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1512 result(s) for 'natural language processing' within BMC Bioinformatics

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  1. The volume of biomedical literature and clinical data is growing at an exponential rate. Therefore, efficient access to data described in unstructured biomedical texts is a crucial task for the biomedical indu...

    Authors: Renzo M. Rivera-Zavala and Paloma Martínez
    Citation: BMC Bioinformatics 2021 22(Suppl 1):601
    Content type: Research Published on:

    This article is part of a Supplement: Volume 22 Supplement 1

  2. Tokenization is an important component of language processing yet there is no widely accepted tokenization method for English texts, including biomedical texts. Other than rule based techniques, tokenization i...

    Authors: Neil Barrett and Jens Weber-Jahnke
    Citation: BMC Bioinformatics 2011 12(Suppl 3):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 3

  3. Our method allows efficient and complete search of OMIM phenotypes as well as improved data-mining of the OMIM phenome. Applying natural language processing, each phrase is tagged with additional semantic...

    Authors: Raphael Cohen, Avitan Gefen, Michael Elhadad and Ohad S Birk
    Citation: BMC Bioinformatics 2011 12:65
    Content type: Database Published on:

  4. Here, we build an integrative platform, the E ncyclopedia of H epatocellular C arcinoma genes O nline, dubbed EHCO http://​ehco.​iis.​sinica.​edu.​tw..., to syste...

    Authors: Chun-Nan Hsu, Jin-Mei Lai, Chia-Hung Liu, Huei-Hun Tseng, Chih-Yun Lin, Kuan-Ting Lin, Hsu-Hua Yeh, Ting-Yi Sung, Wen-Lian Hsu, Li-Jen Su, Sheng-An Lee, Chang-Han Chen, Gen-Cher Lee, DT Lee, Yow-Ling Shiue, Chang-Wei Yeh…
    Citation: BMC Bioinformatics 2007 8:66
    Content type: Methodology article Published on:

  5. We extracted semantic relations with the SemRep natural language processing system from 122,421,765 sentences, which ... organized in a relational database. The QA process is implemented as a search in this...

    Authors: Dimitar Hristovski, Dejan Dinevski, Andrej Kastrin and Thomas C Rindflesch
    Citation: BMC Bioinformatics 2015 16:6
    Content type: Research article Published on:

  7. The evolving complexity of genome-scale experiments has increasingly centralized the role of a highly computable, accurate, and comprehensive resource spanning multiple biological scales and viewpoints. To provid...

    Authors: Lee T Sam, Eneida A Mendonça, Jianrong Li, Judith Blake, Carol Friedman and Yves A Lussier
    Citation: BMC Bioinformatics 2009 10(Suppl 2):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 2

  8. In this research, we proposed a model based on representation and attention mechanism based deep learning methods, to automatic annotate E3-substrate interaction sentences in biomedical literature. Focusing on th...

    Authors: Mengqi Luo, Zhongyan Li, Shangfu Li and Tzong-Yi Lee
    Citation: BMC Bioinformatics 2021 22:507
    Content type: Research Published on:

  10. When developing models for clinical information retrieval and decision support systems, the discrete outcomes required for training are often missing. These labels need to be extracted from free text in electr...

    Authors: Bram van Es, Leon C. Reteig, Sander C. Tan, Marijn Schraagen, Myrthe M. Hemker, Sebastiaan R. S. Arends, Miguel A. R. Rios and Saskia Haitjema
    Citation: BMC Bioinformatics 2023 24:10
    Content type: Research Published on:

  12. Relation extraction is an essential procedure in literature mining. It focuses on extracting semantic relations between parts of text, called mentions. Biomedical literature includes an enormous amount of textual...

    Authors: Slavko Žitnik, Marinka Žitnik, Blaž Zupan and Marko Bajec
    Citation: BMC Bioinformatics 2015 16(Suppl 16):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 16

  13. Current search engines are keyword-based. Semantic technologies promise a next generation of semantic search engines, which will be able to answer questions. Current approaches either apply natural language processing

    Authors: Heiko Dietze and Michael Schroeder
    Citation: BMC Bioinformatics 2009 10(Suppl 10):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 10

  14. Biomedical processes can provide essential information about the (mal-) functioning of an organism and are thus frequently represented in biomedical terminologies and ontologies, including the GO Biological Pr...

