave, Boston, MA, USA
BMC Med Inform Decis Mak 6:12. 2006..1800 new pathology reports were then processed. Each report was reviewed manually before and after deidentification to catalog all identifiers and note those that were not removed...
- MedScan, a natural language processing engine for MEDLINE abstractsSvetlana Novichkova
Ariadne Genomics, Inc, 9100 Great Seneca HWY, Rockville, MD 20850, USA
Bioinformatics 19:1699-706. 2003..Most proposals to date make rather simplistic assumptions about the syntactic aspect of natural language. There is an urgent need for a system that has broad coverage and performs well in real-text applications...
- Abbreviation definition identification based on automatic precision estimatesSunghwan Sohn
National Centre for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
BMC Bioinformatics 9:402. 2008..The pseudo-precisions determine the order in which the algorithm applies the strategies in seeking to identify the definition of an abbreviation...
- Recognizing speculative language in biomedical research articles: a linguistically motivated perspectiveHalil Kilicoglu
Department of Computer Science and Software Engineering, 1455 De Maisonneuve Blvd West, H3G1M8 Montréal, Quebec, Canada
BMC Bioinformatics 9:S10. 2008..Weights of hedging cues are used to determine the speculative strength of sentences...
- Use of natural language processing to translate clinical information from a database of 889,921 chest radiographic reportsGeorge Hripcsak
Department of Medical Informatics, Columbia University, 622 W 168th St, VC 5, New York, NY 10032, USA
Radiology 224:157-63. 2002To evaluate translation of chest radiographic reports by using natural language processing and to compare the findings with those in the literature.
- Frontiers of biomedical text mining: current progressPierre Zweigenbaum
LIMSI CNRS, BP 133, 91403 Orsay Cedex, France
Brief Bioinform 8:358-75. 2007..In this article we review the current state of the art in biomedical text mining or 'BioNLP' in general, focusing primarily on papers published within the past year...
- Medical i2b2 NLP smoking challenge: the A-Life system architecture and methodologyDaniel T Heinze
A Life Medical, Inc, San Diego, CA, USA
J Am Med Inform Assoc 15:40-3. 2008We describe the architecture of LifeCode (A-Life Medical, Inc.), a natural language processing system for free-text clinical information extraction, our methodology in applying LifeCode to the i2b2 smoking challenge, and statistical ..
- Evaluating temporal relations in clinical text: 2012 i2b2 ChallengeWeiyi Sun
Department of Informatics, University at Albany, SUNY, Albany, New York, USA
J Am Med Inform Assoc 20:806-13. 2013The Sixth Informatics for Integrating Biology and the Bedside (i2b2) Natural Language Processing Challenge for Clinical Records focused on the temporal relations in clinical narratives...
- A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing toolsKarin Verspoor
Computational Bioscience Program, U, Colorado School of Medicine, 12801 E 17th Ave, Aurora, MS 8303, CO 80045, USA
BMC Bioinformatics 13:207. 2012..We further assess the performance of existing tools for performing sentence splitting, tokenization, syntactic parsing, and named entity recognition on this corpus...
- Automatically extracting cancer disease characteristics from pathology reports into a Disease Knowledge Representation ModelAnni Coden
IBM T J Watson Research Center, 19 Skyline Drive, Hawthorne, NY 10532, USA
J Biomed Inform 42:937-49. 2009..MedTAS/P is based on an open-source framework and its components use natural language processing principles, machine learning and rules to discover and populate elements of the model...
- Towards comprehensive syntactic and semantic annotations of the clinical narrativeDaniel Albright
Department of Linguistics, University of Colorado, Boulder, Colorado, USA
J Am Med Inform Assoc 20:922-30. 2013To create annotated clinical narratives with layers of syntactic and semantic labels to facilitate advances in clinical natural language processing (NLP). To develop NLP algorithms and open source components.
- Automatic generation of natural language nursing shift summaries in neonatal intensive care: BT-NurseJames Hunter
Department of Computing Science, University of Aberdeen, King s College, Aberdeen AB24 3UE, UK
Artif Intell Med 56:157-72. 2012..Our objective was to determine whether and how a computer system could automatically generate helpful natural language nursing shift summaries solely from an electronic patient record system, in a neonatal intensive care unit (NICU)...
