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DESM: portal for microbial knowledge exploration systems
- Source :
- Nucleic Acids Research
- Publication Year :
- 2015
- Publisher :
- Oxford University Press, 2015.
-
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.
- Subjects :
- 0301 basic medicine
Databases, Factual
Knowledge Bases
030106 microbiology
Antitubercular Agents
Dictionaries as Topic
Biology
03 medical and health sciences
Industrial Microbiology
Controlled vocabulary
Genetics
Database Issue
Data Mining
Humans
Internet
Bacteria
business.industry
Entrez Gene
Drug Repositioning
Fungi
Industrial microbiology
Data science
Archaea
Variety (cybernetics)
Biotechnology
Knowledge exploration
Vocabulary, Controlled
Viruses
The Internet
User interface
business
Subjects
Details
- Language :
- English
- ISSN :
- 13624962 and 03051048
- Volume :
- 44
- Database :
- OpenAIRE
- Journal :
- Nucleic Acids Research
- Accession number :
- edsair.doi.dedup.....063d8a6eeae45191802947d86392815d