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. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. Research article

    Automatic classification of registered clinical trials towards the Global Burden of Diseases taxonomy of diseases and injuries

    Clinical trial registries may allow for producing a global mapping of health research. However, health conditions are not described with standardized taxonomies in registries. Previous work analyzed clinical t...

    Ignacio Atal, Jean-David Zeitoun, Aurélie Névéol, Philippe Ravaud, Raphaël Porcher and Ludovic Trinquart

    BMC Bioinformatics 2016 17:392

    Published on: 22 September 2016

  8. Research Article

    A corpus for plant-chemical relationships in the biomedical domain

    Plants are natural products that humans consume in various ways including food and medicine. They have a long empirical history of treating diseases with relatively few side effects. Based on these strengths, ...

    Wonjun Choi, Baeksoo Kim, Hyejin Cho, Doheon Lee and Hyunju Lee

    BMC Bioinformatics 2016 17:386

    Published on: 20 September 2016

  9. Methodology Article

    Interactive knowledge discovery and data mining on genomic expression data with numeric formal concept analysis

    Gene Expression Data (GED) analysis poses a great challenge to the scientific community that can be framed into the Knowledge Discovery in Databases (KDD) and Data Mining (DM) paradigm. Biclustering has emerge...

    Jose M González-Calabozo, Francisco J Valverde-Albacete and Carmen Peláez-Moreno

    BMC Bioinformatics 2016 17:374

    Published on: 15 September 2016

  10. Methodology Article

    Tilting the lasso by knowledge-based post-processing

    It is useful to incorporate biological knowledge on the role of genetic determinants in predicting an outcome. It is, however, not always feasible to fully elicit this information when the number of determinan...

    Kukatharmini Tharmaratnam, Matthew Sperrin, Thomas Jaki, Sjur Reppe and Arnoldo Frigessi

    BMC Bioinformatics 2016 17:344

    Published on: 2 September 2016

  11. Methodology article

    TopoICSim: a new semantic similarity measure based on gene ontology

    The Gene Ontology (GO) is a dynamic, controlled vocabulary that describes the cellular function of genes and proteins according to tree major categories: biological process, molecular function and cellular com...

    Rezvan Ehsani and Finn Drabløs

    BMC Bioinformatics 2016 17:296

    Published on: 29 July 2016

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