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dc.contributor.authorSalhi, Adil
dc.contributor.authorEssack, Magbubah
dc.contributor.authorRadovanovic, Aleksandar
dc.contributor.authorMarchand, Benoit
dc.contributor.authorBougouffa, Salim
dc.contributor.authorAntunes, Andre
dc.contributor.authorSimoes, Marta
dc.contributor.authorLafi, Feras Fawzi
dc.contributor.authorMotwalli, Olaa Amin
dc.contributor.authorBokhari, Ameerah
dc.contributor.authorMalas, Tareq Majed Yasin
dc.contributor.authorAl Amoudi, Soha
dc.contributor.authorOthum, Ghofran
dc.contributor.authorAlam, Intikhab
dc.contributor.authorMineta, Katsuhiko
dc.contributor.authorGao, Xin
dc.contributor.authorHoehndorf, Robert
dc.contributor.authorArcher, John A.C.
dc.contributor.authorGojobori, Takashi
dc.contributor.authorBajic, Vladimir B.
dc.date.accessioned2016-01-05T07:33:11Z
dc.date.available2016-01-05T07:33:11Z
dc.date.issued2015-11-05
dc.identifier.citationDESM: portal for microbial knowledge exploration systems 2015:gkv1147 Nucleic Acids Research
dc.identifier.issn0305-1048
dc.identifier.issn1362-4962
dc.identifier.pmid26546514
dc.identifier.doi10.1093/nar/gkv1147
dc.identifier.urihttp://hdl.handle.net/10754/592836
dc.description.abstractMicroorganisms produce an enormous variety of chemical compounds. It is of general interest for microbiology and biotechnology researchers to have means to explore information about molecular and genetic basis of functioning of different microorganisms and their ability for bioproduction. To enable such exploration, we compiled 45 topic-specific knowledgebases (KBs) accessible through DESM portal (www.cbrc.kaust.edu.sa/desm). The KBs contain information derived through text-mining of PubMed information and complemented by information data-mined from various other resources (e.g. ChEBI, Entrez Gene, GO, KOBAS, KEGG, UniPathways, BioGrid). All PubMed records were indexed using 4 538 278 concepts from 29 dictionaries, with 1 638 986 records utilized in KBs. Concepts used are normalized whenever possible. Most of the KBs focus on a particular type of microbial activity, such as production of biocatalysts or nutraceuticals. Others are focused on specific categories of microorganisms, e.g. streptomyces or cyanobacteria. KBs are all structured in a uniform manner and have a standardized user interface. Information exploration is enabled through various searches. Users can explore statistically most significant concepts or pairs of concepts, generate hypotheses, create interactive networks of associated concepts and export results. We believe DESM will be a useful complement to the existing resources to benefit microbiology and biotechnology research.
dc.language.isoen
dc.publisherOxford University Press (OUP)
dc.relation.urlhttp://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkv1147
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.
dc.titleDESM: portal for microbial knowledge exploration systems
dc.typeArticle
dc.contributor.departmentApplied Mathematics and Computational Science Program
dc.contributor.departmentBio-Ontology Research Group (BORG)
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentBioscience Program
dc.contributor.departmentChemical Engineering Program
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentComputer Science Program
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
dc.contributor.departmentDesert Agriculture Initiative
dc.contributor.departmentPhysical Science and Engineering (PSE) Division
dc.contributor.departmentStructural and Functional Bioinformatics Group
dc.identifier.journalNucleic Acids Research
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionNew York University, Abu Dhabi, UAE
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)
kaust.personSalhi, Adil
kaust.personEssack, Magbubah
kaust.personRadovanovic, Aleksandar
kaust.personBougouffa, Salim
kaust.personAntunes, Andre
kaust.personSimoes, Marta
kaust.personLafi, Feras Fawzi
kaust.personMotwalli, Olaa Amin
kaust.personBokhari, Ameerah
kaust.personMalas, Tareq Majed Yasin
kaust.personAl Amoudi, Soha
kaust.personOthum, Ghofran
kaust.personAlam, Intikhab
kaust.personMineta, Katsuhiko
kaust.personGao, Xin
kaust.personHoehndorf, Robert
kaust.personArcher, John A.C.
kaust.personGojobori, Takashi
kaust.personBajic, Vladimir B.
refterms.dateFOA2018-06-13T16:40:52Z
dc.date.published-online2015-11-05
dc.date.published-print2016-01-04


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