Strategies towards digital and semi-automated curation in RegulonDB

Database (Oxford). 2017 Jan 1;2017(1):bax012. doi: 10.1093/database/bax012.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Data Curation / methods*
  • Data Curation / standards
  • Data Mining / methods*
  • Databases, Factual*
  • Regulon / physiology*