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https://www.readbyqxmd.com/read/29186491/clamp-a-toolkit-for-efficiently-building-customized-clinical-natural-language-processing-pipelines
#1
Ergin Soysal, Jingqi Wang, Min Jiang, Yonghui Wu, Serguei Pakhomov, Hongfang Liu, Hua Xu
Existing general clinical natural language processing (NLP) systems such as MetaMap and Clinical Text Analysis and Knowledge Extraction System have been successfully applied to information extraction from clinical text. However, end users often have to customize existing systems for their individual tasks, which can require substantial NLP skills. Here we present CLAMP (Clinical Language Annotation, Modeling, and Processing), a newly developed clinical NLP toolkit that provides not only state-of-the-art NLP components, but also a user-friendly graphic user interface that can help users quickly build customized NLP pipelines for their individual applications...
November 24, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28986329/detecting-clinically-related-content-in-online-patient-posts
#2
Courtland VanDam, Shaheen Kanthawala, Wanda Pratt, Joyce Chai, Jina Huh
Patients with chronic health conditions use online health communities to seek support and information to help manage their condition. For clinically related topics, patients can benefit from getting opinions from clinical experts, and many are concerned about misinformation and biased information being spread online. However, a large volume of community posts makes it challenging for moderators and clinical experts, if there are any, to provide necessary information. Automatically identifying forum posts that need validated clinical resources can help online health communities efficiently manage content exchange...
November 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28883198/analysis-of-annotated-data-models-for-improving-data-quality
#3
Hannes Ulrich, Ann-Kristin Kock-Schoppenhauer, Björn Andersen, Josef Ingenerf
The public Medical Data Models (MDM) portal with more than 9.000 annotated forms from clinical trials and other sources provides many research opportunities for the medical informatics community. It is mainly used to address the problem of heterogeneity by searching, mediating, reusing, and assessing data models, e. g. the semi-interactive curation of core data records in a special domain. Furthermore, it can be used as a benchmark for evaluating algorithms that create, transform, annotate, and analyse structured patient data...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28816337/a-bag-of-concepts-approach-for-biomedical-document-classification-using-wikipedia-knowledge-spanish-english-cross-language-case-study
#4
Marcos A Mouriño-García, Roberto Pérez-Rodríguez, Luis E Anido-Rifón
OBJECTIVES: The ability to efficiently review the existing literature is essential for the rapid progress of research. This paper describes a classifier of text documents, represented as vectors in spaces of Wikipedia concepts, and analyses its suitability for classification of Spanish biomedical documents when only English documents are available for training. We propose the cross-language concept matching (CLCM) technique, which relies on Wikipedia interlanguage links to convert concept vectors from the Spanish to the English space...
October 26, 2017: Methods of Information in Medicine
https://www.readbyqxmd.com/read/28815108/monitoring-biomedical-literature-for-post-market-safety-purposes-by-analyzing-networks-of-text-based-coded-information
#5
Taxiarchis Botsis, Matthew Foster, Kory Kreimeyer, Abhishek Pandey, Richard Forshee
Literature review is critical but time-consuming in the post-market surveillance of medical products. We focused on the safety signal of intussusception after the vaccination of infants with the Rotashield Vaccine in 1999 and retrieved all PubMed abstracts for rotavirus vaccines published after January 1, 1998. We used the Event-based Text-mining of Health Electronic Records system, the MetaMap tool, and the National Center for Biomedical Ontologies Annotator to process the abstracts and generate coded terms stamped with the date of publication...
2017: AMIA Summits on Translational Science Proceedings
https://www.readbyqxmd.com/read/28664200/an-ontology-enabled-natural-language-processing-pipeline-for-provenance-metadata-extraction-from-biomedical-text-short-paper
#6
Joshua Valdez, Michael Rueschman, Matthew Kim, Susan Redline, Satya S Sahoo
Extraction of structured information from biomedical literature is a complex and challenging problem due to the complexity of biomedical domain and lack of appropriate natural language processing (NLP) techniques. High quality domain ontologies model both data and metadata information at a fine level of granularity, which can be effectively used to accurately extract structured information from biomedical text. Extraction of provenance metadata, which describes the history or source of information, from published articles is an important task to support scientific reproducibility...
October 2016: On the Move to Meaningful Internet Systems ...: CoopIS, DOA, and ODBASE: Confederated International Conferences, CoopIS, DOA, and ODBASE ... Proceedings
https://www.readbyqxmd.com/read/28552401/rysannmd-a-biomedical-semantic-annotator-balancing-speed-and-accuracy
#7
John Cuzzola, Jelena Jovanović, Ebrahim Bagheri
Recently, both researchers and practitioners have explored the possibility of semantically annotating large and continuously evolving collections of biomedical texts such as research papers, medical reports, and physician notes in order to enable their efficient and effective management and use in clinical practice or research laboratories. Such annotations can be automatically generated by biomedical semantic annotators - tools that are specifically designed for detecting and disambiguating biomedical concepts mentioned in text...
