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928 Result(s) for 'natural language processing' within BMC Bioinformatics

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  3. Software

    Natural Language Processing in aid of FlyBase curators

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

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

    BMC Bioinformatics 2008 9:193

    Published on: 14 April 2008

  5. Database

    Text-mining of PubMed abstracts by natural language processing to create a public knowledge base on molecular mechanisms of bacterial enteropathogens

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

    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

    BMC Bioinformatics 2009 10:177

    Published on: 10 June 2009

  6. Research article

    A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools

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

    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

    BMC Bioinformatics 2012 13:207

    Published on: 17 August 2012

  7. Research article

    Microbial phenomics information extractor (MicroPIE): a natural language processing tool for the automated acquisition of prokaryotic phenotypic characters from text sources

    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....

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

    BMC Bioinformatics 2016 17:528

    Published on: 13 December 2016

  10. Research article

    Exploring subdomain variation in biomedical language

    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...

    Thomas Lippincott, Diarmuid Ó Séaghdha and Anna Korhonen

    BMC Bioinformatics 2011 12:212

    Published on: 27 May 2011

  11. Software

    iMS2Flux– a high–throughput processing tool for stable isotope labeled mass spectrometric data used for metabolic flux analysis

    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...

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

    BMC Bioinformatics 2012 13:295

    Published on: 12 November 2012

  12. Software

    PyMS: a Python toolkit for processing of gas chromatography-mass spectrometry (GC-MS) data. Application and comparative study of selected tools

    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...

    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

    BMC Bioinformatics 2012 13:115

    Published on: 30 May 2012

  13. Software

    Workflows for microarray data processing in the Kepler environment

    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...

    Thomas Stropp, Timothy McPhillips, Bertram Ludäscher and Mark Bieda

    BMC Bioinformatics 2012 13:102

    Published on: 17 May 2012

  15. Review

    Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information

    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 ...

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

    BMC Bioinformatics 2014 15(Suppl 1):S2

    Published on: 10 January 2014

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

  16. Software

    Processing methods for differential analysis of LC/MS profile data

    Liquid chromatography coupled to mass spectrometry (LC/MS) has been widely used in proteomics and metabolomics research. In this context, the technology has been increasingly used for differential profiling, i...

    Mikko Katajamaa and Matej Orešič

    BMC Bioinformatics 2005 6:179

    Published on: 18 July 2005

  17. Software

    OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression

    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 ...

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

    BMC Bioinformatics 2008 9:78

    Published on: 31 January 2008

  18. Research

    Recognizing speculative language in biomedical research articles: a linguistically motivated perspective

    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...

    Halil Kilicoglu and Sabine Bergler

    BMC Bioinformatics 2008 9(Suppl 11):S10

    Published on: 19 November 2008

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

  19. Software

    A modular framework for biomedical concept recognition

    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...

    David Campos, Sérgio Matos and José Luís Oliveira

    BMC Bioinformatics 2013 14:281

    Published on: 24 September 2013

  20. Methodology article

    Calcium (Ca2+) waves data calibration and analysis using image processing techniques

    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...

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

    BMC Bioinformatics 2013 14:162

    Published on: 16 May 2013

  21. Methodology article

    The language of gene ontology: a Zipf’s law analysis

    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...

    Leila Ranandeh Kalankesh, Robert Stevens and Andy Brass

    BMC Bioinformatics 2012 13:127

    Published on: 7 June 2012

  22. Research

    Removing duplicate reads using graphics processing units

    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...

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

    BMC Bioinformatics 2016 17(Suppl 12):346

    Published on: 8 November 2016

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

  23. Research Article

    Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles

    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...

    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

    BMC Bioinformatics 2017 18:372

    Published on: 17 August 2017

  24. Research article

    Natural computation meta-heuristics for the in silico optimization of microbial strains

    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...

    Miguel Rocha, Paulo Maia, Rui Mendes, José P Pinto, Eugénio C Ferreira, Jens Nielsen, Kiran Raosaheb Patil and Isabel Rocha

    BMC Bioinformatics 2008 9:499

    Published on: 27 November 2008

  25. Software

    Software LS-MIDA for efficient mass isotopomer distribution analysis in metabolic modelling

    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...

    Zeeshan Ahmed, Saman Zeeshan, Claudia Huber, Michael Hensel, Dietmar Schomburg, Richard Münch, Wolfgang Eisenreich and Thomas Dandekar

    BMC Bioinformatics 2013 14:218

    Published on: 9 July 2013

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