- An evaluation of the NQF Quality Data Model for representing Electronic Health Record driven phenotyping algorithmsWilliam K Thompson
Northwestern University, Chicago, IL, USA
AMIA Annu Symp Proc 2012:911-20. 2012..However, we also found areas in which the QDM could be usefully extended, such as representing information extracted from clinical text, and the ability to handle algorithms that do not consist of Boolean combinations of criteria...
- Evaluation of natural language processing from emergency department computerized medical records for intra-hospital syndromic surveillanceSolweig Gerbier
Hospices Civils de Lyon, Hopital de la Croix Rousse, Unité d hygiène et d épidémiologie, F 69317 Lyon, France
BMC Med Inform Decis Mak 11:50. 2011..The purpose of the present article is to describe and evaluate this natural language processing system.
- Natural language processing with dynamic classification improves P300 speller accuracy and bit rateWilliam Speier
Biomedical Engineering Interdepartmental Program, University of California, Los Angeles, CA, USA
J Neural Eng 9:016004. 2012..With integration of natural language processing, we observed significant improvements in accuracy and 40-60% increases in bit rate for all six subjects ..
- Automatic classification of mammography reports by BI-RADS breast tissue composition classBethany Percha
Biomedical Informatics Program, Stanford University, Stanford, California 94305 5488, USA
J Am Med Inform Assoc 19:913-6. 2012..Since large-scale studies of breast cancer rely heavily on breast tissue composition information, this method could facilitate this research by helping mine large datasets to correlate breast composition with other covariates...
- Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databasesAndrew Chatr-Aryamontri
School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, UK
BMC Bioinformatics 12:S8. 2011..The development of efficient tools based on natural language processing (NLP) systems is essential for the selection of relevant publications, identification of data ..
- Automatic computation of CHA2DS2-VASc score: information extraction from clinical texts for thromboembolism risk assessmentCyril Grouin
LIMSI CNRS, F 91043 Orsay, France
AMIA Annu Symp Proc 2011:501-10. 2011..In this article, we present a system based on natural language processing (lexicon and linguistic modules), including negation and speculation handling, which extracts medical ..
- Extracting information on pneumonia in infants using natural language processing of radiology reportsEneida A Mendonca
Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA
J Biomed Inform 38:314-21. 2005b>Natural language processing (NLP) is critical for improvement of the healthcare process because it can encode clinical data in patient documents...
- Named entity recognition for bacterial Type IV secretion systemsSophia Ananiadou
School of Computer Science, University of Manchester, Manchester, United Kingdom
PLoS ONE 6:e14780. 2011..Contrastive experiments highlighted the effectiveness of alternate recognition strategies; results of term extraction on contrasting document sets demonstrated the utility of these classes for identifying T4SS-related documents...
- Rutabaga by any other name: extracting biological namesLynette Hirschman
The MITRE Corporation, MS K312, 202 Burlington Rd, Bedford, MA 01730, USA
J Biomed Inform 35:247-59. 2002..Information extraction has been an active area of research in natural language processing and there are promising results for information extraction applied to news stories, e.g...
- Semantic classification of diseases in discharge summaries using a context-aware rule-based classifierIllés Solt
Department of Media Informatics and Telematics, Budapest University of Technology and Economics, Budapest, Hungary
J Am Med Inform Assoc 16:580-4. 2009....
- Detection of interaction articles and experimental methods in biomedical literatureGerold Schneider
Institute of Computational Linguistics, University of Zurich, 8050 Zurich, Switzerland
BMC Bioinformatics 12:S13. 2011....
- Building a high-quality sense inventory for improved abbreviation disambiguationNaoaki Okazaki
Graduate School of Information Science and Technology, University of Tokyo, Tokyo, Japan
Bioinformatics 26:1246-53. 2010..Consequently, a list of expanded forms should be structured into a sense inventory, which provides possible concepts or senses for abbreviation disambiguation...