July 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28391809/leveraging-medical-taxonomies-to-improve-knowledge-management-within-online-communities-of-practice-the-knowledge-maps-system
#8
Samuel Alan Stewart, Syed Sibte Raza Abidi
BACKGROUND AND OBJECTIVE: Online communities of practice contain a wealth of information, stored in the free text of shared communications between community members. The Knowledge Maps (KMaps) system is designed to facilitate Knowledge Translation in online communities through multi-level analyses of the shared messages of these communications. METHODS: Using state-of-the-art semantic mapping technologies (Metamap) the contents of the messages shared within an online community are mapped to terms from the MeSH medical lexicon, providing a multi-level topic-specific summary of the knowledge being shared within the community...
May 2017: Computer Methods and Programs in Biomedicine
https://www.readbyqxmd.com/read/28337503/gut-microbiome-related-metabolic-changes-in-plasma-of-antibiotic-treated-rats
#9
C Behr, H Kamp, E Fabian, G Krennrich, W Mellert, E Peter, V Strauss, T Walk, I M C M Rietjens, B van Ravenzwaay
The intestinal microbiota contributes to the metabolism of its host. Adequate identification of the microbiota's impact on the host plasma metabolites is lacking. As antibiotics have a profound effect on the microbial composition and hence on the mammalian-microbiota co-metabolism, we studied the effects of antibiotics on the "functionality of the microbiome"-defined as the production of metabolites absorbed by the host. This metabolomics study presents insights into the mammalian-microbiome co-metabolism of endogenous metabolites...
March 23, 2017: Archives of Toxicology
https://www.readbyqxmd.com/read/28131722/development-and-empirical-user-centered-evaluation-of-semantically-based-query-recommendation-for-an-electronic-health-record-search-engine
#10
David A Hanauer, Danny T Y Wu, Lei Yang, Qiaozhu Mei, Katherine B Murkowski-Steffy, V G Vinod Vydiswaran, Kai Zheng
OBJECTIVE: The utility of biomedical information retrieval environments can be severely limited when users lack expertise in constructing effective search queries. To address this issue, we developed a computer-based query recommendation algorithm that suggests semantically interchangeable terms based on an initial user-entered query. In this study, we assessed the value of this approach, which has broad applicability in biomedical information retrieval, by demonstrating its application as part of a search engine that facilitates retrieval of information from electronic health records (EHRs)...
March 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28130331/metamap-lite-an-evaluation-of-a-new-java-implementation-of-metamap
#11
Dina Demner-Fushman, Willie J Rogers, Alan R Aronson
MetaMap is a widely used named entity recognition tool that identifies concepts from the Unified Medical Language System Metathesaurus in text. This study presents MetaMap Lite, an implementation of some of the basic MetaMap functions in Java. On several collections of biomedical literature and clinical text, MetaMap Lite demonstrated real-time speed and precision, recall, and F1 scores comparable to or exceeding those of MetaMap and other popular biomedical text processing tools, clinical Text Analysis and Knowledge Extraction System (cTAKES) and DNorm...
July 1, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/27903489/finding-important-terms-for-patients-in-their-electronic-health-records-a-learning-to-rank-approach-using-expert-annotations
#12
Jinying Chen, Jiaping Zheng, Hong Yu
BACKGROUND: Many health organizations allow patients to access their own electronic health record (EHR) notes through online patient portals as a way to enhance patient-centered care. However, EHR notes are typically long and contain abundant medical jargon that can be difficult for patients to understand. In addition, many medical terms in patients' notes are not directly related to their health care needs. One way to help patients better comprehend their own notes is to reduce information overload and help them focus on medical terms that matter most to them...
November 30, 2016: JMIR Medical Informatics
https://www.readbyqxmd.com/read/27683667/v3nlp-framework-tools-to-build-applications-for-extracting-concepts-from-clinical-text
#13
Guy Divita, Marjorie E Carter, Le-Thuy Tran, Doug Redd, Qing T Zeng, Scott Duvall, Matthew H Samore, Adi V Gundlapalli
INTRODUCTION: Substantial amounts of clinically significant information are contained only within the narrative of the clinical notes in electronic medical records. The v3NLP Framework is a set of "best-of-breed" functionalities developed to transform this information into structured data for use in quality improvement, research, population health surveillance, and decision support. BACKGROUND: MetaMap, cTAKES and similar well-known natural language processing (NLP) tools do not have sufficient scalability out of the box...
2016: EGEMS
https://www.readbyqxmd.com/read/27577335/attempting-to-use-metamap-in-clinical-practice-a-feasibility-study-on-the-identification-of-medical-concepts-from-italian-clinical-notes
#14
Emma Chiaramello, Alessia Paglialonga, Francesco Pinciroli, Gabriella Tognola
This study assessed the feasibility of using MetaMap to identify medical concepts from clinical notes written in Italian. We performed two experiments: in "EXP 1", we used MetaMap to annotate Italian texts using a knowledge source consisting of Italian UMLS sources only; in "EXP 2", we used MetaMap to analyze an English unsupervised translated version of the original Italian texts. We considered medical concepts related to three semantic categories: "Disorders", "Findings" and "Symptoms". Average recall, precision and F-measure were equal to 0...