    Authors: André Q Andrade, Ward Blondé, Janna Hastings and Stefan Schulz
    Citation: BMC Bioinformatics 2012 13:217
    Content type: Research article Published on:

  16. ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible plug-in architecture, ImageJ enjoys contributions f...

    Authors: Curtis T. Rueden, Johannes Schindelin, Mark C. Hiner, Barry E. DeZonia, Alison E. Walter, Ellen T. Arena and Kevin W. Eliceiri
    Citation: BMC Bioinformatics 2017 18:529
    Content type: Software Published on:

  17. We sketch our species identification tool for palm sized computers that helps knowledgeable observers with census activities. An algorithm turns an identification matrix into a minimal length series of questio...

    Authors: Aswath Manoharan, Jeannie Stamberger, YuanYuan Yu and Andreas Paepcke
    Citation: BMC Bioinformatics 2008 9:150
    Content type: Research article Published on:

  18. Hydrogen/deuterium exchange mass spectrometry (H/DX-MS) experiments implemented to characterize protein interaction and protein folding generate large quantities of data. Organizing, processing and visualizing...

    Authors: Gordon W Slysz, Charles AH Baker, Benjamin M Bozsa, Anthony Dang, Andrew J Percy, Melissa Bennett and David C Schriemer
    Citation: BMC Bioinformatics 2009 10:162
    Content type: Software Published on:

  19. Saccharomyces cerevisiae is recognized as a model system representing a simple eukaryote whose genome can be easily manipulated. Information solicited by scientists on its biological entities (Proteins, Genes, RN...

    Authors: Abdelaali Briache, Kamar Marrakchi, Amine Kerzazi, Ismael Navas-Delgado, Badr D Rossi Hassani, Khalid Lairini and José F Aldana-Montes
    Citation: BMC Bioinformatics 2012 13(Suppl 1):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 1

  22. Flow cytometry technology is widely used in both health care and research. The rapid expansion of flow cytometry applications has outpaced the development of data storage and analysis tools. Collaborative effo...

    Authors: Yu Qian, Olga Tchuvatkina, Josef Spidlen, Peter Wilkinson, Maura Gasparetto, Andrew R Jones, Frank J Manion, Richard H Scheuermann, Rafick-Pierre Sekaly and Ryan R Brinkman
    Citation: BMC Bioinformatics 2009 10:184
    Content type: Correspondence Published on:

  23. Statistics are reported on corpus size, ambiguity levels and the consistency of annotations. The corpus is accessible for academic purposes and is free of charge. Apart from the intended goal of serving as a comm...

    Authors: Veronika Vincze, György Szarvas, Richárd Farkas, György Móra and János Csirik
    Citation: BMC Bioinformatics 2008 9(Suppl 11):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 11

  24. Despite a wide adoption of English in science, a significant amount of biomedical data are produced in other languages, such as French. Yet a majority of natural language processing or semantic tools as well as d...

    Authors: Andon Tchechmedjiev, Amine Abdaoui, Vincent Emonet, Stella Zevio and Clement Jonquet
    Citation: BMC Bioinformatics 2018 19:405
    Content type: Software Published on:

  25. In recent years, the recognition of semantic types from the biomedical scientific literature has been focused on named entities like protein and gene names (PGNs) and gene ontology terms (GO terms). Other sema...

    Authors: Antonio Jimeno, Ernesto Jimenez-Ruiz, Vivian Lee, Sylvain Gaudan, Rafael Berlanga and Dietrich Rebholz-Schuhmann
    Citation: BMC Bioinformatics 2008 9(Suppl 3):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 3

  26. The reliability and reproducibility of experimental procedures is a cornerstone of scientific practice. There is a pressing technological need for the better representation of biomedical protocols to enable ot...

