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

• Published in: Biochimica et biophysica acta. Gene regulatory mechanisms 2021-11, Vol.1864 (11-12), p.194753-194753, Article 194753
• Main Authors: 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, Julio
• Format: Article
• Language: English
• Subjects: Bacterial transcriptional regulation; Biocuration; Curation tool; Data Curation - methods; Databases, Genetic; Escherichia coli - genetics; Escherichia coli K-12; Gene Expression Regulation, Bacterial; Text mining; Transcription Initiation, Genetic
• ISSN: 1874-9399; 1876-4320
• DOI: 10.1016/j.bbagrm.2021.194753

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. •Lisen&Curate is a platform to assist curation of transcriptional regulation.•Lisen&Curate links curated objects with their supporting evidence in articles.•Lisen&Curate changes traditional access to knowledge by textual sources of evidence.•Lisen&Curate helps to develop text mining approaches and controlled vocabularies.•Lisen&Curate is a new interconnected application to facilitate access to knowledge.