1. 2641-2664 of 2664 « 1 2 ... 108 109 110 111
    1. Modeling and acquisition of drug-drug interaction knowledge.

      Related Articles Modeling and acquisition of drug-drug interaction knowledge. Medinfo. 2007;12(Pt 2):900-4 Authors: Mille F, Degoulet P, Jaulent MC OBJECTIVES: The effectiveness of computerized clinical decision support systems (CDSS) depends on the quality of the knowledge they refer to. In this article, we are interested in the acquisition, modeling and representation of the knowledge embedded in the "national reference framework of drug-drug interaction" published by the French Health Products Safety Agency. METHODS: A model of drug-drug interactions has been designed using bottom-up and top-down approaches. This model is the basis for the design of an XML format ...
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      Mentions: France Paris
    2. PICO Linguist and BabelMeSH: development and partial evaluation of evidence-based multilanguage search tools for MEDLINE/PubMed.

      Related Articles PICO Linguist and BabelMeSH: development and partial evaluation of evidence-based multilanguage search tools for MEDLINE/PubMed. Medinfo. 2007;12(Pt 1):817-21 Authors: Fontelo P, Liu F, Leon S, Anne A, Ackerman M PICO Linguist and BabelMeSH are multilanguage search tools intended for users whose native language is not English. A database of medical terms was created using concept identification equivalents of English terms to other languages. The primary sources of vocabularies were UMLS, MeSH, WHO EMRO and UMLF. The search interface changes according to the language selected which allows search terms to be entered in the native ...
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      Mentions: Bethesda
    3. Health on the Net Foundation: assessing the quality of health web pages all over the world.

      Related Articles Health on the Net Foundation: assessing the quality of health web pages all over the world. Medinfo. 2007;12(Pt 2):1017-21 Authors: Boyer C, Gaudinat A, Baujard V, Geissbühler A The Internet provides a great amount of information and has become one of the communication media which is most widely used [1]. However, the problem is no longer finding information but assessing the credibility of the publishers as well as the relevance and accuracy of the documents retrieved from the web. This problem is particularly relevant in the medical area which has a direct impact on ...
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    4. Identifying QT prolongation from ECG impressions using natural language processing and negation detection.

      Related Articles Identifying QT prolongation from ECG impressions using natural language processing and negation detection. Medinfo. 2007;12(Pt 2):1283-8 Authors: Denny JC, Peterson JF Electrocardiogram (ECG) impressions provide significant information for decision support and clinical research. We investigated the presence of QT prolongation, an important risk factor for sudden cardiac death, compared to the automated calculation of corrected QT (QTc) by ECG machines. We integrated a negation tagging algorithm into the KnowledgeMap concept identifier (KMCI), then applied it to impressions from 44,080 ECGs to identify Unified Medical Language System concepts. We compared the instances of QT prolongation ...
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    5. User-centered evaluation of Arizona BioPathway: an information extraction, integration, and visualization system.

      Related Articles User-centered evaluation of Arizona BioPathway: an information extraction, integration, and visualization system. IEEE Trans Inf Technol Biomed. 2007 Sep;11(5):527-36 Authors: Quiñones KD, Su H, Marshall B, Eggers S, Chen H Explosive growth in biomedical research has made automated information extraction, knowledge integration, and visualization increasingly important and critically needed. The Arizona BioPathway (ABP) system extracts and displays biological regulatory pathway information from the abstracts of journal articles. This study uses relations extracted from more than 200 PubMed abstracts presented in a tabular and graphical user interface with built-in search and aggregation functionality. This paper ...
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    6. Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases.

      Related Articles Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases. BMC Bioinformatics. 2007;8:372 Authors: Berger SI, Posner JM, Ma'ayan A BACKGROUND: In recent years, mammalian protein-protein interaction network databases have been developed. The interactions in these databases are either extracted manually from low-throughput experimental biomedical research literature, extracted automatically from literature using techniques such as natural language processing (NLP), generated experimentally using high-throughput methods such as yeast-2-hybrid screens, or interactions are predicted using an assortment of computational approaches. Genes or proteins identified as significantly changing in proteomic experiments, or identified as susceptibility disease genes ...
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    7. Developmental word acquisition and grammar learning by humanoid robots through a self-organizing incremental neural network.

