title: Assisted curation of regulatory interactions and growth conditions of OxyR in E. coli K-12.
abstract: Given the current explosion of data within original publications generated in the field of genomics, a recognized bottleneck is the transfer of such knowledge into comprehensive databases. We have for years organized knowledge on transcriptional regulation reported in the original literature of Escherichia coli K-12 into RegulonDB (http://regulondb.ccg.unam.mx), our database that is currently supported by >5000 papers. Here, we report a first step towards the automatic biocuration of growth conditions in this corpus. Using the OntoGene text-mining system (http://www.ontogene.org), we extracted and manually validated regulatory interactions and growth conditions in a new approach based on filters that enable the curator to select informative sentences from preprocessed full papers. Based on a set of 48 papers dealing with oxidative stress by OxyR, we were able to retrieve 100% of the OxyR regulatory interactions present in RegulonDB, including the transcription factors and their effect on target genes. Our strategy was designed to extract, as we did, their growth conditions. This result provides a proof of concept for a more direct and efficient curation process, and enables us to define the strategy of the subsequent steps to be implemented for a semi-automatic curation of original literature dealing with regulation of gene expression in bacteria. This project will enhance the efficiency and quality of the curation of knowledge present in the literature of gene regulation, and contribute to a significant increase in the encoding of the regulatory network of E. coli. RegulonDB Database URL: http://regulondb.ccg.unam.mx OntoGene URL: http://www.ontogene.org.
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland.
authors.forename: Socorro
authors.initials: S
authors.lastname: Gama-Castro
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland collado@ccg.unam.mx.
authors.forename: Fabio
authors.initials: F
authors.lastname: Rinaldi
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland.
authors.forename: Alejandra
authors.initials: A
authors.lastname: López-Fuentes
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland.
authors.forename: Yalbi Itzel
authors.initials: YI
authors.lastname: Balderas-Martínez
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland.
authors.forename: Simon
authors.initials: S
authors.lastname: Clematide
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland.
authors.forename: Tilia Renate
authors.initials: TR
authors.lastname: Ellendorff
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland.
authors.forename: Alberto
authors.initials: A
authors.lastname: Santos-Zavaleta
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland.
authors.forename: Hernani
authors.initials: H
authors.lastname: Marques-Madeira
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland collado@ccg.unam.mx.
authors.forename: Julio
authors.initials: J
authors.lastname: Collado-Vides
mesh_terms: D057225:Data Mining; D030541:Databases, Genetic; D048168:Escherichia coli K12 / Q000235:genetics* / Q000254:growth & development* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D018085:Regulon / Q000235:genetics; D012097:Repressor Proteins / Q000378:metabolism*; D012660:Semantics; D009626:Terminology as Topic
chemical_list: D029968:Escherichia coli Proteins; D012097:Repressor Proteins; C499299:oxyR protein, E coli