Dragon exploratory system on Hepatitis C Virus (DESHCV)

Handle URI:
http://hdl.handle.net/10754/561787
Title:
Dragon exploratory system on Hepatitis C Virus (DESHCV)
Authors:
Kwofie, Samuel K.; Radovanovic, Aleksandar; Sundararajan, Vijayaraghava Seshadri; Maqungo, Monique; Christoffels, Alan G.; Bajic, Vladimir B. ( 0000-0001-5435-4750 )
Abstract:
Even though Hepatitis C Virus (HCV) cDNA was characterized about 20 years ago, there is insufficient understanding of the molecular etiology underlying HCV infections. Current global rates of infection and its increasingly chronic character are causes of concern for health policy experts. Vast amount of data accumulated from biochemical, genomic, proteomic, and other biological analyses allows for novel insights into the HCV viral structure, life cycle and functions of its proteins. Biomedical text-mining is a useful approach for analyzing the increasing corpus of published scientific literature on HCV. We report here the first comprehensive HCV customized biomedical text-mining based online web resource, dragon exploratory system on Hepatitis C Virus (DESHCV), a biomedical text-mining and relationship exploring knowledgebase was developed by exploring literature on HCV. The pre-compiled dictionaries existing in the dragon exploratory system (DES) were enriched with biomedical concepts pertaining to HCV proteins, their name variants and symbols to make it suitable for targeted information exploration and knowledge extraction as focused on HCV. A list of 32,895 abstracts retrieved via PubMed database using specific keywords searches related to HCV were processed based on concept recognition of terms from several dictionaries. The web query interface enables retrieval of information using specified concepts, keywords and phrases, generating text-derived association networks and hypotheses, which could be tested to identify potentially novel relationship between different concepts. Such an approach could also augment efforts in the search for diagnostic or even therapeutic targets. DESHCV thus represents online literature-based discovery resource freely accessible for academic and non-profit users via http://apps.sanbi.ac.za/DESHCV/ and its mirror site http://cbrc.kaust.edu.sa/deshcv/. © 2010 Elsevier B.V.
KAUST Department:
Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division; Applied Mathematics and Computational Science Program
Publisher:
Elsevier
Journal:
Infection, Genetics and Evolution
Issue Date:
Jun-2011
DOI:
10.1016/j.meegid.2010.12.006
PubMed ID:
21194573
Type:
Article
ISSN:
15671348
Sponsors:
This work was partly supported by grants from the National Research Foundation (South Africa), National Bioinformatics Network (to S.K.K.), and DST/NRF Research Chair (to A.C.). We are also grateful to A.R. and V.B.B. for making available the DES resource.
Appears in Collections:
Articles; Applied Mathematics and Computational Science Program; Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorKwofie, Samuel K.en
dc.contributor.authorRadovanovic, Aleksandaren
dc.contributor.authorSundararajan, Vijayaraghava Seshadrien
dc.contributor.authorMaqungo, Moniqueen
dc.contributor.authorChristoffels, Alan G.en
dc.contributor.authorBajic, Vladimir B.en
dc.date.accessioned2015-08-03T09:04:37Zen
dc.date.available2015-08-03T09:04:37Zen
dc.date.issued2011-06en
dc.identifier.issn15671348en
dc.identifier.pmid21194573en
dc.identifier.doi10.1016/j.meegid.2010.12.006en
dc.identifier.urihttp://hdl.handle.net/10754/561787en
dc.description.abstractEven though Hepatitis C Virus (HCV) cDNA was characterized about 20 years ago, there is insufficient understanding of the molecular etiology underlying HCV infections. Current global rates of infection and its increasingly chronic character are causes of concern for health policy experts. Vast amount of data accumulated from biochemical, genomic, proteomic, and other biological analyses allows for novel insights into the HCV viral structure, life cycle and functions of its proteins. Biomedical text-mining is a useful approach for analyzing the increasing corpus of published scientific literature on HCV. We report here the first comprehensive HCV customized biomedical text-mining based online web resource, dragon exploratory system on Hepatitis C Virus (DESHCV), a biomedical text-mining and relationship exploring knowledgebase was developed by exploring literature on HCV. The pre-compiled dictionaries existing in the dragon exploratory system (DES) were enriched with biomedical concepts pertaining to HCV proteins, their name variants and symbols to make it suitable for targeted information exploration and knowledge extraction as focused on HCV. A list of 32,895 abstracts retrieved via PubMed database using specific keywords searches related to HCV were processed based on concept recognition of terms from several dictionaries. The web query interface enables retrieval of information using specified concepts, keywords and phrases, generating text-derived association networks and hypotheses, which could be tested to identify potentially novel relationship between different concepts. Such an approach could also augment efforts in the search for diagnostic or even therapeutic targets. DESHCV thus represents online literature-based discovery resource freely accessible for academic and non-profit users via http://apps.sanbi.ac.za/DESHCV/ and its mirror site http://cbrc.kaust.edu.sa/deshcv/. © 2010 Elsevier B.V.en
dc.description.sponsorshipThis work was partly supported by grants from the National Research Foundation (South Africa), National Bioinformatics Network (to S.K.K.), and DST/NRF Research Chair (to A.C.). We are also grateful to A.R. and V.B.B. for making available the DES resource.en
dc.publisherElsevieren
dc.subjectBiomedical conceptsen
dc.subjectDatabaseen
dc.subjectDictionariesen
dc.subjectHepatitis C Virusen
dc.subjectHypotheses generationen
dc.subjectText-miningen
dc.titleDragon exploratory system on Hepatitis C Virus (DESHCV)en
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Divisionen
dc.contributor.departmentApplied Mathematics and Computational Science Programen
dc.identifier.journalInfection, Genetics and Evolutionen
dc.contributor.institutionSouth African National Bioinformatics Institute, University of the Western Cape, Private Bag- X17, Modderdam Road, Bellville, Cape Town, South Africaen
kaust.authorRadovanovic, Aleksandaren
kaust.authorBajic, Vladimir B.en

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