      Related Articles Developmental word acquisition and grammar learning by humanoid robots through a self-organizing incremental neural network. IEEE Trans Syst Man Cybern B Cybern. 2007 Oct;37(5):1357-72 Authors: He X, Ogura T, Satou A, Hasegawa O We present a new approach for online incremental word acquisition and grammar learning by humanoid robots. Using no data set provided in advance, the proposed system grounds language in a physical context, as mediated by its perceptual capacities. It is carried out using show-and-tell procedures, interacting with its human partner. Moreover, this procedure is open-ended for new words and multiword utterances. These ...
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    8. Classification of Cancer Stage from Free-text Histology Reports.

      Related Articles Classification of Cancer Stage from Free-text Histology Reports. Conf Proc IEEE Eng Med Biol Soc. 2006;1:5153-6 Authors: McCowan I, Moore D, Fry MJ This article investigates the classification of a patient's lung cancer stage based on analysis of their free-text medical reports. The system uses natural language processing to transform the report text, including identification of UMLS terms and detection of negated findings. The transformed report is then classified using statistical machine learning techniques. A support vector machine is trained for each stage category based on word occurrences in a corpus of histology reports for ...
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      Mentions: Brisbane
    9. Medical i2b2 NLP Smoking Challenge: The A-Life System Architecture and Methodology.

      Related Articles Medical i2b2 NLP Smoking Challenge: The A-Life System Architecture and Methodology. J Am Med Inform Assoc. 2008 January-February;15(1):40-43 Authors: Heinze DT, Morsch ML, Potter BC, Sheffer RE We describe the architecture of LifeCode(R) (A-Life Medical, Inc.), a natural language processing system for free-text clinical information extraction, our methodology in applying LifeCode(R) to the i2b2 smoking challenge, and statistical measures for performance evaluation. Due to the limited test size and the coefficient of variation in the test standard, it is difficult to draw conclusions regarding the relative efficacy of approaches that were applied to ...
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      Mentions: San Diego
    10. Mayo Clinic NLP System for Patient Smoking Status Identification.

      Related Articles Mayo Clinic NLP System for Patient Smoking Status Identification. J Am Med Inform Assoc. 2008 January-February;15(1):25-28 Authors: Savova GK, Ogren PV, Duffy PH, Buntrock JD, Chute CG This 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. Our system makes the simplifying assumption that patient-level smoking status determination can be achieved by accurately classifying individual sentences from a patient's record. We created our system with reusable text analysis components built on the Unstructured Information Management ...
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    11. Identifying Patient Smoking Status from Medical Discharge Records.

      Related Articles Identifying Patient Smoking Status from Medical Discharge Records. J Am Med Inform Assoc. 2008 January-February;15(1):14-24 Authors: Uzuner O, Goldstein I, Luo Y, Kohane I The authors organized a Natural Language Processing (NLP) challenge on automatically determining the smoking status of patients from information found in their discharge records. This challenge was issued as a part of the i2b2 (Informatics for Integrating Biology to the Bedside) project, to survey, facilitate, and examine studies in medical language understanding for clinical narratives. This article describes the smoking challenge, details the data and the annotation process, explains the evaluation ...
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      Mentions: Uzuner O Albany
    12. An Electronic Health Record Based on Structured Narrative.

      Related Articles An Electronic Health Record Based on Structured Narrative. J Am Med Inform Assoc. 2008 January-February;15(1):54-64 Authors: Johnson SB, Bakken S, Dine D, Hyun S, Mendonça E, Morrison F, Bright T, Van Vleck T, Wrenn J, Stetson P OBJECTIVE To develop an electronic health record that facilitates rapid capture of detailed narrative observations from clinicians, with partial structuring of narrative information for integration and reuse. DESIGN We propose a design in which unstructured text and coded data are fused into a single model called structured narrative. Each major clinical event (e.g., encounter or procedure ...
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      Mentions: New York Johnson SB
    13. An active visual search interface for Medline.

