RegulonDB


Since January 2013 the OntoGene group has established a strategic collaboration with the RegulonDB group, based at the Center for Genomic Sciences, of the National Autonomous University of Mexico. The goal of the collaboration is to develop novel strategies for assisted curation of the biomedical literature. RegulonDB is the primary database on transcriptional regulation in E. coli K-12, containing knowledge manually curated from original scientific publications. Together we have participated in the interactive task of BioCreative 2013. Joint experiments on assisted curation using the ODIN platform have been performed, and a journal paper is currently under evaluation. 

We have customized OntoGene/ODIN for specific subtasks within the RegulonDB curation workflow, in particular using goal-specific terminology provided by RegulonDB for the annotation of full-text articles. Additional filters have been added to ODIN, which allow RegulonDB curators to focus their attention on subsets of the paper which are likely to be particularly relevant for their curation tasks. Specific experiments for the curation of experimental conditional and experimental methods have been described in recent conference presentations.

A recently published journal paper provides a good overview of this line of research.



Related publications

Fabio Rinaldi, Socorro Gama-Castro, Alejandra López-Fuentes, Yalbi Balderas-Martínez, Julio Collado-Vides. Digital Curation Experiments for RegulonDB, BioCuration 2013, April 10th, 2013, Cambridge, UK.

Socorro Gama-Castro, Fabio Rinaldi, Alejandra López-Fuentes, Yalbi Itzel Balderas-Martínez, Simon Clematide, Tilia Renate Ellendorff, Julio Collado-Vides. Assisted curation of growth conditions that affect gene expression in E. coli K-12. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop, vol. 1, pages 214-218. Bethesda, Maryland, October 7-9, 2013.

Fabio Rinaldi, Socorro Gama-Castro, Alejandra López-Fuentes, Alberto Santos-Zavaleta, Simon Clematide, Tilia Renate Ellendorff, Julio Collado-Vides. Assisted curation of experimental methods in RegulonDB. BioCuration 2014, April 7th, 2014, Toronto, Canada.

Socorro Gama-Castro, Fabio Rinaldi, Alejandra Lopez-Fuentes, Yalbi Itzel Balderas-Martinez, Simon Clematide, Tilia Renate Ellendorff, Alberto Santos-Zavaleta, Hernani Marques-Madeira, Julio Collado-Vides. Assisted curation of regulatory interactions and growth conditions of OxyR in E. coli K-12.Database 2014: bau049, Oxford Journals, 2014. doi:10.1093/database/bau049




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