ArticleBioinformatics (Oxford, England)2019
MCO: towards an ontology and unified vocabulary for a framework-based annotation of microbial growth conditions.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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7 citing papers in PubMed.
- The allostery principle supports the symbolic character of signaling circuits: gene regulation provides a form of intelligence to living systems.Theory in biosciences = Theorie in den Biowissenschaften · 2026Article
- RegulonDB v12.0: a comprehensive resource of transcriptional regulation in E. coli K-12.Nucleic acids research · 2024Article
- RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation inMicrobial genomics · 2022Article
- An assessment of genome annotation coverage across the bacterial tree of life.Microbial genomics · 2020Article
- Visualization and prediction of CRISPR incidence in microbial trait-space to identify drivers of antiviral immune strategy.The ISME journal · 2019Article
- 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
- A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0.BMC biology · 2018Article
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8 authors.
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Abstract
motivationA major component in increasing our understanding of the biology of an organism is the mapping of its genotypic potential into its phenotypic expression profiles. This mapping is executed by the machinery of gene regulation, which is essentially studied by changes in growth conditions. Although many efforts have been made to systematize the annotation of experimental conditions in microbiology, the available annotations are not based on a consistent and controlled vocabulary, making difficult the identification of biologically meaningful comparisons of knowledge derived from different experiments or laboratories.
resultsWe curated terms related to experimental conditions that affect gene expression in Escherichia coli K-12. Since this is the best-studied microorganism, the collected terms are the seed for the Microbial Conditions Ontology (MCO), a controlled and structured vocabulary that can be expanded to annotate microbial conditions in general. Moreover, we developed an annotation framework to describe experimental conditions, providing the foundation to identify regulatory networks that operate under particular conditions. AVAILABILITY AND IMPLEMENTATION: As far as we know, MCO is the first ontology for growth conditions of any bacterial organism, and it is available at http://regulondb.ccg.unam.mx and https://github.com/microbial-conditions-ontology. Furthermore, we will disseminate MCO throughout the Open Biological and Biomedical Ontology (OBO) Foundry in order to set a standard for the annotation of gene expression data. This will enable comparison of data from diverse data sources. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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