- Natural language processing: an introductionPrakash M Nadkarni
Yale University School of Medicine, New Haven, Connecticut, USA
J Am Med Inform Assoc 18:544-51. 2011To provide an overview and tutorial of natural language processing (NLP) and modern NLP-system design.
- 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..Analysis reveals that these differences are caused by the nature of each ambiguity type. These results should be taken into account when deciding which information to use for WSD and the level of performance that can be expected...
- Exploring hedge identification in biomedical literatureBen Medlock
University of Cambridge, Computer Laboratory, William Gates Building, 15 JJ Thomson Avenue, Cambridge CB3OFD, UK
J Biomed Inform 41:636-54. 2008..Finally, we examine the errors made by our approach and point toward avenues for future research...
- Corpus annotation for mining biomedical events from literatureJin Dong Kim
Department of Computer Science, School of Information Science and Technology, University of Tokyo, Tokyo, Japan
BMC Bioinformatics 9:10. 2008..However, due to the complexity of the task, semantic annotation has never been tried on a large scale, apart from relatively simple term annotation...
- Natural Language Processing methods and systems for biomedical ontology learningKaihong Liu
Department of Biomedical Informatics, University of Pittsburgh School of Medicine, PA 15232, USA
J Biomed Inform 44:163-79. 2011..Methodologies developed in the fields of Natural Language Processing, information extraction, information retrieval and machine learning provide techniques for automating ..
- 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. 2012..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...
- Enhancing clinical concept extraction with distributional semanticsSiddhartha Jonnalagadda
Department of Biomedical Informatics, Arizona State University, Phoenix, AZ, USA
J Biomed Inform 45:129-40. 2012..Thus, distributional semantic features significantly improve the performance of concept extraction from clinical narratives by taking advantage of word distribution information obtained from unannotated data...
- 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..We have released all tools developed as part of this study as open source, available at http://code.google.com/p/ytex...
- Integrating existing natural language processing tools for medication extraction from discharge summariesSon Doan
Department of Biomedical Informatics, Vanderbilt University, School of Medicine, Nashville, TN, USA
J Am Med Inform Assoc 17:528-31. 2010..system to extract medications and related information from discharge summaries as part of the 2009 i2b2 natural language processing (NLP) challenge...
- Measures of semantic similarity and relatedness in the biomedical domainTed Pedersen
Department of Computer Science, 1114 Kirby Drive, University of Minnesota, Duluth, MN 55812, USA
J Biomed Inform 40:288-99. 2007Measures of semantic similarity between concepts are widely used in Natural Language Processing. In this article, we show how six existing domain-independent measures can be adapted to the biomedical domain...
- A rule-based approach for identifying obesity and its comorbidities in medical discharge summariesNinad K Mishra
Centers for Disease Control and Prevention, 1600 Clifton Rd, Mail Stop E76, Atlanta, GA, USA
J Am Med Inform Assoc 16:576-9. 2009..Further, the approach held up well in relation to more complex approaches applied to this classification task. The approach could be enhanced by the addition of expert rules to model more complex medical reasoning...
- Textractor: a hybrid system for medications and reason for their prescription extraction from clinical text documentsStephane M Meystre
Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah, USA
J Am Med Inform Assoc 17:559-62. 2010..OBJECTIVE To describe a new medication information extraction system-Textractor-developed for the 'i2b2 medication extraction challenge'. The development, functionalities, and official evaluation of the system are detailed...
- Terminology-driven mining of biomedical literatureGoran Nenadic
Computer Science, University of Salford, Salford M5 4WT, UK
Bioinformatics 19:938-43. 2003..Although the knowledge is organized around sets of domain-specific terms, few literature mining systems incorporate deep and dynamic terminology processing...
- Biomedical text summarization to support genetic database curation: using Semantic MEDLINE to create a secondary database of genetic informationT Elizabeth Workman
Department of Biomedical Informatics, University of Utah, 26 S 2000 E, HSEB 5700, Salt Lake City, UT 84112, USA
J Med Libr Assoc 98:273-81. 2010....
