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1513 result(s) for 'natural language processing' within BMC Bioinformatics

Page 5 of 31

  1. 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
  2. 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

  3. 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

  4. 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

  5. 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
  6. 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

  7. 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
  8. 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
  9. 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

  10. 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
  11. 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

  12. 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

  13. 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
  14. 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
  15. 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
  16. 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
  17. Streptomycetes are filamentous microorganisms of high biotechnological relevance, especially for the production of antibiotics. In submerged cultures, the productivity of these microorganisms is closely linked...

    Authors: Christian Carsten Sachs, Joachim Koepff, Wolfgang Wiechert, Alexander Grünberger and Katharina Nöh
    Citation: BMC Bioinformatics 2019 20:452
  18. 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

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

  19. Although rare diseases are characterized by low prevalence, approximately 400 million people are affected by a rare disease. The early and accurate diagnosis of these conditions is a major challenge for general p...

    Authors: Isabel Segura-Bedmar, David Camino-Perdones and Sara Guerrero-Aspizua
    Citation: BMC Bioinformatics 2022 23:263
  20. 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
  21. Orphan gene play an important role in the environmental stresses of many species and their identification is a critical step to understand biological functions. Moso bamboo has high ecological, economic and cu...

    Authors: Xiaodan Zhang, Jinxiang Xuan, Chensong Yao, Qijuan Gao, Lianglong Wang, Xiu Jin and Shaowen Li
    Citation: BMC Bioinformatics 2022 23:162
  22. Stroke has an acute onset and a high mortality rate, making it one of the most fatal diseases worldwide. Its underlying biology and treatments have been widely studied both in the “Western” biomedicine and the...

    Authors: Xi Yang, Chengkun Wu, Goran Nenadic, Wei Wang and Kai Lu
    Citation: BMC Bioinformatics 2021 22(Suppl 10):387

    This article is part of a Supplement: Volume 22 Supplement 10

    The Correction to this article has been published in BMC Bioinformatics 2021 22:585

  23. Computing semantic relatedness between textual labels representing biological and medical concepts is a crucial task in many automated knowledge extraction and processing applications relevant to the biomedica...

    Authors: Maciej Rybinski and José Francisco Aldana-Montes
    Citation: BMC Bioinformatics 2014 15(Suppl 14):S2

    This article is part of a Supplement: Volume 15 Supplement 14

  24. In this paper, a novel building block of proteins called Top-n-grams is presented, which contains the evolutionary information extracted from the protein sequence frequency profiles. The protein sequence frequenc...

    Authors: Bin Liu, Xiaolong Wang, Lei Lin, Qiwen Dong and Xuan Wang
    Citation: BMC Bioinformatics 2008 9:510
  25. Sphingosine 1-phosphate (S1P), a lysophospholipid, is involved in various cellular processes such as migration, proliferation, and survival. To date, the impact of S1P on human glioblastoma is not fully unders...

    Authors: Jeyakumar Natarajan, Daniel Berrar, Werner Dubitzky, Catherine Hack, Yonghong Zhang, Catherine DeSesa, James R Van Brocklyn and Eric G Bremer
    Citation: BMC Bioinformatics 2006 7:373
  26. Text mining has become a useful tool for biologists trying to understand the genetics of diseases. In particular, it can help identify the most interesting candidate genes for a disease for further experimenta...

    Authors: Shi Yu, Leon-Charles Tranchevent, Bart De Moor and Yves Moreau
    Citation: BMC Bioinformatics 2010 11:28
  27. Three-dimensional (3-D) visualization of multimodality neuroimaging data provides a powerful technique for viewing the relationship between structure and function. A number of applications are available that i...

    Authors: Eider B Moore, Andrew V Poliakov, Peter Lincoln and James F Brinkley
    Citation: BMC Bioinformatics 2007 8:389
  28. Today, an unprecedented volume of primary biodiversity data are being generated worldwide, yet significant amounts of these data have been and will continue to be lost after the conclusion of the projects task...

    Authors: Anthony Goddard, Nathan Wilson, Phil Cryer and Grant Yamashita
    Citation: BMC Bioinformatics 2011 12(Suppl 15):S5

    This article is part of a Supplement: Volume 12 Supplement 15

  29. The widely spreading coronavirus disease (COVID-19) has three major spreading properties: pathogenic mutations, spatial, and temporal propagation patterns. We know the spread of the virus geographically and te...

    Authors: Inyoung Sung, Sangseon Lee, Minwoo Pak, Yunyol Shin and Sun Kim
    Citation: BMC Bioinformatics 2022 23(Suppl 3):149

    This article is part of a Supplement: Volume 23 Supplement 3

  30. The Turku Event Extraction System (TEES) is a text mining program developed for the extraction of events, complex biomedical relationships, from scientific literature. Based on a graph-generation approach, the...

