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README.md

Build Status DOI

microbial-conditions-ontology

MCO is a domain ontology that provides a controlled vocabulary for the unambiguous description of microbial growth conditions. The purpose of this ontology is to set an standard for the structured annotation of the experimental conditions in public repositories.

It builds upon extant OBO foundry ontologies and adds 828 terms to describe microbial experimental conditions as a result of Escherichia coli literature curation. It is currently being used in RegulonDB (http://regulondb.ccg.unam.mx/) to relate gene expression data to growth conditions. To this purpose, in parallel, a set of minimal requirements to describe growth conditions was developed based on Neidhardt recommendations for reproducibility [1].

More details can be found in the ontology pre-print:

Tierrafría, V. H., Mejía-Almonte, C., Camacho-Zaragoza, J. M., Salgado, H., Alquicira, K., Gama-Castro, S., & Collado-Vides, J. (2017). MCO: towards an ontology and unified vocabulary for a framework-based annotation of microbial growth conditions. bioRxiv, 218289. https://www.biorxiv.org/content/early/2017/11/12/218289

  1. Neidhardt, F. C., & Curtiss, R. (1999). Escherichia coli and Salmonella: cellular and molecular biology. Washington, DC:: ASM press.

Versions

Stable release versions

The latest version of the ontology can always be found at:

http://purl.obolibrary.org/obo/mco.owl

(note this will not show up until the request has been approved by obofoundry.org)

Editors' version

Editors of this ontology should use the edit version, src/ontology/mco-edit.owl

Contact

Please use this GitHub repository's Issue tracker to request new terms/classes or report errors or specific concerns related to the ontology.

Acknowledgements

This ontology repository was created using the ontology starter kit

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