Lafi, Feras Fawzi
Motwalli, Olaa Amin
Malas, Tareq Majed Yasin
Al Amoudi, Soha
Archer, John A.C.
Bajic, Vladimir B.
KAUST DepartmentComputational Bioscience Research Center (CBRC)
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Desert Agriculture Initiative
Biological and Environmental Sciences and Engineering (BESE) Division
Computer Science Program
Physical Sciences and Engineering (PSE) Division
Chemical and Biological Engineering Program
Applied Mathematics and Computational Science Program
Permanent link to this recordhttp://hdl.handle.net/10754/592836
MetadataShow full item record
AbstractMicroorganisms 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.
CitationDESM: portal for microbial knowledge exploration systems 2015:gkv1147 Nucleic Acids Research
PublisherOxford University Press (OUP)
JournalNucleic Acids Research
CollectionsArticles; Biological and Environmental Sciences and Engineering (BESE) Division; Bioscience Program; Applied Mathematics and Computational Science Program; Physical Sciences and Engineering (PSE) Division; Computer Science Program; Chemical and Biological Engineering Program; Computational Bioscience Research Center (CBRC); Desert Agriculture Initiative; Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
- DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining.
- Authors: Salhi A, Essack M, Alam T, Bajic VP, Ma L, Radovanovic A, Marchand B, Schmeier S, Zhang Z, Bajic VB
- Issue date: 2017 Jul 3
- Dragon exploratory system on hepatitis C virus (DESHCV).
- Authors: Kwofie SK, Radovanovic A, Sundararajan VS, Maqungo M, Christoffels A, Bajic VB
- Issue date: 2011 Jun
- DESTAF: a database of text-mined associations for reproductive toxins potentially affecting human fertility.
- Authors: Dawe AS, Radovanovic A, Kaur M, Sagar S, Seshadri SV, Schaefer U, Kamau AA, Christoffels A, Bajic VB
- Issue date: 2012 Jan
- Global catalogue of microorganisms (gcm): a comprehensive database and information retrieval, analysis, and visualization system for microbial resources.
- Authors: Wu L, Sun Q, Sugawara H, Yang S, Zhou Y, McCluskey K, Vasilenko A, Suzuki K, Ohkuma M, Lee Y, Robert V, Ingsriswang S, Guissart F, Philippe D, Ma J
- Issue date: 2013 Dec 30
- Information exploration system for sickle cell disease and repurposing of hydroxyfasudil.
- Authors: Essack M, Radovanovic A, Bajic VB
- Issue date: 2013