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1512 result(s) for 'natural language processing' within BMC Bioinformatics

Page 4 of 31

  1. The genome sequencing projects have shown our limited knowledge regarding gene function, e.g. S. cerevisiae has 5–6,000 genes of which nearly 1,000 have an uncertain function. Their gross influence on the behavio...

    Authors: Irena Spasić, Warwick B Dunn, Giles Velarde, Andy Tseng, Helen Jenkins, Nigel Hardy, Stephen G Oliver and Douglas B Kell
    Citation: BMC Bioinformatics 2006 7:281
    Content type: Database Published on:

  3. Model card reports aim to provide informative and transparent description of machine learning models to stakeholders. This report document is of interest to the National Institutes of Health’s Bridge2AI initia...

    Authors: Muhammad Tuan Amith, Licong Cui, Degui Zhi, Kirk Roberts, Xiaoqian Jiang, Fang Li, Evan Yu and Cui Tao
    Citation: BMC Bioinformatics 2022 23(Suppl 6):281
    Content type: Research Published on:

    This article is part of a Supplement: Volume 23 Supplement 6

  4. Most biomedical information extraction focuses on binary relations within single sentences. However, extracting n-ary relations that span multiple sentences is in huge demand. At present, in the cross-sentence...

    Authors: Di Zhao, Jian Wang, Yijia Zhang, Xin Wang, Hongfei Lin and Zhihao Yang
    Citation: BMC Bioinformatics 2020 21:312
    Content type: Methodology article Published on:

  6. In this study, we developed MHCSeqNet, an open-source deep learning model, which not only outperforms state-of-the-art predictors on both MHC binding affinity and MHC ligand peptidome datasets but also exhibits p...

    Authors: Poomarin Phloyphisut, Natapol Pornputtapong, Sira Sriswasdi and Ekapol Chuangsuwanich
    Citation: BMC Bioinformatics 2019 20:270
    Content type: Software Published on:

  7. Computer-based pathway discovery is concerned with two important objectives: pathway identification and analysis. Conventional mining and modeling approaches aimed at pathway discovery are often effective at a...

    Authors: George Zheng and Athman Bouguettaya
    Citation: BMC Bioinformatics 2009 10(Suppl 10):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 10

  8. Ontology construction for any domain is a labour intensive and complex process. Any methodology that can reduce the cost and increase efficiency has the potential to make a major impact in the life sciences. T...

    Authors: Christopher Brewster, Simon Jupp, Joanne Luciano, David Shotton, Robert D Stevens and Ziqi Zhang
    Citation: BMC Bioinformatics 2009 10(Suppl 5):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 5

  9. The Internet is a major source of health information but most seekers are not familiar with medical vocabularies. Hence, their searches fail due to bad query formulation. Several methods have been proposed to ...

    Authors: Lina F Soualmia, Elise Prieur-Gaston, Zied Moalla, Thierry Lecroq and Stéfan J Darmoni
    Citation: BMC Bioinformatics 2012 13(Suppl 14):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 14

  11. Quantitative proteomics holds great promise for identifying proteins that are differentially abundant between populations representing different physiological or disease states. A range of computational tools ...

    Authors: Mi-Youn Brusniak, Bernd Bodenmiller, David Campbell, Kelly Cooke, James Eddes, Andrew Garbutt, Hollis Lau, Simon Letarte, Lukas N Mueller, Vagisha Sharma, Olga Vitek, Ning Zhang, Ruedi Aebersold and Julian D Watts
    Citation: BMC Bioinformatics 2008 9:542
    Content type: Methodology article Published on:

  12. It is understood that cancer is a clonal disease initiated by a single cell, and that metastasis, which is the spread of cancer from the primary site, is also initiated by a single cell. The seemingly natural ...

    Authors: Erich A Peterson, Michael A Bauer, Shweta S Chavan, Cody Ashby, Niels Weinhold, Christoph J Heuck, Gareth J Morgan and Donald J Johann
    Citation: BMC Bioinformatics 2015 16(Suppl 13):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 13

  13. In task 1A of the BioCreAtIvE evaluation, systems had to be devised that recognize words and phrases forming gene or protein names in natural language sentences. We approach this problem by building ... Machine, ...

