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DESM: portal for microbial knowledge exploration systems.

Adil Salhi1, Magbubah Essack1, Aleksandar Radovanovic1

  • 1King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Kingdom of Saudi Arabia.

Nucleic Acids Research
|November 8, 2015
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Summary
This summary is machine-generated.

Researchers can now explore microbial functions and bioproduction using 45 specialized knowledgebases (KBs) in the DESM portal. This resource aids microbiology and biotechnology by integrating diverse data for molecular and genetic insights.

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Area of Science:

  • Microbiology
  • Biotechnology
  • Bioinformatics

Background:

  • Microorganisms synthesize diverse chemical compounds, necessitating tools to explore their molecular and genetic underpinnings.
  • Understanding microbial bioproduction capabilities is crucial for biotechnology advancements.

Purpose of the Study:

  • To develop and present the Database for Exploration of Secondary Metabolites (DESM) portal, offering 45 topic-specific knowledgebases (KBs).
  • To facilitate the exploration of the molecular and genetic basis of microbial functioning and bioproduction.

Main Methods:

  • Compiled 45 topic-specific knowledgebases (KBs) from text-mined PubMed records and other biological databases (ChEBI, KEGG, GO, etc.).
  • Indexed PubMed records using 4,538,278 concepts from 29 dictionaries, utilizing 1,638,986 records in the KBs.
  • Structured KBs uniformly with a standardized interface for information exploration via searches, hypothesis generation, and network analysis.

Main Results:

  • The DESM portal provides access to 45 KBs focused on microbial activities (biocatalysts, nutraceuticals) and specific microorganisms (Streptomyces, cyanobacteria).
  • Information is integrated from multiple sources, with normalized concepts for enhanced data consistency.
  • Users can perform advanced searches, identify significant concepts, generate hypotheses, and visualize concept associations.

Conclusions:

  • The DESM portal offers a valuable, integrated resource for microbiology and biotechnology researchers.
  • It enhances the exploration of microbial molecular and genetic information, supporting bioproduction research.