Knowledge-based analysis

Section edited by Hagit Shatkay

This section incorporates all aspects of knowledge-based analysis in biology including but not limited to: methods for the processing of text, ontologies and other computational representations of biological knowledge, as well as applications of knowledge-based systems for gaining insight into biology and biological data.

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  1. Methodology Article

    A strategy for evaluating pathway analysis methods

    Researchers have previously developed a multitude of methods designed to identify biological pathways associated with specific clinical or experimental conditions of interest, with the aim of facilitating biol...

    Chenggang Yu, Hyung Jun Woo, Xueping Yu, Tatsuya Oyama, Anders Wallqvist and Jaques Reifman

    BMC Bioinformatics 2017 18:453

    Published on: 13 October 2017

  2. Research Article

    An attention-based effective neural model for drug-drug interactions extraction

    Drug-drug interactions (DDIs) often bring unexpected side effects. The clinical recognition of DDIs is a crucial issue for both patient safety and healthcare cost control. However, although text-mining-based s...

    Wei Zheng, Hongfei Lin, Ling Luo, Zhehuan Zhao, Zhengguang Li, Yijia Zhang, Zhihao Yang and Jian Wang

    BMC Bioinformatics 2017 18:445

    Published on: 10 October 2017

  3. Research Article

    A new synonym-substitution method to enrich the human phenotype ontology

    Named entity recognition is critical for biomedical text mining, where it is not unusual to find entities labeled by a wide range of different terms. Nowadays, ontologies are one of the crucial enabling techno...

    Maria Taboada, Hadriana Rodriguez, Ranga C. Gudivada and Diego Martinez

    BMC Bioinformatics 2017 18:446

    Published on: 10 October 2017

  4. Research Article

    Interpretation of microbiota-based diagnostics by explaining individual classifier decisions

    The human microbiota is associated with various disease states and holds a great promise for non-invasive diagnostics. However, microbiota data is challenging for traditional diagnostic approaches: It is high-...

    A. Eck, L. M. Zintgraf, E. F. J. de Groot, T. G. J. de Meij, T. S. Cohen, P. H. M. Savelkoul, M. Welling and A. E. Budding

    BMC Bioinformatics 2017 18:441

    Published on: 4 October 2017

  5. Research Article

    Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles

    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...

    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

    BMC Bioinformatics 2017 18:372

    Published on: 17 August 2017

  6. Research article

    Drug voyager: a computational platform for exploring unintended drug action

    The dominant paradigm in understanding drug action focuses on the intended therapeutic effects and frequent adverse reactions. However, this approach may limit opportunities to grasp unintended drug actions, w...

    Min Oh, Jaegyoon Ahn, Taekeon Lee, Giup Jang, Chihyun Park and Youngmi Yoon

    BMC Bioinformatics 2017 18:131

    Published on: 28 February 2017

  7. Research article

    Microbial phenomics information extractor (MicroPIE): a natural language processing tool for the automated acquisition of prokaryotic phenotypic characters from text sources

    The large-scale analysis of phenomic data (i.e., full phenotypic traits of an organism, such as shape, metabolic substrates, and growth conditions) in microbial bioinformatics has been hampered by the lack of ...

    Jin Mao, Lisa R. Moore, Carrine E. Blank, Elvis Hsin-Hui Wu, Marcia Ackerman, Sonali Ranade and Hong Cui

    BMC Bioinformatics 2016 17:528

    Published on: 13 December 2016

  8. Research article

    Introducing Explorer of Taxon Concepts with a case study on spider measurement matrix building

    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...

    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

    BMC Bioinformatics 2016 17:471

    Published on: 17 November 2016

  9. Methodology Article

    Unsupervised gene set testing based on random matrix theory

    Gene set testing, or pathway analysis, is a bioinformatics technique that performs statistical testing on biologically meaningful sets of genomic variables. Although originally developed for supervised analyse...

    H. Robert Frost and Christopher I. Amos

    BMC Bioinformatics 2016 17:442

    Published on: 4 November 2016

  10. Research article

    A decision analysis model for KEGG pathway analysis

    The knowledge base-driven pathway analysis is becoming the first choice for many investigators, in that it not only can reduce the complexity of functional analysis by grouping thousands of genes into just sev...

    Junli Du, Manlin Li, Zhifa Yuan, Mancai Guo, Jiuzhou Song, Xiaozhen Xie and Yulin Chen

    BMC Bioinformatics 2016 17:407

    Published on: 6 October 2016

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