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Lisen&Curate: a platform to facilitate gathering textual evidence for curation of regulation of transcription initiation in bacteria

2021 Martín Díaz-Rodríguez et al. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license http://creativecommons.org/licenses/by-nc-nd/4.0/ http://creativecommons.org/licenses/by-nc-nd/4.0/ info:eu-repo/semantics/openAccess ;ISSN: 1874-9399 ;EISSN: 1876-4320 ;DOI: 10.1016/j.bbagrm.2021.194753

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  • Title:
    Lisen&Curate: a platform to facilitate gathering textual evidence for curation of regulation of transcription initiation in bacteria
  • Author: Díaz-Rodríguez, Martín ; Lithgow-Serrano, Oscar ; Guadarrama-García, Francisco ; Tierrafría, Víctor H ; Gama-Castro, Socorro ; Solano-Lira, Hilda ; Salgado, Heladia ; Rinaldi, Fabio ; Méndez-Cruz, Carlos-Francisco ; Collado Vides, Pedro Julio
  • Subjects: Bacteris ; Informàtica ; Programari
  • Description: The number of published papers in biomedical research makes it rather impossible for a researcher to keep up to date. This is where manually curated databases contribute facilitating the access to knowledge. However, the structure required by databases strongly limits the type of valuable information that can be incorporated. Here, we present Lisen&Curate, a curation system that facilitates linking sentences or part of sentences (both considered sources) in articles with their corresponding curated objects, so that rich additional information of these objects is easily available to users. These sources are going to be offered both within RegulonDB and a new database, L-Regulon. To show the relevance of our work, two senior curators performed a curation of 31 articles on the regulation of transcription initiation of E. coli using Lisen&Curate. As a result, 194 objects were curated and 781 sources were recorded. We also found that these sources are useful to develop automatic approaches to detect objects in articles by observing word frequency patterns and by carrying out an open information extraction task. Sources may help to elaborate a controlled vocabulary of experimental methods. Finally, we discuss our ecosystem of interconnected applications, RegulonDB, L-Regulon, and Lisen&Curate, to facilitate the access to knowledge on regulation of transcription initiation in bacteria. We see our proposal as the starting point to change the way experimentalists connect a piece of knowledge with its evidence using RegulonDB. This study was supported by the Universidad Nacional Autónoma de México (UNAM) and the National Institute of General Medical Sciences of the National Institutes of Health [grants number 5RO1-GM110597-04 and 1RO1-GM131643-01A1]
  • Publisher: Elsevier
  • Creation Date: 2021
  • Language: English
  • Identifier: ISSN: 1874-9399
    EISSN: 1876-4320
    DOI: 10.1016/j.bbagrm.2021.194753
  • Source: Repositori Digital de la UPF (Universitat Pompeu Fabra)
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