2016: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/27539197/a-long-journey-to-short-abbreviations-developing-an-open-source-framework-for-clinical-abbreviation-recognition-and-disambiguation-card
#15
Yonghui Wu, Joshua C Denny, S Trent Rosenbloom, Randolph A Miller, Dario A Giuse, Lulu Wang, Carmelo Blanquicett, Ergin Soysal, Jun Xu, Hua Xu
Objective: The goal of this study was to develop a practical framework for recognizing and disambiguating clinical abbreviations, thereby improving current clinical natural language processing (NLP) systems' capability to handle abbreviations in clinical narratives. Methods: We developed an open-source framework for clinical abbreviation recognition and disambiguation (CARD) that leverages our previously developed methods, including: (1) machine learning based approaches to recognize abbreviations from a clinical corpus, (2) clustering-based semiautomated methods to generate possible senses of abbreviations, and (3) profile-based word sense disambiguation methods for clinical abbreviations...
April 1, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/27444186/use-of-off-the-shelf-information-extraction-algorithms-in-clinical-informatics-a-feasibility-study-of-metamap-annotation-of-italian-medical-notes
#16
Emma Chiaramello, Francesco Pinciroli, Alberico Bonalumi, Angelo Caroli, Gabriella Tognola
Information extraction from narrative clinical notes is useful for patient care, as well as for secondary use of medical data, for research or clinical purposes. Many studies focused on information extraction from English clinical texts, but less dealt with clinical notes in languages other than English. This study tested the feasibility of using "off the shelf" information extraction algorithms to identify medical concepts from Italian clinical notes. Among all the available and well-established information extraction algorithms, we used MetaMap to map medical concepts to the Unified Medical Language System (UMLS)...
July 18, 2016: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/27203858/text-mining-of-journal-articles-for-sleep-disorder-terminologies
#17
Calvin Lam, Fu-Chih Lai, Chia-Hui Wang, Mei-Hsin Lai, Nanly Hsu, Min-Huey Chung
OBJECTIVE: Research on publication trends in journal articles on sleep disorders (SDs) and the associated methodologies by using text mining has been limited. The present study involved text mining for terms to determine the publication trends in sleep-related journal articles published during 2000-2013 and to identify associations between SD and methodology terms as well as conducting statistical analyses of the text mining findings. METHODS: SD and methodology terms were extracted from 3,720 sleep-related journal articles in the PubMed database by using MetaMap...
2016: PloS One
https://www.readbyqxmd.com/read/27153797/metabolite-profiles-of-rats-in-repeated-dose-toxicological-studies-after-oral-and-inhalative-exposure
#18
COMPARATIVE STUDY
E Fabian, N Bordag, M Herold, H Kamp, G Krennrich, R Looser, L Ma-Hock, W Mellert, G Montoya, E Peter, A Prokudin, M Spitzer, V Strauss, T Walk, R Zbranek, B van Ravenzwaay
The MetaMap(®)-Tox database contains plasma-metabolome and toxicity data of rats obtained from oral administration of 550 reference compounds following a standardized adapted OECD 407 protocol. Here, metabolic profiles for aniline (A), chloroform (CL), ethylbenzene (EB), 2-methoxyethanol (ME), N,N-dimethylformamide (DMF) and tetrahydrofurane (THF), dosed inhalatively for six hours/day, five days a week for 4 weeks were compared to oral dosing performed daily for 4 weeks. To investigate if the oral and inhalative metabolome would be comparable statistical analyses were performed...
July 25, 2016: Toxicology Letters
https://www.readbyqxmd.com/read/27026618/efficient-identification-of-nationally-mandated-reportable-cancer-cases-using-natural-language-processing-and-machine-learning
#19
John D Osborne, Matthew Wyatt, Andrew O Westfall, James Willig, Steven Bethard, Geoff Gordon
OBJECTIVE: To help cancer registrars efficiently and accurately identify reportable cancer cases. MATERIAL AND METHODS: The Cancer Registry Control Panel (CRCP) was developed to detect mentions of reportable cancer cases using a pipeline built on the Unstructured Information Management Architecture - Asynchronous Scaleout (UIMA-AS) architecture containing the National Library of Medicine's UIMA MetaMap annotator as well as a variety of rule-based UIMA annotators that primarily act to filter out concepts referring to nonreportable cancers...
November 2016: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/26323337/automatically-detecting-failures-in-natural-language-processing-tools-for-online-community-text
#20
Albert Park, Andrea L Hartzler, Jina Huh, David W McDonald, Wanda Pratt
BACKGROUND: The prevalence and value of patient-generated health text are increasing, but processing such text remains problematic. Although existing biomedical natural language processing (NLP) tools are appealing, most were developed to process clinician- or researcher-generated text, such as clinical notes or journal articles. In addition to being constructed for different types of text, other challenges of using existing NLP include constantly changing technologies, source vocabularies, and characteristics of text...
2015: Journal of Medical Internet Research
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