Skip to main content


1435 result(s) for 'natural language processing' within BMC Bioinformatics

Page 4 of 29

  1. 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

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

  2. 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

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

  3. 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
  4. 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

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

  5. 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
  6. 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

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

  7. 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
  8. 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
  9. 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

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

  10. 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

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

  11. 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

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

  12. 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

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

  13. 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

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

  14. 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
  15. 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
  16. 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

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

  17. 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
  18. 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

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

  19. 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

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

  20. 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

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

  21. 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

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

  22. 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
  23. 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
  24. 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

    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

  25. 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
  26. 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
  27. Based on the promising results obtained so far we suggest that the co-authorship information and the circumstances of the articles' release (like the title of the journal, the year of publication) can be a crucia...

    Authors: Richárd Farkas
    Citation: BMC Bioinformatics 2008 9:69
  28. The investigation of possible interactions between two proteins in intracellular signaling is an expensive and laborious procedure in the wet-lab, therefore, several in silico approaches have been implemented ...

    Authors: Olivér M. Balogh, Bettina Benczik, András Horváth, Mátyás Pétervári, Péter Csermely, Péter Ferdinandy and Bence Ágg
    Citation: BMC Bioinformatics 2022 23:78
  29. 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

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

  30. 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

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

  31. Traditional genome annotation systems were developed in a very different computing era, one where the World Wide Web was just emerging. Consequently, these systems are built as centralized black boxes focused ...

    Authors: Daniel J Quest, Miriam L Land, Thomas S Brettin and Robert W Cottingham
    Citation: BMC Bioinformatics 2010 11(Suppl 6):S15

    This article is part of a Supplement: Volume 11 Supplement 6

  32. Recent years have brought great progress in efforts to digitize the world’s biodiversity data, but integrating data from many different providers, and across research domains, remains challenging. Semantic Web...

    Authors: Brian J Stucky, John Deck, Tom Conlin, Lukasz Ziemba, Nico Cellinese and Robert Guralnick
    Citation: BMC Bioinformatics 2014 15:257
  33. In pursuing personalized medicine, pharmacogenomic (PGx) knowledge may help guide prescribing drugs based on a person’s genotype. Here we evaluate the feasibility of incorporating PGx knowledge, combined with ...

    Authors: Casey Lynnette Overby, Peter Tarczy-Hornoch, James I Hoath, Ira J Kalet and David L Veenstra
    Citation: BMC Bioinformatics 2010 11(Suppl 9):S10

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

  34. The Pan-African bioinformatics network, H3ABioNet, comprises 27 research institutions in 17 African countries. H3ABioNet is part of the Human Health and Heredity in Africa program (H3Africa), an African-led re...

    Authors: Shakuntala Baichoo, Yassine Souilmi, Sumir Panji, Gerrit Botha, Ayton Meintjes, Scott Hazelhurst, Hocine Bendou, Eugene de Beste, Phelelani T. Mpangase, Oussema Souiai, Mustafa Alghali, Long Yi, Brian D. O’Connor, Michael Crusoe, Don Armstrong, Shaun Aron…
    Citation: BMC Bioinformatics 2018 19:457
  35. Examining the distribution of variation has proven an extremely profitable technique in the effort to identify sequences of biological significance. Most approaches in the field, however, evaluate only the con...

    Authors: Andrew Butterfield, Vivek Vedagiri, Edward Lang, Cath Lawrence, Matthew J Wakefield, Alexander Isaev and Gavin A Huttley
    Citation: BMC Bioinformatics 2004 5:1
  36. Extracting protein-protein interactions from biomedical literature is an important task in biomedical text mining. Supervised machine learning methods have been used with great success in this task but they te...

    Authors: Yanpeng Li, Xiaohua Hu, Hongfei Lin and Zhihao Yang
    Citation: BMC Bioinformatics 2010 11(Suppl 2):S7

    This article is part of a Supplement: Volume 11 Supplement 2

  37. The package pyMeSHSim recognizes bio-NEs by using MetaMap which produces Unified Medical Language System (UMLS) concepts in natural language process. To map the UMLS concepts to Medical...> 0.94, precision > 0.56...

    Authors: Zhi-Hui Luo, Meng-Wei Shi, Zhuang Yang, Hong-Yu Zhang and Zhen-Xia Chen
    Citation: BMC Bioinformatics 2020 21:252
  38. Functional annotation of proteins remains a challenging task. Currently the scientific literature serves as the main source for yet uncurated functional annotations, but curation work is slow and expensive. Au...

    Authors: Samira Jaeger, Sylvain Gaudan, Ulf Leser and Dietrich Rebholz-Schuhmann
    Citation: BMC Bioinformatics 2008 9(Suppl 8):S2

    This article is part of a Supplement: Volume 9 Supplement 8

  39. We propose MKEM, a Multi-level Knowledge Emergence Model, to discover implicit relationships using Natural Language Processing techniques such as Link Grammar and Ontologies such as Unified Medical Language Syste...

    Authors: Ali Z Ijaz, Min Song and Doheon Lee
    Citation: BMC Bioinformatics 2010 11(Suppl 2):S3

    This article is part of a Supplement: Volume 11 Supplement 2

Featured videos

View featured videos from across the BMC-series journals

Annual Journal Metrics

  • Speed
    15 days to first decision for all manuscripts
    70 days to first decision for reviewed manuscripts only
    163 days from submission to acceptance
    36 days from acceptance to publication

    Citation Impact
    3.169 - 2-year Impact Factor
    3.629 - 5-year Impact Factor
    1.276 - Source Normalized Impact per Paper (SNIP)
    1.567 - SCImago Journal Rank (SJR)

    6,337,109 Downloads (2021)
    5089 Altmetric Mentions

Sign up for article alerts and news from this journal