- The ODIE Toolkit - Software for Information Extraction and Biomedical Ontology DeRebecca S Crowley; Fiscal Year: 2010..Additionally, the project would contribute to the software for developing other applications by helping researchers build more comprehensive ontologies. The results of this work may benefit both medical research and patient care. ..
- Automated Literature Mining for Validation of High-Throughput Function PredictionKARIN MARIA VERSPOOR; Fiscal Year: 2010..It is time to truly integrate the biological literature into the protein function prediction problem. By doing so, we will enable a critical advance in high-throughput protein function prediction ..
- Assisting Systematic Review Preparation Using Automated Document ClassificationAaron Cohen; Fiscal Year: 2009..Since up-to-date systematic reviews are essential for establishing widespread high quality practice standards and guidelines, the overall public health will benefit from this work. ..
- Improving Guideline Development and ImplementationRichard N Shiffman; Fiscal Year: 2010..In addition, the proposed activities focus on systems that will preferentially impact children - a particularly vulnerable population. ..
- Flexible NLP system for MEDLINE information extractionNikolai Daraselia; Fiscal Year: 2003..The system we proposed will be based on advanced natural language processing (NLP) technologies, and uses it as a fast and reliable way to extract information about protein ..
- Interoperation of Genome Databases and ToolsKei Hoi Cheung; Fiscal Year: 2005..We will extend our approach to other types of genomic data such as microarray data, which both laboratories and others will soon be generating in large quantities. ..
- PubAssist - an NLP-based document search systemNikolai Daraselia; Fiscal Year: 2005..Customers who install the server-based semantic indexing engine in addition to the PubAssist client will be able to process their proprietary documents and customize the NLP algorithm. ..
- Automating Assessment of Asthma Care QualityBrian Hazlehurst; Fiscal Year: 2008..At each study site, the MediClass system will extract coded data and use natural language processing (NLP) on free-text clinical notes to identify ACQ-relevant clinical events in the electronic medical ..
- A Toxicological Knowledge Base PrototypeNikolai Daraselia; Fiscal Year: 2007..We believe that such a knowledge base can facilitate research in the pharmaceutical and drug discovery fields and will be highly useful to many researchers in these areas. [unreadable] [unreadable] [unreadable]..
- 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. ..
- Pramipexole in Treatment-Resistant DepressionRoy Perlis; Fiscal Year: 2007..The proposed investigation and training program will provide critical skills, experience and data to aid the candidate in writing an R01 and becoming an independent investigator. ..
- Cost-effectiveness of automated telephone outreach in patients with lung diseaseDavid H Smith; Fiscal Year: 2010..We will carry out an evaluation of the cost-effectiveness (efficiency) of the automated phone calls. (End of Abstract) ..
- Signal Detection for Prescription Opioid OutbreaksStephen Butler; Fiscal Year: 2008..This system should be perceived by stakeholders as highly valuable. Thus, we believe this product has enormous commercial viability and public health importance. [unreadable] [unreadable] [unreadable] [unreadable]..
- Cancer Narratives for Low-Literacy Adult LearnersCOLLEEN CRANGLE; Fiscal Year: 2003..Phase I locates its evaluation activities within Project Read, a library-based adult learning service in California. ..
- WEB-BASED MANAGEMENT TRAINING: ADDICTION-RESOURCES.COMStephen Butler; Fiscal Year: 2003..An analogue field trial will examine, in contrast to a written booklet and wait-list control, the website's effectiveness in facilitating managers to more use of clinical data in decision-making. ..
- Protein Functional Site Characterization and AnalysisPhilip E Bourne; Fiscal Year: 2010..The results of this effort will be disseminated through the Protein Data Bank which is used by over 10,000 scientists every day. ..
- Searching Genomes for Non-Coding RNAs by Their StructureLiming Cai; Fiscal Year: 2009..Our proposed research will help biologists find RNA molecules of interest in the mass of genome sequence data being generated. ..
- 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. ..
- Tools & Data Resources in Support of Structural GenomicsPHILIP BOURNE; Fiscal Year: 2006..The proposed public resource will complement the private software and data resulting from the individual structural genomics centers as they undertake competitive high throughput structure determination. ..
