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    DESM: portal for microbial knowledge exploration systems

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    Type
    Article
    Authors
    Salhi, Adil
    Essack, Magbubah cc
    Radovanovic, Aleksandar
    Marchand, Benoit
    Bougouffa, Salim cc
    Antunes, Andre cc
    Simoes, Marta
    Lafi, Feras Fawzi
    Motwalli, Olaa Amin cc
    Bokhari, Ameerah cc
    Malas, Tareq Majed Yasin cc
    Al Amoudi, Soha cc
    Othum, Ghofran
    Alam, Intikhab
    Mineta, Katsuhiko cc
    Gao, Xin cc
    Hoehndorf, Robert cc
    Archer, John A.C. cc
    Gojobori, Takashi cc
    Bajic, Vladimir B. cc
    KAUST Department
    Applied Mathematics and Computational Science Program
    Bio-Ontology Research Group (BORG)
    Biological and Environmental Science and Engineering (BESE) Division
    Bioscience Program
    Center for Desert Agriculture
    Chemical Engineering Program
    Computational Bioscience Research Center (CBRC)
    Computer Science Program
    Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division
    Physical Science and Engineering (PSE) Division
    Structural and Functional Bioinformatics Group
    Date
    2015-11-05
    Online Publication Date
    2015-11-05
    Print Publication Date
    2016-01-04
    Permanent link to this record
    http://hdl.handle.net/10754/592836
    
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    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.
    Citation
    DESM: portal for microbial knowledge exploration systems 2015:gkv1147 Nucleic Acids Research
    Publisher
    Oxford University Press (OUP)
    Journal
    Nucleic Acids Research
    DOI
    10.1093/nar/gkv1147
    PubMed ID
    26546514
    Additional Links
    http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkv1147
    ae974a485f413a2113503eed53cd6c53
    10.1093/nar/gkv1147
    Scopus Count
    Collections
    Articles; Bio-Ontology Research Group (BORG); Biological and Environmental Science and Engineering (BESE) Division; Bioscience Program; Applied Mathematics and Computational Science Program; Physical Science and Engineering (PSE) Division; Structural and Functional Bioinformatics Group; Computer Science Program; Chemical Engineering Program; Computational Bioscience Research Center (CBRC); Center for Desert Agriculture; Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division

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