MOTIVATION: A 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. RESULTS: We 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.
MOTIVATION: A 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. RESULTS: We 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.
Authors: Georgios V Gkoutos; Chris Mungall; Sandra Dolken; Michael Ashburner; Suzanna Lewis; John Hancock; Paul Schofield; Sebastian Kohler; Peter N Robinson Journal: Conf Proc IEEE Eng Med Biol Soc Date: 2009
Authors: Alberto Santos-Zavaleta; Mishael Sánchez-Pérez; Heladia Salgado; David A Velázquez-Ramírez; Socorro Gama-Castro; Víctor H Tierrafría; Stephen J W Busby; Patricia Aquino; Xin Fang; Bernhard O Palsson; James E Galagan; Julio Collado-Vides Journal: BMC Biol Date: 2018-08-16 Impact factor: 7.431
Authors: Matthew A Richards; Victor Cassen; Benjamin D Heavner; Nassim E Ajami; Andrea Herrmann; Evangelos Simeonidis; Nathan D Price Journal: PLoS One Date: 2014-08-06 Impact factor: 3.240
Authors: Mark D Wilkinson; Michel Dumontier; I Jsbrand Jan Aalbersberg; Gabrielle Appleton; Myles Axton; Arie Baak; Niklas Blomberg; Jan-Willem Boiten; Luiz Bonino da Silva Santos; Philip E Bourne; Jildau Bouwman; Anthony J Brookes; Tim Clark; Mercè Crosas; Ingrid Dillo; Olivier Dumon; Scott Edmunds; Chris T Evelo; Richard Finkers; Alejandra Gonzalez-Beltran; Alasdair J G Gray; Paul Groth; Carole Goble; Jeffrey S Grethe; Jaap Heringa; Peter A C 't Hoen; Rob Hooft; Tobias Kuhn; Ruben Kok; Joost Kok; Scott J Lusher; Maryann E Martone; Albert Mons; Abel L Packer; Bengt Persson; Philippe Rocca-Serra; Marco Roos; Rene van Schaik; Susanna-Assunta Sansone; Erik Schultes; Thierry Sengstag; Ted Slater; George Strawn; Morris A Swertz; Mark Thompson; Johan van der Lei; Erik van Mulligen; Jan Velterop; Andra Waagmeester; Peter Wittenburg; Katherine Wolstencroft; Jun Zhao; Barend Mons Journal: Sci Data Date: 2016-03-15 Impact factor: 6.444
Authors: Anita Bandrowski; Ryan Brinkman; Mathias Brochhausen; Matthew H Brush; Bill Bug; Marcus C Chibucos; Kevin Clancy; Mélanie Courtot; Dirk Derom; Michel Dumontier; Liju Fan; Jennifer Fostel; Gilberto Fragoso; Frank Gibson; Alejandra Gonzalez-Beltran; Melissa A Haendel; Yongqun He; Mervi Heiskanen; Tina Hernandez-Boussard; Mark Jensen; Yu Lin; Allyson L Lister; Phillip Lord; James Malone; Elisabetta Manduchi; Monnie McGee; Norman Morrison; James A Overton; Helen Parkinson; Bjoern Peters; Philippe Rocca-Serra; Alan Ruttenberg; Susanna-Assunta Sansone; Richard H Scheuermann; Daniel Schober; Barry Smith; Larisa N Soldatova; Christian J Stoeckert; Chris F Taylor; Carlo Torniai; Jessica A Turner; Randi Vita; Patricia L Whetzel; Jie Zheng Journal: PLoS One Date: 2016-04-29 Impact factor: 3.240
Authors: Alberto Santos-Zavaleta; Heladia Salgado; Socorro Gama-Castro; Mishael Sánchez-Pérez; Laura Gómez-Romero; Daniela Ledezma-Tejeida; Jair Santiago García-Sotelo; Kevin Alquicira-Hernández; Luis José Muñiz-Rascado; Pablo Peña-Loredo; Cecilia Ishida-Gutiérrez; David A Velázquez-Ramírez; Víctor Del Moral-Chávez; César Bonavides-Martínez; Carlos-Francisco Méndez-Cruz; James Galagan; Julio Collado-Vides Journal: Nucleic Acids Res Date: 2019-01-08 Impact factor: 16.971
Authors: Víctor H Tierrafría; Claire Rioualen; Heladia Salgado; Paloma Lara; Socorro Gama-Castro; Patrick Lally; Laura Gómez-Romero; Pablo Peña-Loredo; Andrés G López-Almazo; Gabriel Alarcón-Carranza; Felipe Betancourt-Figueroa; Shirley Alquicira-Hernández; J Enrique Polanco-Morelos; Jair García-Sotelo; Estefani Gaytan-Nuñez; Carlos-Francisco Méndez-Cruz; Luis J Muñiz; César Bonavides-Martínez; Gabriel Moreno-Hagelsieb; James E Galagan; Joseph T Wade; Julio Collado-Vides Journal: Microb Genom Date: 2022-05