Research Topics
| Carol FriedmanSummaryAffiliation: Columbia University Country: USA Publications
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Detail Information
Publications
Bio-Ontology and text: bridging the modeling gapCarol Friedman
Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA
Bioinformatics 22:2421-9. 2006....- Mapping abbreviations to full forms in biomedical articlesHong Yu
Department of Medical Informatics, Columbia University, New York, New York 10032, USA
J Am Med Inform Assoc 9:262-72. 2002..To develop methods that automatically map abbreviations to their full forms in biomedical articles... - 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... 
ISO reference terminology models for nursing: applicability for natural language processing of nursing narrativesSuzanne Bakken
School of Nursing, Columbia University, New York, NY 10032, USA
Int J Med Inform 74:615-22. 2005..Our analysis also suggests areas for extension of MedLEE particularly in regard to represent nursing actions...- Qualitative assessment of the International Classification of Functioning, Disability, and Health with respect to the desiderata for controlled medical vocabulariesMichael E Bales
Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA
Int J Med Inform 75:384-95. 2006..Therefore, it could serve as a base from which to develop a formal terminology of functioning and disability. This assessment is a key next step in the development of the ICF as a sensitive, universal measure of functional status... - 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..Our results demonstrate that the framework is feasible although there are some challenging issues. To the best of our knowledge, this is the first study using comprehensive unstructured data from the EHR for pharmacovigilance... - A vocabulary development and visualization tool based on natural language processing and the mining of textual patient reportsCarol Friedman
Department of Medical Informatics, Columbia University, 622 West 168 Street, VC 5 Bldg, New York, NY 10032, USA
J Biomed Inform 36:189-201. 2003.... - Natural language processing and visualization in the molecular imaging domainP Karina Tulipano
Department of Biomedical Informatics, Columbia University, 622 West 168th Street, Vanderbilt Clinic Floor 5, NY 10032, USA
J Biomed Inform 40:270-81. 2007..74 (95% CI: [.70-.76]) and 0.70 (95% CI [.63-.76]), respectively. We adapt a JAVA viewer known as PGviewer for the simultaneous visualization of images with NLP extracted information... - Gene symbol disambiguation using knowledge-based profilesHua Xu
Department of Biomedical Informatics, Columbia University, New York City, New York, USA
Bioinformatics 23:1015-22. 2007..Existing knowledge sources, such as Entrez Gene and the MEDLINE database, contain information concerning the characteristics of a particular gene that could be used to disambiguate gene symbols... - GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway dataAndrey Rzhetsky
Columbia Genome Center, Columbia University, New York, NY 10032, USA
J Biomed Inform 37:43-53. 2004..GeneWays is designed as an open platform, allowing researchers to query, review, and critique stored information... - Terminology model discovery using natural language processing and visualization techniquesLi Zhou
Department of Biomedical Informatics, Columbia University, New York, NY, USA
J Biomed Inform 39:626-36. 2006..We believe that a general method based on NLP and information visualization will facilitate the modeling of medical terminologies... - 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... - Probabilistic inference of molecular networks from noisy data sourcesIvan Iossifov
Department of Medical Informatics, Columbia University, New York, NY 10032, USA
Bioinformatics 20:1205-13. 2004..We further explore the prediction limits, given experimental data that cover only part of the underlying protein networks. This approach can be extended naturally to include other types of biological data sources... - Gene name ambiguity of eukaryotic nomenclaturesLifeng Chen
Department of Biomedical Informatics, Columbia University New York, NY 10032, USA
Bioinformatics 21:248-56. 2005..However, gene name ambiguity is a serious problem because it affects the appropriate identification of gene entities. In this paper, we explore the extent of the problem and suggest ways to address it... - Visualizing information across multidimensional post-genomic structured and textual databasesYing Tao
Department of Biomedical Informatics, Columbia University, 622 West 168th Street, Vanderbilt Clinic, 5th Floor, New York, NY 10032, USA
Bioinformatics 21:1659-67. 2005..AVAILABILITY: PhenogenesViewer as well as its support and tutorial are available at http://www.dbmi.columbia.edu/pgviewer/ CONTACT: ... - Of truth and pathways: chasing bits of information through myriads of articlesMichael Krauthammer
Department of Medical Informatics, Columbia University, New York, NY 10032, USA
Bioinformatics 18:S249-57. 2002..We hope that in the future such a model can be useful for automatically producing consensus views of molecular interaction data... - Characterizing environmental and phenotypic associations using information theory and electronic health recordsXiaoyan Wang
