Information Exploration System for Sickle Cell Disease and Repurposing of Hydroxyfasudil
KAUST DepartmentComputational Bioscience Research Center (CBRC)
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
MetadataShow full item record
AbstractBackground:Sickle cell disease (SCD) is a fatal monogenic disorder with no effective cure and thus high rates of morbidity and sequelae. Efforts toward discovery of disease modifying drugs and curative strategies can be augmented by leveraging the plethora of information contained in available biomedical literature. To facilitate research in this direction we have developed a resource, Dragon Exploration System for Sickle Cell Disease (DESSCD) (http://cbrc.kaust.edu.sa/desscd/) that aims to promote the easy exploration of SCD-related data.Description:The Dragon Exploration System (DES), developed based on text mining and complemented by data mining, processed 419,612 MEDLINE abstracts retrieved from a PubMed query using SCD-related keywords. The processed SCD-related data has been made available via the DESSCD web query interface that enables: a/information retrieval using specified concepts, keywords and phrases, and b/the generation of inferred association networks and hypotheses. The usefulness of the system is demonstrated by: a/reproducing a known scientific fact, the "Sickle_Cell_Anemia-Hydroxyurea" association, and b/generating novel and plausible "Sickle_Cell_Anemia-Hydroxyfasudil" hypothesis. A PCT patent (PCT/US12/55042) has been filed for the latter drug repurposing for SCD treatment.Conclusion:We developed the DESSCD resource dedicated to exploration of text-mined and data-mined information about SCD. No similar SCD-related resource exists. Thus, we anticipate that DESSCD will serve as a valuable tool for physicians and researchers interested in SCD. © 2013 Essack et al.
CitationEssack M, Radovanovic A, Bajic VB (2013) Information Exploration System for Sickle Cell Disease and Repurposing of Hydroxyfasudil. PLoS ONE 8: e65190. doi:10.1371/journal.pone.0065190.
PublisherPublic Library of Science (PLoS)
PubMed Central IDPMC3677893
- 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
- Novel approaches to the treatment of sickle cell disease: the potential of histone deacetylase inhibitors.
- Authors: Okam MM, Ebert BL
- Issue date: 2012 Jun
- Hydroxyurea for children with sickle cell disease.
- Authors: Heeney MM, Ware RE
- Issue date: 2008 Apr
- Hydroxyurea therapy in children severely affected with sickle cell disease.
- Authors: Scott JP, Hillery CA, Brown ER, Misiewicz V, Labotka RJ
- Issue date: 1996 Jun
- Advances in sickle cell disease treatment: from drug discovery until the patient monitoring.
- Authors: dos Santos JL, Lanaro C, Chin CM
- Issue date: 2011 Apr 1
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