    Authors: Jörg Hakenberg, Steffen Bickel, Conrad Plake, Ulf Brefeld, Hagen Zahn, Lukas Faulstich, Ulf Leser and Tobias Scheffer
    Citation: BMC Bioinformatics 2005 6(Suppl 1):S9
    Content type: Report Published on:

    This article is part of a Supplement: Volume 6 Supplement 1

  14. The detection and interpretation of CNVs are of clinical importance in genetic testing. Several databases and web services are already being used by clinical geneticists to interpret the medical relevance of i...

    Authors: Xi Yang, Zhuo Song, Chengkun Wu, Wei Wang, Gen Li, Wei Zhang, Lingqian Wu and Kai Lu
    Citation: BMC Bioinformatics 2018 19(Suppl 19):528
    Content type: Research Published on:

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

  15. The development of bioinformatics databases, algorithms, and tools throughout the last years has lead to a highly distributed world of bioinformatics services. Without adequate management and development suppo...

    Authors: Anna-Lena Lamprecht, Tiziana Margaria and Bernhard Steffen
    Citation: BMC Bioinformatics 2009 10(Suppl 10):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 10

  16. Many medical imaging techniques utilize fitting approaches for quantitative parameter estimation and analysis. Common examples are pharmacokinetic modeling in dynamic contrast-enhanced (DCE) magnetic resonance...

    Authors: Charlotte Debus, Ralf Floca, Michael Ingrisch, Ina Kompan, Klaus Maier-Hein, Amir Abdollahi and Marco Nolden
    Citation: BMC Bioinformatics 2019 20:31
    Content type: Software Published on:

  18. Small molecules are of increasing interest for bioinformatics in areas such as metabolomics and drug discovery. The recent release of large open access chemistry databases generates a demand for flexible tools...

    Authors: Thomas Kuhn, Egon L Willighagen, Achim Zielesny and Christoph Steinbeck
    Citation: BMC Bioinformatics 2010 11:159
    Content type: Software Published on:

  19. In this work we describe an approach that facilitates the automatic recognition of eight relationships defined between medical problems, treatments and tests. Unlike the traditional bag-of-words representation, i...

    Authors: Rezarta Islamaj Doğan, Aurélie Névéol and Zhiyong Lu
    Citation: BMC Bioinformatics 2011 12(Suppl 3):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 3

  20. Lately, there has been a great interest in the application of information extraction methods to the biomedical domain, in particular, to the extraction of relationships of genes, proteins, and RNA from scienti...

    Authors: Sampo Pyysalo, Filip Ginter, Juho Heimonen, Jari Björne, Jorma Boberg, Jouni Järvinen and Tapio Salakoski
    Citation: BMC Bioinformatics 2007 8:50
    Content type: Research article Published on:

  22. Biological contextual information helps understand various phenomena occurring in the biological systems consisting of complex molecular relations. The construction of context-specific relational resources vas...

    Authors: Jaehyun Lee, Doheon Lee and Kwang Hyung Lee
    Citation: BMC Bioinformatics 2020 21(Suppl 5):250
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 5

  23. A fundamental goal of the U.S. National Institute of Health (NIH) "Roadmap" is to strengthen Translational Research, defined as the movement of discoveries in basic research to application at the clinical level. ...

    Authors: Alan Ruttenberg, Tim Clark, William Bug, Matthias Samwald, Olivier Bodenreider, Helen Chen, Donald Doherty, Kerstin Forsberg, Yong Gao, Vipul Kashyap, June Kinoshita, Joanne Luciano, M Scott Marshall, Chimezie Ogbuji, Jonathan Rees, Susie Stephens…
    Citation: BMC Bioinformatics 2007 8(Suppl 3):S2
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 8 Supplement 3

  24. With advancements in omics technologies, the range of biological processes where long non-coding RNAs (lncRNAs) are involved, is expanding extensively, thereby generating the need to develop lncRNA annotation ...

    Authors: Swapna Vidhur Daulatabad, Rajneesh Srivastava and Sarath Chandra Janga
    Citation: BMC Bioinformatics 2021 22:279
    Content type: Database Published on:

  26. The Clinical E-Science Framework (CLEF) project has built a system to extract clinically significant information from the textual component of medical records in order to support clinical research, evidence-ba...