Dept of Biomedical Informatics, Columbia University, New York 10032, USA
BMC Bioinformatics 10:S13. 2009..In particular, some associations are indirect relations due to interdependencies among the data... - Human and automated coding of rehabilitation discharge summaries according to the International Classification of Functioning, Disability, and HealthRita Kukafka
Department of Biomedical Informatics, Vanderbilt Clinic, New York, NY 10032, USA
J Am Med Inform Assoc 13:508-15. 2006..The goal of this research was to investigate human and automated coding of functional status information using the ICF framework... - Two biomedical sublanguages: a description based on the theories of Zellig HarrisCarol Friedman
Department of Medical Informatics, Columbia University, VC5, Vanderbilt Building, 622 West 168th Street, New York, NY 10032 3720, USA
J Biomed Inform 35:222-35. 2002..The two domains and their associated sublanguages discussed are: the clinical domain, where the text consists of patient reports, and the biomolecular domain, where the text consists of complete journal articles... - 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..The new classification is useful for auditing the original UMLS semantic classification and for building biomedical text mining applications. AVAILABILITY: http://www.dbmi.columbia.edu/~juf7002/reclassify_production.. - Information theory applied to the sparse gene ontology annotation network to predict novel gene functionYing Tao
Department of Biomedical Informatics, Columbia University, 622 West 168th Street, VC5, New York, NY 10032, USA
Bioinformatics 23:i529-38. 2007..To our knowledge, no prediction method has been demonstrated to be highly accurate for sparsely annotated GO terms (those associated to fewer than 10 genes)... - A drug-adverse event extraction algorithm to support pharmacovigilance knowledge mining from PubMed citationsWei Wang
Dept of Biomedical Informatics, Columbia University, New York, NY, USA
AMIA Annu Symp Proc 2011:1464-70. 2011..For further proof of concept this method was applied to 48 drugs to determine whether they caused another AE, myocardial infarction. Results showed that AUROC was 0.93 and 0.86 respectively... 
A new clustering method for detecting rare senses of abbreviations in clinical notesHua Xu
Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37203, USA
J Biomed Inform 45:1075-83. 2012..Further analysis demonstrated that the improvement by the TCRS method was mainly from additionally detected rare senses, thus indicating its usefulness for building more complete sense inventories of clinical abbreviations...- Facilitating adverse drug event detection in pharmacovigilance databases using molecular structure similarity: application to rhabdomyolysisSantiago Vilar
Department of Biomedical Informatics, Columbia University Medical Center, New York, New York 10032, USA
J Am Med Inform Assoc 18:i73-80. 2011..Various data mining approaches have been developed that use AERS to detect signals identifying associations between drugs and ADE. The signals must then be monitored further by domain experts, which is a time-consuming task... - Selecting information in electronic health records for knowledge acquisitionXiaoyan Wang
Department of Biomedical Informatics, Columbia University, New York, NY 10032, United States
J Biomed Inform 43:595-601. 2010..Further investigation of complementary methods, such as more sophisticated statistical methods, more complex temporal models and use of information from other knowledge sources, is needed... - Using distributional analysis to semantically classify UMLS conceptsJung Wei Fan
Department of Biomedical Informatics, Columbia University, USA
Stud Health Technol Inform 129:519-23. 2007..54 and recall of 0.654 was achieved by the top prediction; precision of 0.64 and recall of 0.769 was achieved by the top 2 predictions. Error analysis revealed problems in the current method, and provided insight into future improvements... - 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..In this paper, we introduce another classification approach based on words of the concept strings and compare it to the contextual syntactic approach... - 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. 2005..We estimated sensitivity, specificity, and positive predictive value by comparing results with clinicians' judgments. Sensitivity was 71% and specificity was 99%. Our results demonstrated that the automated method was feasible... - Enhancing adverse drug event detection in electronic health records using molecular structure similarity: application to pancreatitisSantiago Vilar
Department of Biomedical Informatics, Columbia University Medical Center, New York, New York, United States of America
PLoS ONE 7:e41471. 2012..Although different data mining approaches have been shown to be valuable, it is still crucial to improve the quality of the generated signals... - 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... - Combing signals from spontaneous reports and electronic health records for detection of adverse drug reactionsRave Harpaz
Department of Biomedical Informatics, Columbia University Medical Center, New York, New York, USA