      Related Articles An active visual search interface for Medline. Comput Syst Bioinformatics Conf. 2007;6:359-69 Authors: Xuan W, Dai M, Mirel B, Wilson J, Athey B, Watson SJ, Meng F Searching the Medline database is almost a daily necessity for many biomedical researchers. However, available Medline search solutions are mainly designed for the quick retrieval of a small set of most relevant documents. Because of this search model, they are not suitable for the large-scale exploration of literature and the underlying biomedical conceptual relationships, which are common tasks in the age of high throughput experimental data analysis and cross-discipline ...
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    14. CBioC: beyond a prototype for collaborative annotation of molecular interactions from the literature.

      Related Articles CBioC: beyond a prototype for collaborative annotation of molecular interactions from the literature. Comput Syst Bioinformatics Conf. 2007;6:381-4 Authors: Baral C, Gonzalez G, Gitter A, Teegarden C, Zeigler A, Joshi-Topé G In molecular biology research, looking for information on a particular entity such as a gene or a protein may lead to thousands of articles, making it impossible for a researcher to individually read these articles and even just their abstracts. Thus, there is a need to curate the literature to get various nuggets of knowledge, such as an interaction between two proteins, and store them ...
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    15. Rule-based human gene normalization in biomedical text with confidence estimation.

      Related Articles Rule-based human gene normalization in biomedical text with confidence estimation. Comput Syst Bioinformatics Conf. 2007;6:371-9 Authors: Lau WW, Johnson CA, Becker KG The ability to identify gene mentions in text and normalize them to the proper unique identifiers is crucial for "down-stream" text mining applications in bioinformatics. We have developed a rule-based algorithm that divides the normalization task into two steps. The first step includes pattern matching for gene symbols and an approximate term searching technique for gene names. Next, the algorithm measures several features based on morphological, statistical, and contextual information to estimate the level ...
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    16. Extracting semantic predications from Medline citations for pharmacogenomics.

      Related Articles Extracting semantic predications from Medline citations for pharmacogenomics. Pac Symp Biocomput. 2007;:209-20 Authors: Ahlers CB, Fiszman M, Demner-Fushman D, Lang FM, Rindflesch TC We describe a natural language processing system (Enhanced SemRep) to identify core assertions on pharmacogenomics in Medline citations. Extracted information is represented as semantic predications covering a range of relations relevant to this domain. The specific relations addressed by the system provide greater precision than that achievable with methods that rely on entity co-occurrence. The development of Enhanced SemRep is based on the adaptation of an existing system and crucially depends on domain knowledge ...
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    17. Integrating natural language processing with FlyBase curation.

      Related Articles Integrating natural language processing with FlyBase curation. Pac Symp Biocomput. 2007;:245-56 Authors: Karamanis N, Lewin I, Seal R, Drysdale R, Briscoe E Applying Natural Language Processing techniques to biomedical text as a potential aid to curation has become the focus of intensive research. However, developing integrated systems which address the curators' real-world needs has been studied less rigorously. This paper addresses this question and presents generic tools developed to assist FlyBase curators. We discuss how they have been integrated into the curation workflow and present initial evidence about their effectiveness. PMID: 17990496 [PubMed - in process]
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    18. Multiple approaches to fine-grained indexing of the biomedical literature.

      Related Articles Multiple approaches to fine-grained indexing of the biomedical literature. Pac Symp Biocomput. 2007;:292-303 Authors: Neveol A, Shooshan SE, Humphrey SM, Rindflesh TC, Aronson AR The number of articles in the MEDLINE database is expected to increase tremendously in the coming years. To ensure that all these documents are indexed with continuing high quality, it is necessary to develop tools and methods that help the indexers in their daily task. We present three methods addressing a novel aspect of automatic indexing of the biomedical literature, namely producing MeSH main heading/subheading pair recommendations. The methods, (dictionary-based, post- processing ...
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    19. Mining gene-disease relationships from biomedical literature: weighting protein-protein interactions and connectivity measures.