- 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. ..
- ISMB 2005 Conf. Support for Students & Young ScientistsPHILIP BOURNE; Fiscal Year: 2005..This proposal seeks to assist them at this critical but resource-limited stage in their careers. ..
- Communicating probabilities through interactive computer graphicsRita Kukafka; Fiscal Year: 2007..unreadable] [unreadable] [unreadable]..
- INTERPERSONAL DISCLOSURE PROCESSES AND HEALTHJames Pennebaker; Fiscal Year: 2004..Measures of physician use, autonomic functioning, and illness reports will serve as outcome measures and correlates in each of the studies. ..
- A DNA SEQUENCE ASSEMBLY PROGRAMXiaoqiu Huang; Fiscal Year: 2003..The investigators will also assist the integration of their assembly program into sequencing environments at other genome centers. ..
- Tool to Integrate Genomic and Proteomic Data of AgingZOE LACROIX; Fiscal Year: 2002..Aim 2: Enhance the access to information related to age-related diseases, disorders and disabilities through the exploration of multiple data sources. ..
- 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. ..
- I-Talk: Eye Controlled, Direct Selection AAC DeviceGREGORY LESHER; Fiscal Year: 2002..abstract_text> ..
- Statewide Implementation of Electronic Health RecordsDavid Bates; Fiscal Year: 2006..Dissemination of the results of this work should speed efforts toward the establishment of a national health information infrastructure. [unreadable] [unreadable]..
- Determinants of arterial function in hypertensionIftikhar J Kullo; Fiscal Year: 2010..The aim of our investigation is to identify novel proteins and genes that influence arterial function. Such work will help in identifying those at risk of developing arterial disease and facilitate development of new therapies. ..
- Functional Arterial Changes in AtherogenesisIftikhar Kullo; Fiscal Year: 2007..abstract_text> ..
- Allergy Alerts in Computerized Physician EntryDavid Bates; Fiscal Year: 2001..We believe the results of our work will improve patient safety and the overall quality of pharmacotherapy. We also believe that the results of our study will be applicabe to other healthcare systems ..
- Internet Based Patient-Centered Asthma Management SystemDimitri Christakis; Fiscal Year: 2009..Children in AsthmaNet families will be more likely to report using written care plans. Aim 4: to decrease the number of symptom days for children with asthma H4. Children in AsthmaNet families will experience fewer symptom days. ..
- ASI-MV.net: A Prescription Medication Monitoring ToolStephen Butler; Fiscal Year: 2006..Phase II will fully develop the ASI-MV.net website and establish its reliability and validity. The ASI-MV.net will be an innovative solution to problems collecting product-specific addictions data in real time. [unreadable] [unreadable]..
- The Role of Microsatellite Instability in CancerHarold Garner; Fiscal Year: 2005..We will also (Aim 3) investigate the effects of these mutations identified in Aim 2 on splicing by correlating them with the results of a quantitative global survey of splicing isoforms. ..
- Internet Monitoring Of Prescription Drug AbuseStephen Butler; Fiscal Year: 2006..Phase II will see development of a full prototype of PRISM and demonstration of its reliability and internal and external validity. [unreadable] [unreadable] [unreadable] [unreadable]..
- A Literature Curation Tool for Organism DatabasesSeung Rhee; Fiscal Year: 2003..The system will be central to the curation efforts of the collaborating databases and will be useable as a whole or in parts by other existing or emerging MODs. ..
- Data Structuring and Visualization System for Neuro-oncologyRicky K Taira; Fiscal Year: 2010..The structuring tools should lead to improvements in the quality of clinical research databases. ..
- Force and Measurement Device - Phase IIRory Cooper; Fiscal Year: 2003..g. playgrounds, parks, etc.). ..
- First International Biocurator MeetingSeung Rhee; Fiscal Year: 2006..unreadable] [unreadable] [unreadable]..
- Enhancing Organism Based Disease Knowledge Via Name Based Taxonomic IntelligenceIndra N Sarkar; Fiscal Year: 2010..Through regular collaboration events, such as annual workshops, the proposed research will continually evaluate the value of the deliverables and findings with a team of experts and potential beneficiaries from around the world. ..
