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1661 result(s) for 'natural language processing' within BMC Bioinformatics

Page 2 of 34

  2. Automated assignment of specific ontology concepts to mentions in text is a critical task in biomedical natural language processing, and the subject of many open shared ... the art involves the use of neural netw...

    Authors: Mayla R. Boguslav, Negacy D. Hailu, Michael Bada, William A. Baumgartner Jr. and Lawrence E. Hunter
    Citation: BMC Bioinformatics 2021 22(Suppl 1):598
    Content type: Research Published on:

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

  3. One of the greatest challenges in Metabolic Engineering is to develop quantitative models and algorithms to identify a set of genetic manipulations that will result in a microbial strain with a desirable metab...

    Authors: Miguel Rocha, Paulo Maia, Rui Mendes, José P Pinto, Eugénio C Ferreira, Jens Nielsen, Kiran Raosaheb Patil and Isabel Rocha
    Citation: BMC Bioinformatics 2008 9:499
    Content type: Research article Published on:

  4. The resulting event-annotated corpus is the largest and one of the best in quality among similar annotation efforts. We expect it to become a valuable resource for NLP (Natural Language Processing)-based TM in th...

    Authors: Jin-Dong Kim, Tomoko Ohta and Jun'ichi Tsujii
    Citation: BMC Bioinformatics 2008 9:10
    Content type: Research article Published on:

  5. The knowledge of metabolic pathways and fluxes is important to understand the adaptation of organisms to their biotic and abiotic environment. The specific distribution of stable isotope labelled precursors in...

    Authors: Zeeshan Ahmed, Saman Zeeshan, Claudia Huber, Michael Hensel, Dietmar Schomburg, Richard Münch, Wolfgang Eisenreich and Thomas Dandekar
    Citation: BMC Bioinformatics 2013 14:218
    Content type: Software Published on:

  6. Many systems biology studies leverage the integration of multiple data types (across different data sources) to offer a more comprehensive view of the biological system being studied. While SQL (Structured Que...

    Authors: Syed Ahmad Chan Bukhari, Shrikant Pawar, Jeff Mandell, Steven H. Kleinstein and Kei-Hoi Cheung
    Citation: BMC Bioinformatics 2021 22(Suppl 9):105
    Content type: Research Published on:

    This article is part of a Supplement: Volume 22 Supplement 9

  7. Genomic functional information is valuable for biomedical research. However, such information frequently needs to be extracted from the scientific literature and structured in order to be exploited by automatic s...

    Authors: Marco Masseroli, Halil Kilicoglu, François-Michel Lang and Thomas C Rindflesch
    Citation: BMC Bioinformatics 2006 7:291
    Content type: Research article Published on:

  8. SPARQL query composition is difficult for the lay-person, and even the experienced bioinformatician in cases where the data model is unfamiliar. Moreover, established best-practices and internationalization co...

    Authors: Luke McCarthy, Ben Vandervalk and Mark Wilkinson
    Citation: BMC Bioinformatics 2012 13(Suppl 1):S2
    Content type: Research Published on:

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

  10. The advent of population-scale genome projects has revolutionized our biological understanding of parasitic protozoa. However, while hundreds to thousands of nuclear genomes of parasitic protozoa have been gen...

    Authors: Manon Geerts, Achim Schnaufer and Frederik Van den Broeck
    Citation: BMC Bioinformatics 2021 22:468
    Content type: Software Published on:

  11. Spectral processing and post-experimental data analysis are the major tasks in NMR-based metabonomics studies. While there are commercial and free licensed software tools available to assist these tasks, resea...

    Authors: Tao Wang, Kang Shao, Qinying Chu, Yanfei Ren, Yiming Mu, Lijia Qu, Jie He, Changwen Jin and Bin Xia
    Citation: BMC Bioinformatics 2009 10:83
    Content type: Software Published on:

  12. Data generated from liquid chromatography coupled to high-resolution mass spectrometry (LC-MS)-based studies of a biological sample can contain large amounts of biologically significant information in the form...

    Authors: Navdeep Jaitly, Anoop Mayampurath, Kyle Littlefield, Joshua N Adkins, Gordon A Anderson and Richard D Smith
    Citation: BMC Bioinformatics 2009 10:87
    Content type: Software Published on:

  13. 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

  14. 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

  15. 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:

  17. 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:

  18. 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:

  21. 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

  22. 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:

  24. 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:

  26. 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

  27. 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

  28. 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:

  29. 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:

  31. 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:

  32. 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:

  33. 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

  35. 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:

  37. 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

  38. 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:

  39. 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

  40. 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

  41. 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

  42. Automatic and accurate extraction of diverse biomedical relations from literature is a crucial component of bio-medical text mining. Currently, stacking various classification networks on pre-trained language ...

    Authors: Xiangwen Zheng, Xuanze Wang, Xiaowei Luo, Fan Tong and Dongsheng Zhao
    Citation: BMC Bioinformatics 2023 24:486
    Content type: Research Published on:

  44. 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:

  45. The escalation of viruses over the past decade has highlighted the need to determine their respective hosts, particularly for emerging ones that pose a potential menace to the welfare of both human and animal ...

    Authors: Zhaoyan Ming, Xiangjun Chen, Shunlong Wang, Hong Liu, Zhiming Yuan, Minghui Wu and Han Xia
    Citation: BMC Bioinformatics 2023 24:455
    Content type: Research Published on:

  47. 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

  48. 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:

  49. 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:

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