J Am Med Inform Assoc 20:413-9. 2013..We claim that this approach leads to improved accuracy of signal detection when the goal is to produce a highly selective ranked set of candidate ADRs... - Drug-drug interaction through molecular structure similarity analysisSantiago Vilar
Department of Biomedical Informatics, Columbia University Medical Center, New York, NY, USA
J Am Med Inform Assoc 19:1066-74. 2012..Currently, the US Food and Drug Administration and pharmaceutical companies are showing great interest in the development of improved tools for identifying DDIs... - 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... - Extracting phenotypic information from the literature via natural language processingLifeng Chen
Department of Biomedical Informatics, Columbia University, NY 10032, USA
Stud Health Technol Inform 107:758-62. 2004..4%, (95%CI: [58.0%, 72.8%]) and a recall rate of 73.0%, (95%CI: [66.2%, 80.0%]). BioMedLEE had 64.0% precision and 77.1% recall respectively, according to expert agreements... - Determining the reasons for medication prescriptions in the EHR using knowledge and natural language processingYing Li
Department of Biomedical Informatics, Columbia University, New York, NY, USA
AMIA Annu Symp Proc 2011:768-76. 2011..Future work will focus on increasing the accuracy and coverage of the indication knowledge and evaluating its performance using a much larger set of drugs frequently used in the outpatient population... - Deriving a probabilistic syntacto-semantic grammar for biomedicine based on domain-specific terminologiesJung Wei Fan
Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA
J Biomed Inform 44:805-14. 2011..Although the current performance of the unsupervised solution does not adequately replace manual engineering, we believe once the performance issues are addressed, it could serve as an aide in a semi-supervised solution... - A comparison of semantic categories of the ISO reference terminology models for nursing and the MedLEE natural language processing systemSuzanne Bakken
School of Nursing, Department of Biomedical Informatics, Columbia University, 630 W 168th Street, Mailbox 6, New York, NY 10032, USA
Stud Health Technol Inform 107:472-6. 2004..Our analysis also suggests areas for extension of MedLEE... - Use of computerized surveillance to detect nosocomial pneumonia in neonatal intensive care unit patientsJanet P Haas
School of Nursing and Columbia University, New York, NY, USA
Am J Infect Control 33:439-43. 2005..Pneumonia surveillance is difficult and time-consuming. The definition is complicated, and there are many opportunities for subjectivity in determining infection status... - Detection of drug-drug interactions by modeling interaction profile fingerprintsSantiago Vilar
Department of Biomedical Informatics, Columbia University Medical Center, New York, New York, United States of America
PLoS ONE 8:e58321. 2013.... - Mining multi-item drug adverse effect associations in spontaneous reporting systemsRave Harpaz
Department of Biomedical Informatics, Columbia University, 622 West 168th St, VC5, New York, NY 10032, USA
BMC Bioinformatics 11:S7. 2010.... - Generating quality word sense disambiguation test sets based on MeSH indexingJung Wei Fan
Department of Biomedical Informatics, Columbia University, New York, USA
AMIA Annu Symp Proc 2009:183-7. 2009..We also suggest that, by cross-validating with 2 or 3 annotators, the method should be able to efficiently generate quality WSD test sets. Online supplement is available at: http://www.dbmi.columbia.edu/~juf7002/AMIA09... - Integrating heterogeneous knowledge sources to acquire executable drug-related knowledgeXiaoyan Wang
Department of Biomedical Informatics, Columbia University, New York, NY
AMIA Annu Symp Proc 2010:852-6. 2010..The automated method should also be applicable to integrate other clinical knowledge, such as drug-related knowledge with omics information... - Syndromic surveillance using ambulatory electronic health recordsGeorge Hripcsak
Department of Biomedical Informatics, Columbia University, New York, NY, 10032, USA
J Am Med Inform Assoc 16:354-61. 2009..To assess the performance of electronic health record data for syndromic surveillance and to assess the feasibility of broadly distributed surveillance... - Facilitating cancer research using natural language processing of pathology reportsHua Xu
Department of Biomedical Informatics, College of Physicians and Surgeons, Columbia University, 622 W. 168th Street, VC-5, New York, NY 10032, USA
Medinfo 11:565-72. 2004..The evaluation outcome showed that the extended NLP system had a sensitivity of 90.6% and a precision of 91.6%. Results indicated that this system performed satisfactorily for capturing information for the cancer research project... - Combining Corpus-derived Sense Profiles with Estimated Frequency Information to Disambiguate Clinical AbbreviationsHua Xu
Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, TN, USA
AMIA Annu Symp Proc 2012:1004-13. 2012..875 on the same test set, indicating that integrating sense frequency information with local context is effective for clinical abbreviation disambiguation... - Methods for building sense inventories of abbreviations in clinical notesHua Xu
Department of Biomedical Informatics, Columbia University, New York, NY, USA
