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1325 result(s) for 'natural language processing' within BMC Bioinformatics

Page 1 of 27

  2. 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

    Content type: Methodology article

    Published on:

  3. 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

    Content type: Software

    Published on:

  5. 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

    Content type: Database

    Published on:

  6. 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

    Content type: Research article

    Published on:

  8. Identifying local recurrences in breast cancer from patient data sets is important for clinical research and practice. Developing a model using natural language processing and machine learning to identify local r...

    Authors: Zexian Zeng, Sasa Espino, Ankita Roy, Xiaoyu Li, Seema A. Khan, Susan E. Clare, Xia Jiang, Richard Neapolitan and Yuan Luo

    Citation: BMC Bioinformatics 2018 19(Suppl 17):498

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 17

  9. 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

    Content type: Research article

    Published on:

  12. 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

    Content type: Research article

    Published on:

  13. 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

    Content type: Software

    Published on:

  15. 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

    Content type: Software

    Published on:

  16. 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

    Content type: Review

    Published on:

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

  17. 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

    Content type: Software

    Published on:

  18. We introduced a novel way to represent protein sequences as continuous vectors (embeddings) by using the language model ELMo taken from natural language processing. By modeling protein sequences, ELMo effectively...

    Authors: Michael Heinzinger, Ahmed Elnaggar, Yu Wang, Christian Dallago, Dmitrii Nechaev, Florian Matthes and Burkhard Rost

    Citation: BMC Bioinformatics 2019 20:723

    Content type: Research article

    Published on:

  20. 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

    Content type: Software

    Published on:

  21. 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

    Content type: Research

    Published on:

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

  22. Biomedical question answering (QA) is a sub-task of natural language processing in a specific domain, which aims to ... the neural network and large scale pre-trained language model have largely improved its perf...

    Authors: Gezheng Xu, Wenge Rong, Yanmeng Wang, Yuanxin Ouyang and Zhang Xiong

    Citation: BMC Bioinformatics 2021 22:272

    Content type: Research

    Published on:

  23. 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

    Content type: Software

    Published on:

  24. 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

    Content type: Methodology article

    Published on:

  25. We present a literature-driven workflow involving document delivery and natural language processing steps generating tagged sentences containing lipid, protein...bibliosphere. We illustrate the extent of the desc...

    Authors: Christopher JO Baker, Rajaraman Kanagasabai, Wee Tiong Ang, Anitha Veeramani, Hong-Sang Low and Markus R Wenk

    Citation: BMC Bioinformatics 2008 9(Suppl 1):S5

    Content type: Proceedings

    Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  26. 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

    Content type: Methodology article

    Published on:

  27. 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

    Content type: Research

    Published on:

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

  28. 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

    Content type: Research Article

    Published on:

  29. 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:

  30. 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:

  31. 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:

  32. 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:

  33. 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

  35. 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:

  36. 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:

  37. 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

  38. 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:

  39. 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:

  40. 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:

  42. 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

  43. 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

  45. 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

  46. 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:

  47. 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:

  48. 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:

  49. 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:

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