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1458 result(s) for 'natural language processing' within BMC Bioinformatics

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  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:

  7. 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:

  9. 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

  10. 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:

  13. 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:

  14. 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:

  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. 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:

  18. 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:

  19. The recognition of pharmacological substances, compounds and proteins is essential for biomedical relation extraction, knowledge graph construction, drug discovery, as well as medical question answering. Although...

    Authors: Cong Sun, Zhihao Yang, Lei Wang, Yin Zhang, Hongfei Lin and Jian Wang
    Citation: BMC Bioinformatics 2021 22(Suppl 1):602
    Content type: Research Published on:

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

  20. 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:

  22. 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:

  23. 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:

  24. 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

  25. 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:

  27. 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:

  28. 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

  29. Medical information has rapidly increased on the internet and has become one of the main targets of search engine use. However, medical information on the internet is subject to the problems of quality and acc...

    Authors: Li Zhang, Xiaoran Yang, Shijian Li, Tianyi Liao and Gang Pan
    Citation: BMC Bioinformatics 2022 23:136
    Content type: Software Published on:

  30. 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:

  31. 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

  33. 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:

  34. 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

  35. 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:

  36. 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:

  37. 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:

  38. 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

  39. 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:

  40. 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

  42. 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:

  43. 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:

  44. 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:

  45. 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

  46. 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

  47. 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:

  48. 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:

  49. 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:

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