1. DESM: portal for microbial knowledge exploration systems
- Author
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Takashi Gojobori, Ghofran Othum, Katsuhiko Mineta, Feras F. Lafi, Tariq Malas, Benoit Marchand, Aleksandar Radovanovic, Marta Filipa Simões, Magbubah Essack, André Antunes, Salim Bougouffa, Soha Al Amoudi, John A.C. Archer, Intikhab Allam, Robert Hoehndorf, Adil Salhi, Ameerah Bokhari, Xin Gao, Olaa Amin Motwalli, and Vladimir B. Bajic
- 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 - 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.
- Published
- 2015