title: Strategies towards digital and semi-automated curation in RegulonDB.
abstract: Experimentally generated biological information needs to be organized and structured in order to become meaningful knowledge. However, the rate at which new information is being published makes manual curation increasingly unable to cope. Devising new curation strategies that leverage upon data mining and text analysis is, therefore, a promising avenue to help life science databases to cope with the deluge of novel information. In this article, we describe the integration of text mining technologies in the curation pipeline of the RegulonDB database, and discuss how the process can enhance the productivity of the curators.
  Specifically, a named entity recognition approach is used to pre-annotate terms referring to a set of domain entities which are potentially relevant for the curation process. The annotated documents are presented to the curator, who, thanks to a custom-designed interface, can select sentences containing specific types of entities, thus restricting the amount of text that needs to be inspected. Additionally, a module capable of computing semantic similarity between sentences across the entire collection of articles to be curated is being integrated in the system. We tested the module using three sets of scientific articles and six domain experts. All these improvements are gradually enabling us to obtain a high throughput curation process with the same quality as manual curation.
authors.affiliation: Swiss Institute of Bioinformatics, and Institute of Computational Linguistics, University of Zurich, 8050 Andreasstrasse 14, Zürich.|Institute of Computational Linguistics, University of Zurich, Andreasstrasse 15, Zurich 8050, Switzerland.
authors.forename: Fabio
authors.initials: F
authors.lastname: Rinaldi
authors.affiliation: Swiss Institute of Bioinformatics, and Institute of Computational Linguistics, University of Zurich, 8050 Andreasstrasse 14, Zürich.
authors.forename: Oscar
authors.initials: O
authors.lastname: Lithgow
authors.affiliation: Swiss Institute of Bioinformatics, and Institute of Computational Linguistics, University of Zurich, 8050 Andreasstrasse 14, Zürich.
authors.forename: Socorro
authors.initials: S
authors.lastname: Gama-Castro
authors.affiliation: Swiss Institute of Bioinformatics, and Institute of Computational Linguistics, University of Zurich, 8050 Andreasstrasse 14, Zürich.
authors.forename: Hilda
authors.initials: H
authors.lastname: Solano
authors.affiliation: Swiss Institute of Bioinformatics, and Institute of Computational Linguistics, University of Zurich, 8050 Andreasstrasse 14, Zürich.
authors.forename: Alejandra
authors.initials: A
authors.lastname: Lopez
authors.affiliation: Swiss Institute of Bioinformatics, and Institute of Computational Linguistics, University of Zurich, 8050 Andreasstrasse 14, Zürich.
authors.forename: Luis José
authors.initials: LJ
authors.lastname: Muñiz Rascado
authors.affiliation: Swiss Institute of Bioinformatics, and Institute of Computational Linguistics, University of Zurich, 8050 Andreasstrasse 14, Zürich.
authors.forename: Cecilia
authors.initials: C
authors.lastname: Ishida-Gutiérrez
authors.affiliation: Swiss Institute of Bioinformatics, and Institute of Computational Linguistics, University of Zurich, 8050 Andreasstrasse 14, Zürich.
authors.forename: Carlos-Francisco
authors.initials: CF
authors.lastname: Méndez-Cruz
authors.affiliation: Swiss Institute of Bioinformatics, and Institute of Computational Linguistics, University of Zurich, 8050 Andreasstrasse 14, Zürich.
authors.forename: Julio
authors.initials: J
authors.lastname: Collado-Vides
mesh_terms: D066289:Data Curation / Q000379:methods* / Q000592:standards; D057225:Data Mining / Q000379:methods*; D016208:Databases, Factual; D018085:Regulon / Q000502:physiology*