    Authors: Larisa N Soldatova, Daniel Nadis, Ross D King, Piyali S Basu, Emma Haddi, Véronique Baumlé, Nigel J Saunders, Wolfgang Marwan and Brian B Rudkin
    Citation: BMC Bioinformatics 2014 15(Suppl 14):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 14

  27. Personalised medicine provides patients with treatments that are specific to their genetic profiles. It requires efficient data sharing of disparate data types across a variety of scientific disciplines, such ...

    Authors: Alejandra González-Beltrán, Ben Tagger and Anthony Finkelstein
    Citation: BMC Bioinformatics 2012 13(Suppl 1):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 1

  29. Graph-based notions are increasingly used in biomedical data mining and knowledge discovery tasks. In this paper, we present a clique-clustering method to automatically summarize graphs of semantic predication...

    Authors: Han Zhang, Marcelo Fiszman, Dongwook Shin, Bartlomiej Wilkowski and Thomas C Rindflesch
    Citation: BMC Bioinformatics 2013 14:182
    Content type: Research article Published on:

  31. Due to the rapidly expanding body of biomedical literature, biologists require increasingly sophisticated and efficient systems to help them to search for relevant information. Such systems should account for ...

    Authors: Paul Thompson, John McNaught, Simonetta Montemagni, Nicoletta Calzolari, Riccardo del Gratta, Vivian Lee, Simone Marchi, Monica Monachini, Piotr Pezik, Valeria Quochi, CJ Rupp, Yutaka Sasaki, Giulia Venturi, Dietrich Rebholz-Schuhmann and Sophia Ananiadou
    Citation: BMC Bioinformatics 2011 12:397
    Content type: Research article Published on:

  32. Researchers who use MEDLINE for text mining, information extraction, or natural language processing may benefit from having a copy of ... Medicine (NLM) distributes MEDLINE in eXtensible Markup Language (XML)-for...

    Authors: Diane E Oliver, Gaurav Bhalotia, Ariel S Schwartz, Russ B Altman and Marti A Hearst
    Citation: BMC Bioinformatics 2004 5:146
    Content type: Software Published on:

  34. Deep Learning (DL) has advanced the state-of-the-art capabilities in bioinformatics applications which has resulted in trends of increasingly sophisticated and computationally demanding models trained by larger a...

    Authors: John X. Qiu, Hong-Jun Yoon, Kshitij Srivastava, Thomas P. Watson, J. Blair Christian, Arvind Ramanathan, Xiao C. Wu, Paul A. Fearn and Georgia D. Tourassi
    Citation: BMC Bioinformatics 2018 19(Suppl 18):488
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 18

  35. Since their introduction in 2009, the BioNLP Shared Task events have been instrumental in advancing the development of methods and resources for the automatic extraction of information from the biomedical lite...

    Authors: Sampo Pyysalo, Tomoko Ohta, Rafal Rak, Andrew Rowley, Hong-Woo Chun, Sung-Jae Jung, Sung-Pil Choi, Jun'ichi Tsujii and Sophia Ananiadou
    Citation: BMC Bioinformatics 2015 16(Suppl 10):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 10

  36. In situ hybridisation gene expression information helps biologists identify where a gene is expressed. However, the databases that republish the experimental information online are often both incomplete and incon...

    Authors: Kenneth McLeod, Gus Ferguson and Albert Burger
    Citation: BMC Bioinformatics 2012 13(Suppl 1):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 1

  38. In this work, we develop methods using mutual information (MI) and its property, the data processing inequality (DPI), to help characterize associations that were generated based on use of natural language processing

    Authors: Xiaoyan Wang, George Hripcsak and Carol Friedman
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  39. An increase in work on the full text of journal articles and the growth of PubMedCentral have the opportunity to create a major paradigm shift in how biomedical text mining is done. However, until now there ha...

