ArticleDatabase : the journal of biological databases and curation2014
Assisted curation of regulatory interactions and growth conditions of OxyR in E. coli K-12.
Article in Database : the journal of biological databases and curation, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Fine-tuned GPT-based foundation models effectively reconstruct bacterial transcriptional regulatory networks from literature.Frontiers in artificial intelligence · 2026Article
- Symmetries in metabolic networks ofPNAS nexus · 2025Article
- The master regulator OxyR orchestrates bacterial oxidative stress response genes in space and time.Cell systems · 2024Article
- Automatic extraction of transcriptional regulatory interactions of bacteria from biomedical literature using a BERT-based approach.Database : the journal of biological databases and curation · 2024Article
- RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12.Nucleic acids research · 2019Article
- Accelerating annotation of articles via automated approaches: evaluation of the neXtA5 curation-support tool by neXtProt.Database : the journal of biological databases and curation · 2018Article
- First steps in automatic summarization of transcription factor properties for RegulonDB: classification of sentences about structural domains and regulated processes.Database : the journal of biological databases and curation · 2017Article
- Strategies towards digital and semi-automated curation in RegulonDB.Database : the journal of biological databases and curation · 2017Article
- Improving biocuration of microRNAs in diseases: a case study in idiopathic pulmonary fibrosis.Database : the journal of biological databases and curation · 2017Article
- RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond.Nucleic acids research · 2016Article
- Automated detection of discourse segment and experimental types from the text of cancer pathway results sections.Database : the journal of biological databases and curation · 2016Article
- Every Site Counts: Submitting Transcription Factor-Binding Site Information through the CollecTF Portal.Journal of bacteriology · 2015Article
- Biocuration with insufficient resources and fixed timelines.Database : the journal of biological databases and curation · 2015Article
- OntoGene web services for biomedical text mining.BMC bioinformatics · 2014Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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