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1641 result(s) for 'natural language processing' within BMC Bioinformatics

Page 5 of 33

  1. 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:

  3. 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

  5. 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:

  6. 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:

  7. 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

  8. 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:

  9. 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:

  10. 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:

  11. 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

  12. Understanding gene expression processes necessitates the accurate classification and identification of transcription factors, which is supported by high-throughput sequencing technologies. However, these techn...

    Authors: Jidong Zhang, Bo Liu, Jiahui Wu, Zhihan Wang and Jianqiang Li
    Citation: BMC Bioinformatics 2023 24:345
    Content type: Research Published on:

  14. 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

  16. 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

  17. 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

  18. 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:

  19. 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

  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
    Content type: Proceedings Published on:

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

  21. An abnormal growth or fatty mass of cells in the brain is called a tumor. They can be either healthy (normal) or become cancerous, depending on the structure of their cells. This can result in increased pressu...

    Authors: A. Rohini, Carol Praveen, Sandeep Kumar Mathivanan, V. Muthukumaran, Saurav Mallik, Mohammed S. Alqahtani, Amal Al-Rasheed and Ben Othman Soufiene
    Citation: BMC Bioinformatics 2023 24:382
    Content type: Research Published on:

  22. 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:

  24. 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:

  25. 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

  26. 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

  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
    Content type: Methodology article Published on:

  30. 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
    Content type: Software Published on:

  32. Sequenced Protein–Protein Interaction (PPI) prediction represents a pivotal area of study in biology, playing a crucial role in elucidating the mechanistic underpinnings of diseases and facilitating the design...

    Authors: Jiahui Wu, Bo Liu, Jidong Zhang, Zhihan Wang and Jianqiang Li
    Citation: BMC Bioinformatics 2023 24:473
    Content type: Research Published on:

  33. 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
    Content type: Proceedings Published on:

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

  34. 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
    Content type: Software Published on:

  35. 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
    Content type: Proceedings Published on:

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

  36. Natural History science is characterised by a single immense goal (to document, describe and synthesise all facets pertaining to the diversity of life) that can only be addressed through a seemingly infinite s...

    Authors: Vincent S Smith, Simon D Rycroft, Kehan T Harman, Ben Scott and David Roberts
    Citation: BMC Bioinformatics 2009 10(Suppl 14):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 14

  37. 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
    Content type: Software Published on:

  39. 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
    Content type: Proceedings Published on:

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

  40. 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
    Content type: Proceedings Published on:

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

  41. 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
    Content type: Software Published on:

  44. We developed a method for automatic extraction of protein functional annotation from scientific text based on the Natural Language Processing (NLP) technology. For the protein annotation ... We also expanded the ...

    Authors: Nikolai Daraselia, Anton Yuryev, Sergei Egorov, Ilya Mazo and Iaroslav Ispolatov
    Citation: BMC Bioinformatics 2007 8:243
    Content type: Research article Published on:

  45. 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
    Content type: Software Published on:

  46. Manual curation of experimental data from the biomedical literature is an expensive and time-consuming endeavor. Nevertheless, most biological knowledge bases still rely heavily on manual curation for data ext...

    Authors: Kimberly Van Auken, Joshua Jaffery, Juancarlos Chan, Hans-Michael Müller and Paul W Sternberg
    Citation: BMC Bioinformatics 2009 10:228
    Content type: Methodology article Published on:

  47. The Molecular Interaction Map (MIM) notation offers a standard set of symbols and rules on their usage for the depiction of cellular signaling network diagrams. Such diagrams are essential for disseminating bi...

    Authors: Augustin Luna, Evrim I Karac, Margot Sunshine, Lucas Chang, Ruth Nussinov, Mirit I Aladjem and Kurt W Kohn
    Citation: BMC Bioinformatics 2011 12:167
    Content type: Research article Published on:

  48. Consumers increasingly use online resources for their health information needs. While current search engines can address these needs to some extent, they generally do not take into account that most health inf...

    Authors: Halil Kilicoglu, Asma Ben Abacha, Yassine Mrabet, Sonya E. Shooshan, Laritza Rodriguez, Kate Masterton and Dina Demner-Fushman
    Citation: BMC Bioinformatics 2018 19:34
    Content type: Research Article Published on:

  49. The rapid annotation of genes on a genome-wide scale is now possible for several organisms using high-throughput RNA interference assays to knock down the expression of a specific gene. To date, dozens of RNA ...

    Authors: Matthew T Weirauch, Christopher K Wong, Alexandra B Byrne and Joshua M Stuart
    Citation: BMC Bioinformatics 2008 9:463
    Content type: Research article Published on:

  50. Machine learning (ML) has a rich history in structural bioinformatics, and modern approaches, such as deep learning, are revolutionizing our knowledge of the subtle relationships between biomolecular sequence,...

    Authors: Eli J. Draizen, John Readey, Cameron Mura and Philip E. Bourne
    Citation: BMC Bioinformatics 2024 25:11
    Content type: Software Published on:

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