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BMC Bioinformatics

Articles

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

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  1. Content type: Methodology article

    Manual curation of biological databases, an expensive and labor-intensive process, is essential for high quality integrated data ... the implementation of a state-of-the-art Natural Language Processing system tha...

    Authors: Carlos Rodríguez-Penagos, Heladia Salgado, Irma Martínez-Flores and Julio Collado-Vides

    Citation: BMC Bioinformatics 2007 8:293

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  2. Content type: Software

    Despite increasing interest in applying Natural Language Processing (NLP) to biomedical text, whether this...

    Authors: Nikiforos Karamanis, Ruth Seal, Ian Lewin, Peter McQuilton, Andreas Vlachos, Caroline Gasperin, Rachel Drysdale and Ted Briscoe

    Citation: BMC Bioinformatics 2008 9:193

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  3. Content type: Database

    The Enteropathogen Resource Integration Center (ERIC; http://​www.​ericbrc.​org) has a goal of providing bioinformatics support for the scientific communi...

    Authors: Sam Zaremba, Mila Ramos-Santacruz, Thomas Hampton, Panna Shetty, Joel Fedorko, Jon Whitmore, John M Greene, Nicole T Perna, Jeremy D Glasner, Guy Plunkett III, Matthew Shaker and David Pot

    Citation: BMC Bioinformatics 2009 10:177

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  4. Content type: Research article

    Many biomedical natural language processing systems demonstrated large differences between their previously...

    Authors: Karin Verspoor, Kevin Bretonnel Cohen, Arrick Lanfranchi, Colin Warner, Helen L Johnson, Christophe Roeder, Jinho D Choi, Christopher Funk, Yuriy Malenkiy, Miriam Eckert, Nianwen Xue, William A Baumgartner Jr, Michael Bada, Martha Palmer and Lawrence E Hunter

    Citation: BMC Bioinformatics 2012 13:207

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  5. Content type: Research article

    We report the development and evaluation of Microbial Phenomics Information Extractor (MicroPIE, version 0.1.0). MicroPIE is a natural language processing application that uses a robust supervised classification....

    Authors: Jin Mao, Lisa R. Moore, Carrine E. Blank, Elvis Hsin-Hui Wu, Marcia Ackerman, Sonali Ranade and Hong Cui

    Citation: BMC Bioinformatics 2016 17:528

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  6. Content type: Research article

    Applications of Natural Language Processing (NLP) technology to biomedical texts have...subdomain variation within the biomedical domain, i.e., the extent to which different subject areas of biomedicine are chara...

    Authors: Thomas Lippincott, Diarmuid Ó Séaghdha and Anna Korhonen

    Citation: BMC Bioinformatics 2011 12:212

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  7. Content type: Software

    Metabolic flux analysis has become an established method in systems biology and functional genomics. The most common approach for determining intracellular metabolic fluxes is to utilize mass spectrometry in c...

    Authors: C Hart Poskar, Jan Huege, Christian Krach, Mathias Franke, Yair Shachar-Hill and Björn H Junker

    Citation: BMC Bioinformatics 2012 13:295

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  8. Content type: Software

    Gas chromatography–mass spectrometry (GC-MS) is a technique frequently used in targeted and non-targeted measurements of metabolites. Most existing software tools for processing of raw instrument GC-MS data ti...

    Authors: Sean O'Callaghan, David P De Souza, Andrew Isaac, Qiao Wang, Luke Hodkinson, Moshe Olshansky, Tim Erwin, Bill Appelbe, Dedreia L Tull, Ute Roessner, Antony Bacic, Malcolm J McConville and Vladimir A Likić

    Citation: BMC Bioinformatics 2012 13:115

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  9. Content type: Software

    Microarray data analysis has been the subject of extensive and ongoing pipeline development due to its complexity, the availability of several options at each analysis step, and the development of new analysis...

    Authors: Thomas Stropp, Timothy McPhillips, Bertram Ludäscher and Mark Bieda

    Citation: BMC Bioinformatics 2012 13:102

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  10. Content type: Review

    Many efforts exist to design and implement approaches and tools for data capture, integration and analysis in the life sciences. Challenges are not only the heterogeneity, size and distribution of information ...

    Authors: Marco Masseroli, Barend Mons, Erik Bongcam-Rudloff, Stefano Ceri, Alexander Kel, François Rechenmann, Frederique Lisacek and Paolo Romano

    Citation: BMC Bioinformatics 2014 15(Suppl 1):S2

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    This article is part of a Supplement: Volume 15 Supplement 1

  11. Content type: Software

    Information extraction (IE) efforts are widely acknowledged to be important in harnessing the rapid advance of biomedical knowledge, particularly in areas where important factual information is published in a ...

    Authors: Lawrence Hunter, Zhiyong Lu, James Firby, William A Baumgartner Jr, Helen L Johnson, Philip V Ogren and K Bretonnel Cohen

    Citation: BMC Bioinformatics 2008 9:78

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  12. Content type: Software

    This article presents Neji, an open source framework optimized for biomedical concept recognition built around four key characteristics: modularity, scalability, speed, and usability. It integrates modules for bi...

    Authors: David Campos, Sérgio Matos and José Luís Oliveira

    Citation: BMC Bioinformatics 2013 14:281

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  13. Content type: Research

    Due to the nature of scientific methodology, research articles are rich in speculative and tentative statements, also known as hedges. We explore a linguistically motivated approach to the problem of recognizi...

    Authors: Halil Kilicoglu and Sabine Bergler

    Citation: BMC Bioinformatics 2008 9(Suppl 11):S10

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

  14. Content type: Methodology article

    Calcium (Ca2+) propagates within tissues serving as an important information carrier. In particular, cilia beat frequency in oviduct cells is partially regulated by Ca2+ changes. Thus, measuring the calcium de...

    Authors: Carlos Milovic, Carolina Oses, Manuel Villalón, Sergio Uribe, Carlos Lizama, Claudia Prieto, Marcelo E Andia, Pablo Irarrazaval and Cristian Tejos

    Citation: BMC Bioinformatics 2013 14:162

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  15. Content type: Research

    During library construction polymerase chain reaction is used to enrich the DNA before sequencing. Typically, this process generates duplicate read sequences. Removal of these artifacts is mandatory, as they c...

    Authors: Andrea Manconi, Marco Moscatelli, Giuliano Armano, Matteo Gnocchi, Alessandro Orro and Luciano Milanesi

    Citation: BMC Bioinformatics 2016 17(Suppl 12):346

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    This article is part of a Supplement: Volume 17 Supplement 12

  16. Content type: Methodology article

    Techniques from computational linguistics can provide new insights into the annotation process. GO annotations show similar statistical behaviours to those seen in natural language with measured exponents that pr...

    Authors: Leila Ranandeh Kalankesh, Robert Stevens and Andy Brass

    Citation: BMC Bioinformatics 2012 13:127

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  17. Content type: Research Article

    Coreference resolution is the task of finding strings in text that have the same referent as other strings. Failures of coreference resolution are a common cause of false negatives in information extraction fr...

    Authors: K. Bretonnel Cohen, Arrick Lanfranchi, Miji Joo-young Choi, Michael Bada, William A. Baumgartner Jr., Natalya Panteleyeva, Karin Verspoor, Martha Palmer and Lawrence E. Hunter

    Citation: BMC Bioinformatics 2017 18:372

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  18. Content type: Research article

    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

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  19. Content type: Software

    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

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