    Authors: Jari Björne and Tapio Salakoski
    Citation: BMC Bioinformatics 2015 16(Suppl 16):S4

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

  31. Determining usefulness of biomedical text mining systems requires realistic task definition and data selection criteria without artificial constraints, measuring performance aspects that go beyond traditional ...

    Authors: Martin Krallinger, Miguel Vazquez, Florian Leitner, David Salgado, Andrew Chatr-aryamontri, Andrew Winter, Livia Perfetto, Leonardo Briganti, Luana Licata, Marta Iannuccelli, Luisa Castagnoli, Gianni Cesareni, Mike Tyers, Gerold Schneider, Fabio Rinaldi, Robert Leaman…
    Citation: BMC Bioinformatics 2011 12(Suppl 8):S3

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

  32. From a comparative perspective, the combination of retrieval and natural language processing methods we designed, achieved very competitive performances...

    Authors: Frédéric Ehrler, Antoine Geissbühler, Antonio Jimeno and Patrick Ruch
    Citation: BMC Bioinformatics 2005 6(Suppl 1):S23

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

  33. Protein-protein interactions (PPIs) are critical to normal cellular function and are related to many disease pathways. A range of protein functions are mediated and regulated by protein interactions through po...

    Authors: Aparna Elangovan, Yuan Li, Douglas E. V. Pires, Melissa J. Davis and Karin Verspoor
    Citation: BMC Bioinformatics 2022 23:4
  34. Manual extraction of information from electronic pathology (epath) reports to populate the Surveillance, Epidemiology, and End Result (SEER) database is labor intensive. Systematizing the data extraction automati...

    Authors: Nicolas Hengartner, Leticia Cuellar, Xiao-Cheng Wu, Georgia Tourassi, John Qiu, Blair Christian and Tanmoy Bhattacharya
    Citation: BMC Bioinformatics 2018 19(Suppl 18):485

    This article is part of a Supplement: Volume 19 Supplement 18

  35. Computational Biology needs computer-readable information records. Increasingly, meta-analysed and pre-digested information is being used in the follow up of high throughput experiments and other investigation...

    Authors: Barend Mons
    Citation: BMC Bioinformatics 2005 6:142
  36. The combination of mass spectrometry and solution phase amide hydrogen/deuterium exchange (H/D exchange) experiments is an effective method for characterizing protein dynamics, and protein-protein or protein-l...

    Authors: BD Pascal, MJ Chalmers, SA Busby, CC Mader, MR Southern, NF Tsinoremas and PR Griffin
    Citation: BMC Bioinformatics 2007 8:156
  37. Quantification of gene expression from RNA-seq data is a prerequisite for transcriptome analysis such as differential gene expression analysis and gene co-expression network construction. Individual RNA-seq ex...

    Authors: John A. Hadish, Tyler D. Biggs, Benjamin T. Shealy, M. Reed Bender, Coleman B. McKnight, Connor Wytko, Melissa C. Smith, F. Alex Feltus, Loren Honaas and Stephen P. Ficklin
    Citation: BMC Bioinformatics 2022 23:156
  38. This paper presents the concept annotations of the Colorado Richly Annotated Full-Text (CRAFT) Corpus, a collection of 97 full-length, open-access biomedical journal articles that have been annotated both semanti...

    Authors: Michael Bada, Miriam Eckert, Donald Evans, Kristin Garcia, Krista Shipley, Dmitry Sitnikov, William A Baumgartner Jr, K Bretonnel Cohen, Karin Verspoor, Judith A Blake and Lawrence E Hunter
    Citation: BMC Bioinformatics 2012 13:161
  39. Word sense disambiguation (WSD) is critical in the biomedical domain for improving the precision of natural language processing (NLP), text mining, and information ... the WSD problem for a number of text processing

    Authors: Hua Xu, Marianthi Markatou, Rositsa Dimova, Hongfang Liu and Carol Friedman
    Citation: BMC Bioinformatics 2006 7:334
  40. Biomedical named entity recognition (Bio-NER) is a challenging problem because, in general, biomedical named entities of the same category (e.g., proteins and genes) do not follow one standard nomenclature. Th...

    Authors: Richard Tzong-Han Tsai, Cheng-Lung Sung, Hong-Jie Dai, Hsieh-Chuan Hung, Ting-Yi Sung and Wen-Lian Hsu
    Citation: BMC Bioinformatics 2006 7(Suppl 5):S11

    This article is part of a Supplement: Volume 7 Supplement 5

  41. Recent advances in automation technologies have enabled the use of flow cytometry for high throughput screening, generating large complex data sets often in clinical trials or drug discovery settings. However,...

    Authors: Florian Hahne, Nolwenn LeMeur, Ryan R Brinkman, Byron Ellis, Perry Haaland, Deepayan Sarkar, Josef Spidlen, Errol Strain and Robert Gentleman
    Citation: BMC Bioinformatics 2009 10:106

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