DEOP: a database on osmoprotectants and associated pathways

Handle URI:
http://hdl.handle.net/10754/348510
Title:
DEOP: a database on osmoprotectants and associated pathways
Authors:
Bougouffa, S.; Radovanovic, A.; Essack, M.; Bajic, Vladimir B. ( 0000-0001-5435-4750 )
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.
KAUST Department:
Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Citation:
DEOP: a database on osmoprotectants and associated pathways 2014, 2014 (0):bau100 Database
Publisher:
Oxford University Press (OUP)
Journal:
Database
Issue Date:
17-Oct-2014
DOI:
10.1093/database/bau100
PubMed ID:
25326239
PubMed Central ID:
PMC4201361
Type:
Article
ISSN:
1758-0463
Additional Links:
http://database.oxfordjournals.org/cgi/doi/10.1093/database/bau100
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorBougouffa, S.en
dc.contributor.authorRadovanovic, A.en
dc.contributor.authorEssack, M.en
dc.contributor.authorBajic, Vladimir B.en
dc.date.accessioned2015-04-06T08:43:36Zen
dc.date.available2015-04-06T08:43:36Zen
dc.date.issued2014-10-17en
dc.identifier.citationDEOP: a database on osmoprotectants and associated pathways 2014, 2014 (0):bau100 Databaseen
dc.identifier.issn1758-0463en
dc.identifier.pmid25326239en
dc.identifier.doi10.1093/database/bau100en
dc.identifier.urihttp://hdl.handle.net/10754/348510en
dc.description.abstractMicroorganisms 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.en
dc.publisherOxford University Press (OUP)en
dc.relation.urlhttp://database.oxfordjournals.org/cgi/doi/10.1093/database/bau100en
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.titleDEOP: a database on osmoprotectants and associated pathwaysen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Divisionen
dc.identifier.journalDatabaseen
dc.identifier.pmcidPMC4201361en
dc.eprint.versionPublisher's Version/PDFen
kaust.authorBougouffa, Salimen

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