    Authors: K Bretonnel Cohen, Helen L Johnson, Karin Verspoor, Christophe Roeder and Lawrence E Hunter
    Citation: BMC Bioinformatics 2010 11:492
    Content type: Research article Published on:

  40. Electronic medical record (EMR) systems have become widely used throughout the world to improve the quality of healthcare and the efficiency of hospital services. A bilingual medical lexicon of Chinese and Eng...

    Authors: Yan Xu, Luoxin Chen, Junsheng Wei, Sophia Ananiadou, Yubo Fan, Yi Qian, Eric I-Chao Chang and Junichi Tsujii
    Citation: BMC Bioinformatics 2015 16:149
    Content type: Research article Published on:

  41. This article provides an overview of the first BioASQ challenge, a competition on large-scale biomedical semantic indexing and question answering (QA), which took place between March and September 2013. BioASQ as...

    Authors: George Tsatsaronis, Georgios Balikas, Prodromos Malakasiotis, Ioannis Partalas, Matthias Zschunke, Michael R Alvers, Dirk Weissenborn, Anastasia Krithara, Sergios Petridis, Dimitris Polychronopoulos, Yannis Almirantis, John Pavlopoulos, Nicolas Baskiotis, Patrick Gallinari, Thierry Artiéres, Axel-Cyrille Ngonga Ngomo…
    Citation: BMC Bioinformatics 2015 16:138
    Content type: Research Article Published on:

  42. With the advancements of Next Generation Techniques, a tremendous amount of genomic information has been made available to be analyzed by means of computational methods. Bioinformatics Tertiary Analysis is a c...

    Authors: Sara Pidò, Pietro Crovari and Franca Garzotto
    Citation: BMC Bioinformatics 2021 22(Suppl 13):452
    Content type: Research Published on:

    This article is part of a Supplement: Volume 22 Supplement 13

  44. The biomedical literature continues to grow at a rapid pace, making the challenge of knowledge retrieval and extraction ever greater. Tools that provide a means to search and mine the full text of literature t...

    Authors: H.-M. Müller, K. M. Van Auken, Y. Li and P. W. Sternberg
    Citation: BMC Bioinformatics 2018 19:94
    Content type: Software Published on:

  45. Automatic and accurate recognition of various biomedical named entities from literature is an important task of biomedical text mining, which is the foundation of extracting biomedical knowledge from unstructu...

    Authors: Xiangwen Zheng, Haijian Du, Xiaowei Luo, Fan Tong, Wei Song and Dongsheng Zhao
    Citation: BMC Bioinformatics 2022 23:501
    Content type: Research Published on:

  46. Immunotherapy is a promising route towards personalized cancer treatment. A key algorithmic challenge in this process is to decide if a given peptide (neoepitope) binds with the major histocompatibility comple...

    Authors: Johanna Vielhaben, Markus Wenzel, Wojciech Samek and Nils Strodthoff
    Citation: BMC Bioinformatics 2020 21:279
    Content type: Software Published on:

  47. In systems biology, and many other areas of research, there is a need for the interoperability of tools and data sources that were not originally designed to be integrated. Due to the interdisciplinary nature ...

    Authors: John Boyle, Christopher Cavnor, Sarah Killcoyne and Ilya Shmulevich
    Citation: BMC Bioinformatics 2008 9:295
    Content type: Methodology article Published on:

  48. Enzymatic and chemical reactions are key for understanding biological processes in cells. Curated databases of chemical reactions exist but these databases struggle to keep up with the exponential growth of th...

    Authors: Emily K. Mallory, Matthieu de Rochemonteix, Alex Ratner, Ambika Acharya, Chris Re, Roselie A. Bright and Russ B. Altman
    Citation: BMC Bioinformatics 2020 21:217
    Content type: Research article Published on:

  50. The today's public database infrastructure spans a very large collection of heterogeneous biological data, opening new opportunities for molecular biology, bio-medical and bioinformatics research, but raising ...

    Authors: Marco Mesiti, Ernesto Jiménez-Ruiz, Ismael Sanz, Rafael Berlanga-Llavori, Paolo Perlasca, Giorgio Valentini and David Manset
    Citation: BMC Bioinformatics 2009 10(Suppl 12):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 12

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