| URL: | http://www.cbrc.kaust.edu.sa/desm/home/index.php |
| Full name: | Microbial Knowledge Exploration Systems |
| Description: | Portal for Microbial Knowledge Exploration Systems is a platform for discovery, analysis and exploration of information from a number of topic-specific microbial knowledgebases. The knowledgebases include integrated information from published scientific literature and a number of major databases from biology fields. These include PubMed; ChEBI; Entrez Gene; GO; KOBAS, KEGG; REACTOME; UniPathways; PANTHER; BioGrid; etc.). Information exploration is enabled through a number of different ontologies, controlled vocabularies, taxonomy, and integrated information. |
| Year founded: | 2016 |
| Last update: | 2015-8-18 |
| Version: | v1.0 |
| Accessibility: |
Accessible
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| Country/Region: | Saudi Arabia |
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| University/Institution: | King Abdullah University of Science and Technology |
| Address: | King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC),Thuwal 23955-6900, Kingdom of Saudi Arabia |
| City: | Thuwal |
| Province/State: | |
| Country/Region: | Saudi Arabia |
| Contact name (PI/Team): | Vladimir B. Bajic |
| Contact email (PI/Helpdesk): | vladimir.bajic@kaust.edu.sa |
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DESM: portal for microbial knowledge exploration systems. [PMID: 26546514]
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. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. |