DESM: portal for microbial knowledge exploration systems

Handle URI:
http://hdl.handle.net/10754/592836
Title:
DESM: portal for microbial knowledge exploration systems
Authors:
Salhi, Adil; Essack, Magbubah ( 0000-0003-2709-5356 ) ; Radovanovic, Aleksandar; Marchand, Benoit; Bougouffa, Salim ( 0000-0001-9218-6452 ) ; Antunes, Andre ( 0000-0001-7668-9842 ) ; Simoes, Marta; Lafi, Feras Fawzi; Motwalli, Olaa Amin ( 0000-0002-3392-5734 ) ; Bokhari, Ameerah ( 0000-0003-0137-9027 ) ; Malas, Tareq Majed Yasin ( 0000-0002-4506-9365 ) ; Al Amoudi, Soha ( 0000-0003-1028-7634 ) ; Othum, Ghofran; Alam, Intikhab; Mineta, Katsuhiko ( 0000-0002-4727-045X ) ; Gao, Xin ( 0000-0002-7108-3574 ) ; Hoehndorf, Robert ( 0000-0001-8149-5890 ) ; Archer, John A.C. ( 0000-0002-3302-3933 ) ; Gojobori, Takashi ( 0000-0001-7850-1743 ) ; Bajic, Vladimir B. ( 0000-0001-5435-4750 )
Abstract:
Microorganisms 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.
KAUST Department:
Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division; Desert Agriculture Initiative; Biological and Environmental Sciences and Engineering (BESE) Division; Computer Science Program; Bioscience Program; Physical Sciences and Engineering (PSE) Division; Chemical and Biological Engineering Program; Applied Mathematics and Computational Science Program
Citation:
DESM: portal for microbial knowledge exploration systems 2015:gkv1147 Nucleic Acids Research
Publisher:
Oxford University Press (OUP)
Journal:
Nucleic Acids Research
Issue Date:
5-Nov-2015
DOI:
10.1093/nar/gkv1147
Type:
Article
ISSN:
0305-1048; 1362-4962
Additional Links:
http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkv1147
Appears in Collections:
Articles; Bioscience Program; Applied Mathematics and Computational Science Program; Physical Sciences and Engineering (PSE) Division; Computer Science Program; Chemical and Biological Engineering Program; Computational Bioscience Research Center (CBRC); Desert Agriculture Initiative; Biological and Environmental Sciences and Engineering (BESE) Division; Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorSalhi, Adilen
dc.contributor.authorEssack, Magbubahen
dc.contributor.authorRadovanovic, Aleksandaren
dc.contributor.authorMarchand, Benoiten
dc.contributor.authorBougouffa, Salimen
dc.contributor.authorAntunes, Andreen
dc.contributor.authorSimoes, Martaen
dc.contributor.authorLafi, Feras Fawzien
dc.contributor.authorMotwalli, Olaa Aminen
dc.contributor.authorBokhari, Ameerahen
dc.contributor.authorMalas, Tareq Majed Yasinen
dc.contributor.authorAl Amoudi, Sohaen
dc.contributor.authorOthum, Ghofranen
dc.contributor.authorAlam, Intikhaben
dc.contributor.authorMineta, Katsuhikoen
dc.contributor.authorGao, Xinen
dc.contributor.authorHoehndorf, Roberten
dc.contributor.authorArcher, John A.C.en
dc.contributor.authorGojobori, Takashien
dc.contributor.authorBajic, Vladimir B.en
dc.date.accessioned2016-01-05T07:33:11Zen
dc.date.available2016-01-05T07:33:11Zen
dc.date.issued2015-11-05en
dc.identifier.citationDESM: portal for microbial knowledge exploration systems 2015:gkv1147 Nucleic Acids Researchen
dc.identifier.issn0305-1048en
dc.identifier.issn1362-4962en
dc.identifier.doi10.1093/nar/gkv1147en
dc.identifier.urihttp://hdl.handle.net/10754/592836en
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.en
dc.language.isoenen
dc.publisherOxford University Press (OUP)en
dc.relation.urlhttp://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkv1147en
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.titleDESM: portal for microbial knowledge exploration systemsen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Divisionen
dc.contributor.departmentDesert Agriculture Initiativeen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentComputer Science Programen
dc.contributor.departmentBioscience Programen
dc.contributor.departmentPhysical Sciences and Engineering (PSE) Divisionen
dc.contributor.departmentChemical and Biological Engineering Programen
dc.contributor.departmentApplied Mathematics and Computational Science Programen
dc.identifier.journalNucleic Acids Researchen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionNew York University, Abu Dhabi, UAEen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorSalhi, Adilen
kaust.authorEssack, Magbubahen
kaust.authorRadovanovic, Aleksandaren
kaust.authorBougouffa, Salimen
kaust.authorAntunes, Andreen
kaust.authorSimoes, Martaen
kaust.authorLafi, Feras Fawzien
kaust.authorMotwalli, Olaa Aminen
kaust.authorBokhari, Ameerahen
kaust.authorMalas, Tareq Majed Yasinen
kaust.authorAl Amoudi, Sohaen
kaust.authorOthum, Ghofranen
kaust.authorAlam, Intikhaben
kaust.authorMineta, Katsuhikoen
kaust.authorGao, Xinen
kaust.authorHoehndorf, Roberten
kaust.authorArcher, John A.C.en
kaust.authorGojobori, Takashien
kaust.authorBajic, Vladimir B.en
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