Lafi, Feras Fawzi
Motwalli, Olaa Amin
Malas, Tareq Majed Yasin
Al Amoudi, Soha
Archer, John A.C.
Bajic, Vladimir B.
KAUST DepartmentApplied Mathematics and Computational Science Program
Bio-Ontology Research Group (BORG)
Biological and Environmental Science and Engineering (BESE) Division
Center for Desert Agriculture
Chemical Engineering Program
Computational Bioscience Research Center (CBRC)
Computer Science Program
Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division
Physical Science and Engineering (PSE) Division
Structural and Functional Bioinformatics Group
Online Publication Date2015-11-05
Print Publication Date2016-01-04
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; Bio-Ontology Research Group (BORG); Biological and Environmental Science and Engineering (BESE) Division; Bioscience Program; Applied Mathematics and Computational Science Program; Physical Science and Engineering (PSE) Division; Structural and Functional Bioinformatics Group; Computer Science Program; Chemical Engineering Program; Computational Bioscience Research Center (CBRC); Center for Desert Agriculture; Computer, Electrical and Mathematical Science 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
- IBDDB: a manually curated and text-mining-enhanced database of genes involved in inflammatory bowel disease.
- Authors: Khan F, Radovanovic A, Gojobori T, Kaur M
- Issue date: 2021 Apr 30
- 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