- Sematic Relatedness for Active Medication Safety and Outcomes SurveillanceSerguei V S Pakhomov; Fiscal Year: 2010..Sophisticated natural language processing systems have been developed to find medical terms and their synonyms in the unstructured text and use ..
- A Spanish Adaptation of the ASI-Multimedia VersionStephen Butler; Fiscal Year: 2002..Due to its reliability and low cost, we believe the ASI-MV could become the "Gold Standard" addictions assessment. Under such a circumstance, a Spanish adaptation would enjoy widespread use and profitability. ..
- Computational Methods for Personalized and Adaptive Cognitive TrainingRebecca S Crowley; Fiscal Year: 2010..Work in these areas has the potential to deeply impact the fields of patient safety, medical simulation and competency- based assessment, in addition to guiding the development of future medical training systems. ..
- A Chinese Adaptation of the ASI-Multimedia VersionStephen Butler; Fiscal Year: 2004..The final product will be marketed as part of our extensive suite of substance abuse-related, multimedia tools. ..
- Computerized ASI Follow-up and Outcome SystemStephen Butler; Fiscal Year: 2004..Client acceptance will be evaluated along with correspondence between the IVR and traditional ASI administration. Phase II will evaluate the system's validity, capacity to produce acceptable response rates, and cost-effectiveness. ..
- Integrated Neuroinformatics Resource for Alcoholism (IN*Lawrence Hunter; Fiscal Year: 2005..sequence analysis, gene expression array analysis, characterization of Biochemical pathways, and natural language processing to support hypothesis generation and testing regarding ethanol Consumption and neuroadaptation to ..
- Pain Assessment Interview and Clinical Advisory SystemStephen Butler; Fiscal Year: 2008..Thus, we believe this product has enormous commercial viability and public health importance. [unreadable] [unreadable] [unreadable] [unreadable]..
- Proteomic Markers of ArteriosclerosisIftikhar Kullo; Fiscal Year: 2008..unreadable] [unreadable]..
- Parent Initiated Prevention ProgramDimitri Christakis; Fiscal Year: 2005..3) To improve parental perceptions of the quality of care provided.H3: Compared to controls, PIPP parents will report higher scores on selected Consumer Assessment of Health Plans (CAHPS) items. ..
- Biomarkers of Peripheral Arterial DiseaseIftikhar Kullo; Fiscal Year: 2007..abstract_text> ..
- MULTIMEDIA SMOKING CESSATION FOR ALCOHOLIC CLIENTSStephen Butler; Fiscal Year: 2002..If a computerized, affordable smoking cessation program can be shown, in field trials, to have demonstrable efficacy, the commercial potential can be extraordinary. ..
- Advanced 3D Control Techniques for Powered WheelchairsRory Cooper; Fiscal Year: 2006..This pilot study will provide the means to conduct a large-scale trial designed to implement robust controllers in electric powered wheelchairs and test the effect on safety, mobility, and community participation. ..
- Screening for Addiction Risk in Chronic Opioid TherapyStephen Butler; Fiscal Year: 2005..Substantial Phase III support has been committed by Endo Pharmaceuticals. The resulting measure should be reliable, valid, and easy to use in practice settings. ..
- Biomedical Ontology and Tools for Database CurationCOLLEEN CRANGLE; Fiscal Year: 2005..Evaluate the effectiveness of the new tool and methods by comparing its results to those of the SGD curators for gene products that have GO functional annotations with evidence code IDA (Inferred from Direct Assay). ..
- A Computerized Adaptive Testing Version of the ASIStephen Butler; Fiscal Year: 2007..The availability of this new tool should enhance the quality and reduce the cost of research and treatment in the substance abuse area. [unreadable] [unreadable] [unreadable] [unreadable]..
- HERMES - Help physicians to Extract and aRticulate Multimedia information from liHong Yu; Fiscal Year: 2009..5) Design a usability study to measure efficacy, accuracy and perceived ease of use of HERMES and to compare HERMES with other information systems. ..