      Related Articles Mining gene-disease relationships from biomedical literature: weighting protein-protein interactions and connectivity measures. Pac Symp Biocomput. 2007;:28-39 Authors: Gonzalez G, Uribe JC, Tari L, Brophy C, Baral C MOTIVATION: The promises of the post-genome era disease-related discoveries and advances have yet to be fully realized, with many opportunities for discovery hiding in the millions of biomedical papers published since. Public databases give access to data extracted from the literature by teams of experts, but their coverage is often limited and lags behind recent discoveries. We present a computational method that combines data extracted from the literature with data ...
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    20. Constructing human brain-function association models from FMRI literature.

      Related Articles Constructing human brain-function association models from FMRI literature. Conf Proc IEEE Eng Med Biol Soc. 2007;1:1188-91 Authors: Hsiao MY, Chen DY, Chen JH Toward the goal of understanding the human brain function, we have developed a web-based Human Brain Functional Mapping Knowledge Base (HBFMKB) system to mining human brain-function association model from vast Medline abstracts. Since nomenclature and relationships among cognitive functions have no consensus yet, we use rule-based natural language processing methods to extract behavioral task and cognitive function and do n-gram approximate concept mapping by the Unified Medical Language system (UMLS) knowledge source. The ...
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      Mentions: Taipei Hsiao Chen JH
    21. Automatic mining of the literature to generate new hypotheses for the possible link between periodontitis and atherosclerosis: lipopolysaccharide as a case study.

      Related Articles Automatic mining of the literature to generate new hypotheses for the possible link between periodontitis and atherosclerosis: lipopolysaccharide as a case study. J Clin Periodontol. 2007 Dec;34(12):1016-24 Authors: Hettne KM, Weeber M, Laine ML, Ten Cate H, Boyer S, Kors JA, Loos BG Aim: The aim of the current report was to generate and explore new hypotheses into how, in a pathophysiological sense, atherosclerosis and periodontitis could be linked. Material and Methods: Two different biomedical informatics techniques were used: an association-based technique that generated a ranked list of genes associated with the diseases, and a ...
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    22. Enhanced semantic access to the protein engineering literature using ontologies populated by text mining.

      Related Articles Enhanced semantic access to the protein engineering literature using ontologies populated by text mining. Int J Bioinform Res Appl. 2007;3(3):389-413 Authors: Witte R, Kappler T, Baker CJ The biomedical literature is growing at an ever-increasing rate, which pronounces the need to support scientists with advanced, automated means of accessing knowledge. We investigate a novel approach employing description logics (DL)-based queries made to formal ontologies that have been created using the results of text mining full-text research papers. In this paradigm, an OWL-DL ontology becomes populated with instances detected through natural language processing (NLP). The ...
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    23. Electronic patient records: some answers to the data representation and reuse challenges. Findings from the section on patient records.

      Related Articles Electronic patient records: some answers to the data representation and reuse challenges. Findings from the section on patient records. Methods Inf Med. 2007;46 Suppl 1:47-9 Authors: Meystre S, OBJECTIVES: To summarize current excellent research in the field of patient records. METHOD: Synopsis of the papers selected for the IMIA Yearbook 2007. RESULTS: The Electronic Patient Record encompasses a broad field of research and development. Some current research topics were selected for this IMIA Yearbook: EHR representation and communication standards, and secondary uses of clinical data for research and decision support. Four excellent papers representing the research ...
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    24. Binding Moad, a high-quality protein ligand database.

      Related Articles Binding MOAD, a high-quality protein ligand database. Nucleic Acids Res. 2007 Nov 30; Authors: Benson ML, Smith RD, Khazanov NA, Dimcheff B, Beaver J, Dresslar P, Nerothin J, Carlson HA Binding MOAD (Mother of All Databases) is a database of 9836 protein-ligand crystal structures. All biologically relevant ligands are annotated, and experimental binding-affinity data is reported when available. Binding MOAD has almost doubled in size since it was originally introduced in 2004, demonstrating steady growth with each annual update. Several technologies, such as natural language processing, help drive this constant expansion. Along with increasing data, Binding MOAD has ...
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    2641-2664 of 2664 « 1 2 ... 108 109 110 111
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