    Authors: Angus Roberts, Robert Gaizauskas, Mark Hepple and Yikun Guo
    Citation: BMC Bioinformatics 2008 9(Suppl 11):S3
    Content type: Research Published on:

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

  27. Elucidation of interactive relation between chemicals and genes is of key relevance not only for discovering new drug leads in drug development but also for repositioning existing drugs to novel therapeutic ta...

    Authors: Wei Wang, Xi Yang, Chengkun Wu and Canqun Yang
    Citation: BMC Bioinformatics 2020 21:544
    Content type: Methodology article Published on:

  28. As Twitter has become an active data source for health surveillance research, it is important that efficient and effective methods are developed to identify tweets related to personal health experience. Conven...

    Authors: Keyuan Jiang, Shichao Feng, Qunhao Song, Ricardo A. Calix, Matrika Gupta and Gordon R. Bernard
    Citation: BMC Bioinformatics 2018 19(Suppl 8):210
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 8

  29. Making accurate patient care decision, as early as possible, is a constant challenge, especially for physicians in the emergency department. The increasing volumes of electronic medical records (EMRs) open new...

    Authors: Huaixiao Tou, Lu Yao, Zhongyu Wei, Xiahai Zhuang and Bo Zhang
    Citation: BMC Bioinformatics 2018 19(Suppl 5):117
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 5

  31. Mathematical and computational modelling of biochemical systems has seen a lot of effort devoted to the definition and implementation of high-performance mechanistic simulation frameworks. Within these framewo...

    Authors: Giulio Caravagna, Luca De Sano and Marco Antoniotti
    Citation: BMC Bioinformatics 2015 16(Suppl 9):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 9

  32. The classifier relies on the UMLS® knowledge source (Unified Medical Language System®) and on heuristic algorithms for ... clinical trial record and candidate GBD categories using natural language processing and ...

    Authors: Ignacio Atal, Jean-David Zeitoun, Aurélie Névéol, Philippe Ravaud, Raphaël Porcher and Ludovic Trinquart
    Citation: BMC Bioinformatics 2016 17:392
    Content type: Research article Published on:

  33. Taxonomic descriptions are traditionally composed in natural language and published in a format that cannot be directly used by computers. The Exploring Taxon Concepts (ETC) project has been developing a set o...

    Authors: Hong Cui, Dongfang Xu, Steven S. Chong, Martin Ramirez, Thomas Rodenhausen, James A. Macklin, Bertram Ludäscher, Robert A. Morris, Eduardo M. Soto and Nicolás Mongiardino Koch
    Citation: BMC Bioinformatics 2016 17:471
    Content type: Research article Published on:

  34. Two main achievements are described in this paper: (a) a system for document classification which crucially relies on the results of an advanced pipeline of natural language processing tools; (b) a system which i...

    Authors: Gerold Schneider, Simon Clematide and Fabio Rinaldi
    Citation: BMC Bioinformatics 2011 12(Suppl 8):S13
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 8

  35. Currently, data about age-phenotype associations are not systematically organized and cannot be studied methodically. Searching for scientific articles describing phenotypic changes reported as occurring at a ...

    Authors: Nophar Geifman and Eitan Rubin
    Citation: BMC Bioinformatics 2011 12:229
    Content type: Research article Published on:

  36. The bio-ontology community falls into two camps: first we have biology domain experts, who actually hold the knowledge we wish to capture in ontologies; second, we have ontology specialists, who hold knowledge...

    Authors: Mikel Egaña Aranguren, Sean Bechhofer, Phillip Lord, Ulrike Sattler and Robert Stevens
    Citation: BMC Bioinformatics 2007 8:57
    Content type: Commentary Published on:

  37. The limitations of traditional computer-aided detection (CAD) systems for mammography, the extreme importance of early detection of breast cancer and the high impact of the false diagnosis of patients drive re...

    Authors: Dina Abdelhafiz, Clifford Yang, Reda Ammar and Sheida Nabavi
    Citation: BMC Bioinformatics 2019 20(Suppl 11):281
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 11

  38. Although biomedical publications and literature are growing rapidly, there still lacks structured knowledge that can be easily processed by computer programs. In order to extract such knowledge from plain text...

