DESM: portal for microbial knowledge exploration systems

DESM: portal for microbial knowledge exploration systems

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...

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Published in:Nucleic acids research Vol. 44; no. D1; pp. D624 - D633
Main Authors: Salhi, Adil, Essack, Magbubah, Radovanovic, Aleksandar, Marchand, Benoit, Bougouffa, Salim, Antunes, Andre, Simoes, Marta Filipa, Lafi, Feras F, Motwalli, Olaa A, Bokhari, Ameerah, Malas, Tariq, Amoudi, Soha Al, Othum, Ghofran, Allam, Intikhab, Mineta, Katsuhiko, Gao, Xin, Hoehndorf, Robert, C Archer, John A, Gojobori, Takashi, Bajic, Vladimir B
Format: Journal Article
Language:English
Published: England Oxford University Press 04-01-2016
Subjects:
Antitubercular Agents - pharmacology
Archaea - genetics
Archaea - metabolism
Bacteria - genetics
Bacteria - metabolism
Data Mining
Database Issue
Databases, Factual
Dictionaries as Topic
Drug Repositioning
Fungi - genetics
Fungi - metabolism
Humans
Industrial Microbiology
Internet
Knowledge Bases
Viruses - genetics
Viruses - metabolism
Vocabulary, Controlled
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Summary: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.
Bibliography:ObjectType-Article-1
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ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkv1147