J Am Med Inform Assoc 16:103-8. 2009..To develop methods for building corpus-specific sense inventories of abbreviations occurring in clinical documents... - 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. 2002..To evaluate translation of chest radiographic reports by using natural language processing and to compare the findings with those in the literature... - Statistical Mining of Potential Drug Interaction Adverse Effects in FDA's Spontaneous Reporting SystemRave Harpaz
Dept of Biomedical Informatics, Columbia University, New York, NY
AMIA Annu Symp Proc 2010:281-5. 2010..This paper examines the application of a highly optimized and tailored implementation of the Apriori algorithm, as well as methods addressing data quality issues, to the identification of DIAEs in FDAs SRS... - An automated tool for detecting medication overuse based on the electronic health recordsHojjat Salmasian
Department of Biomedical Informatics, Columbia University, New York, NY, USA
Pharmacoepidemiol Drug Saf 22:183-9. 2013..We developed a framework for automatic identification of medication overuse and applied it to proton pump inhibitors (PPIs)... - Discovering disease associations by integrating electronic clinical data and medical literatureAntony B Holmes
Department of Biomedical Informatics, Columbia University College of Physicians and Surgeons, New York, New York, United States of America
PLoS ONE 6:e21132. 2011..In particular, we report a statistically significant association between Kawasaki disease and diagnosis of autistic disorder... - Quantitative assessment of dictionary-based protein named entity taggingHongfang Liu
Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University Medical Center, Washington, DC 20007, USA
J Am Med Inform Assoc 13:497-507. 2006.... - A multi-aspect comparison study of supervised word sense disambiguationHongfang Liu
Department of Information Systems, University of Maryland at Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
J Am Med Inform Assoc 11:320-31. 2004.... - CliniViewer: a tool for viewing electronic medical records based on natural language processing and XMLHongfang Liu
Department of Information Systems, University of Maryland at Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
Medinfo 11:639-43. 2004..The tool has been fully implemented and tested using patients with multiple discharge summaries... - Automated acquisition of disease drug knowledge from biomedical and clinical documents: an initial studyElizabeth S Chen
Clinical Informatics Research and Development, Partners HealthCare System, 93 Worcester Street, PO Box 81902, Wellesley, MA 02481, USA
J Am Med Inform Assoc 15:87-98. 2008..Explore the automated acquisition of knowledge in biomedical and clinical documents using text mining and statistical techniques to identify disease-drug associations... - Cancer mortality surveillance--United States, 1990-2000Sherri L Stewart
Division of Cancer Prevention and Control, National Center for Chronic Disease Prevention and Health Promotion, USA
MMWR Surveill Summ 53:1-108. 2004..Continued research in primary prevention, screening methods, and therapeutics is needed to further reduce disparities and improve quality of life and survival among all populations... - The influence of year-end bonuses on colorectal cancer screeningBrian S Armour
National Center for Chronic Disease Prevention and Health Promotion, Centers for Disease Control and Prevention, Atlanta, GA 30041, USA
Am J Manag Care 10:617-24. 2004..Study Design: Retrospective study using managed care plan claims data from 2000 and 2001... - Association between health insurance coverage of office visit and cancer screening among womenCarol Friedman
Division of Prevention Research and Analytic Methods, Epidemiology Program Office, Centers for Disease Control and Prevention, Atlanta, Georgia 303411, USA
Med Care 40:1060-7. 2002..Little is known regarding the nuances of insurance benefit design that may affect the receipt of clinical preventive services... - Does health insurance coverage of office visits influence colorectal cancer testing?Reuben K Varghese
National Center for Chronic Disease Prevention and Health Promotion, Centers for Disease Control and Prevention, Atlanta, GA 30341, USA
Cancer Epidemiol Biomarkers Prev 14:744-7. 2005..To assess the effect of differing health insurance coverage of physician office visits on the use of colorectal cancer (CRC) tests among an employed and insured population... - Annual report to the nation on the status of cancer, 1975-2002, featuring population-based trends in cancer treatmentBrenda K Edwards
Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, MD 20892 8315, USA
J Natl Cancer Inst 97:1407-27. 2005..This year's report updates statistics on the 15 most common cancers in the five major racial/ethnic populations in the United States for 1992-2002 and features population-based trends in cancer treatment... - Colorectal cancer in U.S. adults younger than 50 years of age, 1998-2001Temeika L Fairley
Division of Cancer Prevention and Control, National Center for Chronic Disease Prevention and Control, Centers for Disease Control and Prevention, Atlanta, Georgia 30341, USA
Cancer 107:1153-61. 2006..This population-based study focuses primarily on describing the CRC burden for persons in this age group...