title: DEOP: a database on osmoprotectants and associated pathways.
abstract: Microorganisms are known to counteract salt stress through salt influx or by the accumulation of osmoprotectants (also called compatible solutes). Understanding the pathways that synthesize and/or breakdown these osmoprotectants is of interest to studies of crops halotolerance and to biotechnology applications that use microbes as cell factories for production of biomass or commercial chemicals. To facilitate the exploration of osmoprotectants, we have developed the first online resource, 'Dragon Explorer of Osmoprotection associated Pathways' (DEOP) that gathers and presents curated information about osmoprotectants, complemented by information about reactions and pathways that use or affect them. A combined total of 141 compounds were confirmed osmoprotectants, which were matched to 1883 reactions and 834 pathways. DEOP can also be used to map genes or microbial genomes to potential osmoprotection-associated pathways, and thus link genes and genomes to other associated osmoprotection information. Moreover, DEOP provides a text-mining utility to search deeper into the scientific literature for supporting evidence or for new associations of osmoprotectants to pathways, reactions, enzymes, genes or organisms. Two case studies are provided to demonstrate the usefulness of DEOP. The system can be accessed at. Database URL: http://www.cbrc.kaust.edu.sa/deop/
authors.affiliation: King Abdullah University of Science and Technology (KAUST); Computational Bioscience Research Centre (CBRC); Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE); Thuwal, Jeddah, 23955-6900, Saudi Arabia.
authors.forename: Salim
authors.initials: S
authors.lastname: Bougouffa
authors.affiliation: King Abdullah University of Science and Technology (KAUST); Computational Bioscience Research Centre (CBRC); Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE); Thuwal, Jeddah, 23955-6900, Saudi Arabia.
authors.forename: Aleksandar
authors.initials: A
authors.lastname: Radovanovic
authors.affiliation: King Abdullah University of Science and Technology (KAUST); Computational Bioscience Research Centre (CBRC); Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE); Thuwal, Jeddah, 23955-6900, Saudi Arabia.
authors.forename: Magbubah
authors.initials: M
authors.lastname: Essack
authors.affiliation: King Abdullah University of Science and Technology (KAUST); Computational Bioscience Research Centre (CBRC); Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE); Thuwal, Jeddah, 23955-6900, Saudi Arabia vladimir.bajic@kaust.edu.sa.
authors.forename: Vladimir B
authors.initials: VB
authors.lastname: Bajic
mesh_terms: D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D016680:Genome, Bacterial; D053858:Metabolic Networks and Pathways; D056186:Metagenomics / Q000379:methods*; D009997:Osmotic Pressure; D020011:Protective Agents; D012965:Sodium Chloride / Q000378:metabolism*; D013312:Stress, Physiological
chemical_list: D020011:Protective Agents; D012965:Sodium Chloride