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Type
ArticleAuthors
Salhi, AdilEssack, Magbubah

Radovanovic, Aleksandar
Marchand, Benoit
Bougouffa, Salim

Antunes, Andre

Simoes, Marta
Lafi, Feras Fawzi
Motwalli, Olaa Amin

Bokhari, Ameerah

Malas, Tareq Majed Yasin

Al Amoudi, Soha

Othum, Ghofran
Alam, Intikhab
Mineta, Katsuhiko

Gao, Xin

Hoehndorf, Robert

Archer, John A.C.

Gojobori, Takashi

Bajic, Vladimir B.

KAUST Department
Applied Mathematics and Computational Science ProgramBio-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
2015-11-05Online Publication Date
2015-11-05Print Publication Date
2016-01-04Permanent link to this record
http://hdl.handle.net/10754/592836
Metadata
Show full item recordAbstract
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 ResearchPublisher
Oxford University Press (OUP)Journal
Nucleic Acids ResearchPubMed ID
26546514Additional Links
http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkv1147ae974a485f413a2113503eed53cd6c53
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) DivisionRelated articles
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