    Authors: Rui Xing, Jie Luo and Tengwei Song
    Citation: BMC Bioinformatics 2020 21(Suppl 16):543
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 16

  39. With the development of e-Health, it plays a more and more important role in predicting whether a doctor’s answer can be accepted by a patient through online healthcare community. Unlike the previous work whic...

    Authors: Qianlong Liu, Kangenbei Liao, Kelvin Kam-fai Tsoi and Zhongyu Wei
    Citation: BMC Bioinformatics 2019 20(Suppl 18):567
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 18

  41. Visualization concerns the representation of data visually and is an important task in scientific research. Protein-protein interactions (PPI) are discovered using either wet lab techniques, such mass spectrom...

    Authors: Giuseppe Agapito, Pietro Hiram Guzzi and Mario Cannataro
    Citation: BMC Bioinformatics 2013 14(Suppl 1):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  42. Biomedical translational science is increasingly using computational reasoning on repositories of structured knowledge (such as UMLS, SemMedDB, ChEMBL, Reactome, DrugBank, and SMPDB in order to facilitate disc...

    Authors: E. C. Wood, Amy K. Glen, Lindsey G. Kvarfordt, Finn Womack, Liliana Acevedo, Timothy S. Yoon, Chunyu Ma, Veronica Flores, Meghamala Sinha, Yodsawalai Chodpathumwan, Arash Termehchy, Jared C. Roach, Luis Mendoza, Andrew S. Hoffman, Eric W. Deutsch, David Koslicki…
    Citation: BMC Bioinformatics 2022 23:400
    Content type: Database Published on:

  43. The National Center for Biomedical Ontology (NCBO) is developing a system for automated, ontology-based access to online biomedical resources. The system's indexing workflow processes the text metadata of dive...

    Authors: Nigam H Shah, Nipun Bhatia, Clement Jonquet, Daniel Rubin, Annie P Chiang and Mark A Musen
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S14
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  44. Natural products are the source of various functional materials such as medicines, and understanding their biosynthetic pathways can provide information that is helpful for their effective production through t...

    Authors: Kohei Amano, Tsubasa Matsumoto, Kenichi Tanaka, Kimito Funatsu and Masaaki Kotera
    Citation: BMC Bioinformatics 2019 20:728
    Content type: Methodology article Published on:

  45. Word sense disambiguation (WSD) attempts to solve lexical ambiguities by identifying the correct meaning of a word based on its context. WSD has been demonstrated to be an important step in knowledge-based app...

    Authors: Laura Plaza, Antonio J Jimeno-Yepes, Alberto Díaz and Alan R Aronson
    Citation: BMC Bioinformatics 2011 12:355
    Content type: Research article Published on:

  46. The number of natural proteins represents a small fraction of all the possible protein sequences and there is an enormous number of proteins never sampled by nature, the so called "never born proteins" (NBPs)....

    Authors: Giovanni Minervini, Giuseppe Evangelista, Laura Villanova, Debora Slanzi, Davide De Lucrezia, Irene Poli, Pier Luigi Luisi and Fabio Polticelli
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S22
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 6

  47. Ontological concepts are useful for many different biomedical tasks. Concepts are difficult to recognize in text due to a disconnect between what is captured in an ontology and how the concepts are expressed i...

    Authors: Christopher Funk, William Baumgartner Jr, Benjamin Garcia, Christophe Roeder, Michael Bada, K Bretonnel Cohen, Lawrence E Hunter and Karin Verspoor
    Citation: BMC Bioinformatics 2014 15:59
    Content type: Research article Published on:

  48. We participated, as Team 81, in the Article Classification and the Interaction Method subtasks (ACT and IMT, respectively) of the Protein-Protein Interaction...task of the BioCreative III Challenge. For the ACT, ...

    Authors: Anália Lourenço, Michael Conover, Andrew Wong, Azadeh Nematzadeh, Fengxia Pan, Hagit Shatkay and Luis M Rocha
    Citation: BMC Bioinformatics 2011 12(Suppl 8):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 8

    The Erratum to this article has been published in BMC Bioinformatics 2012 13:180

  50. This paper describes the design of an event ontology being developed for application in the machine understanding of infectious disease-related events reported in natural language text. This event ontology is ...

    Authors: Ai Kawazoe, Hutchatai Chanlekha, Mika Shigematsu and Nigel Collier
    Citation: BMC Bioinformatics 2008 9(Suppl 3):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 3

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