DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining

Handle URI:
http://hdl.handle.net/10754/623259
Title:
DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining
Authors:
Salhi, Adil; Essack, Magbubah ( 0000-0003-2709-5356 ) ; Alam, Tanvir ( 0000-0003-4844-0171 ) ; Bajic, Vladan P.; Ma, Lina; Radovanovic, Aleksandar; Marchand, Benoit; Schmeier, Sebastian; Zhang, Zhang; Bajic, Vladimir B. ( 0000-0001-5435-4750 )
Abstract:
Noncoding RNAs (ncRNAs), particularly microRNAs (miRNAs) and long ncRNAs (lncRNAs), are important players in diseases and emerge as novel drug targets. Thus, unraveling the relationships between ncRNAs and other biomedical entities in cells are critical for better understanding ncRNA roles that may eventually help develop their use in medicine. To support ncRNA research and facilitate retrieval of relevant information regarding miRNAs and lncRNAs from the plethora of published ncRNA-related research, we developed DES-ncRNA ( www.cbrc.kaust.edu.sa/des_ncrna ). DES-ncRNA is a knowledgebase containing text- and data-mined information from public scientific literature and other public resources. Exploration of mined information is enabled through terms and pairs of terms from 19 topic-specific dictionaries including, for example, antibiotics, toxins, drugs, enzymes, mutations, pathways, human genes and proteins, drug indications and side effects, mutations, diseases, etc. DES-ncRNA contains approximately 878,000 associations of terms from these dictionaries of which 36,222 (5,373) are with regards to miRNAs (lncRNAs). We provide several ways to explore information regarding ncRNAs to users including controlled generation of association networks as well as hypotheses generation. We show an example how DES-ncRNA can aid research on Alzheimer's disease and suggest potential therapeutic role for Fasudil. DES-ncRNA is a powerful tool that can be used on its own or as a complement to the existing resources, to support research in human ncRNA. To our knowledge, this is the only knowledgebase dedicated to human miRNAs and lncRNAs derived primarily through literature-mining enabling exploration of a broad spectrum of associated biomedical entities, not paralleled by any other resource.
KAUST Department:
Computational Bioscience Research Center (CBRC)
Citation:
Salhi A, Essack M, Alam T, Bajic VP, Ma L, et al. (2017) DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining. RNA Biology: 00–00. Available: http://dx.doi.org/10.1080/15476286.2017.1312243.
Publisher:
Informa UK Limited
Journal:
RNA Biology
KAUST Grant Number:
BAS/1/1606-01-01
Issue Date:
7-Apr-2017
DOI:
10.1080/15476286.2017.1312243
Type:
Article
ISSN:
1547-6286; 1555-8584
Sponsors:
The computational analysis for this study was performed on Dragon and Snapdragon compute clusters of the Computational Bioscience Research Center (CBRC) at King Abdullah University of Science and Technology (KAUST). The King Abdullah University of Science and Technology (KAUST) Base Research Funds [BAS/1/1606-01-01] to VBB supported research reported in this publication. This work was also supported by grants from Strategic Priority Research Program of the Chinese Academy of Sciences [XDB13040500 to ZZ], International Partnership Program of the Chinese Academy of Sciences [153F11KYSB20160008], National Programs for High Technology Research and Development [2015AA020108 to ZZ] and The 100 Talent Program of the Chinese Academy of Sciences (to ZZ). Ministry of Education, Science and Technological Development of the Republic of Serbia, Project No 173034 support VPB.
Additional Links:
http://www.tandfonline.com/doi/full/10.1080/15476286.2017.1312243
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorSalhi, Adilen
dc.contributor.authorEssack, Magbubahen
dc.contributor.authorAlam, Tanviren
dc.contributor.authorBajic, Vladan P.en
dc.contributor.authorMa, Linaen
dc.contributor.authorRadovanovic, Aleksandaren
dc.contributor.authorMarchand, Benoiten
dc.contributor.authorSchmeier, Sebastianen
dc.contributor.authorZhang, Zhangen
dc.contributor.authorBajic, Vladimir B.en
dc.date.accessioned2017-04-20T08:08:15Z-
dc.date.available2017-04-20T08:08:15Z-
dc.date.issued2017-04-07en
dc.identifier.citationSalhi A, Essack M, Alam T, Bajic VP, Ma L, et al. (2017) DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining. RNA Biology: 00–00. Available: http://dx.doi.org/10.1080/15476286.2017.1312243.en
dc.identifier.issn1547-6286en
dc.identifier.issn1555-8584en
dc.identifier.doi10.1080/15476286.2017.1312243en
dc.identifier.urihttp://hdl.handle.net/10754/623259-
dc.description.abstractNoncoding RNAs (ncRNAs), particularly microRNAs (miRNAs) and long ncRNAs (lncRNAs), are important players in diseases and emerge as novel drug targets. Thus, unraveling the relationships between ncRNAs and other biomedical entities in cells are critical for better understanding ncRNA roles that may eventually help develop their use in medicine. To support ncRNA research and facilitate retrieval of relevant information regarding miRNAs and lncRNAs from the plethora of published ncRNA-related research, we developed DES-ncRNA ( www.cbrc.kaust.edu.sa/des_ncrna ). DES-ncRNA is a knowledgebase containing text- and data-mined information from public scientific literature and other public resources. Exploration of mined information is enabled through terms and pairs of terms from 19 topic-specific dictionaries including, for example, antibiotics, toxins, drugs, enzymes, mutations, pathways, human genes and proteins, drug indications and side effects, mutations, diseases, etc. DES-ncRNA contains approximately 878,000 associations of terms from these dictionaries of which 36,222 (5,373) are with regards to miRNAs (lncRNAs). We provide several ways to explore information regarding ncRNAs to users including controlled generation of association networks as well as hypotheses generation. We show an example how DES-ncRNA can aid research on Alzheimer's disease and suggest potential therapeutic role for Fasudil. DES-ncRNA is a powerful tool that can be used on its own or as a complement to the existing resources, to support research in human ncRNA. To our knowledge, this is the only knowledgebase dedicated to human miRNAs and lncRNAs derived primarily through literature-mining enabling exploration of a broad spectrum of associated biomedical entities, not paralleled by any other resource.en
dc.description.sponsorshipThe computational analysis for this study was performed on Dragon and Snapdragon compute clusters of the Computational Bioscience Research Center (CBRC) at King Abdullah University of Science and Technology (KAUST). The King Abdullah University of Science and Technology (KAUST) Base Research Funds [BAS/1/1606-01-01] to VBB supported research reported in this publication. This work was also supported by grants from Strategic Priority Research Program of the Chinese Academy of Sciences [XDB13040500 to ZZ], International Partnership Program of the Chinese Academy of Sciences [153F11KYSB20160008], National Programs for High Technology Research and Development [2015AA020108 to ZZ] and The 100 Talent Program of the Chinese Academy of Sciences (to ZZ). Ministry of Education, Science and Technological Development of the Republic of Serbia, Project No 173034 support VPB.en
dc.publisherInforma UK Limiteden
dc.relation.urlhttp://www.tandfonline.com/doi/full/10.1080/15476286.2017.1312243en
dc.rightsThis is an Accepted Manuscript of an article published by Taylor & Francis in RNA Biology on 07 Apr 2017, available online: http://wwww.tandfonline.com/10.1080/15476286.2017.1312243.en
dc.subjectAlzheimer's diseaseen
dc.subjectBioinformaticsen
dc.subjectNoncoding RNAen
dc.subjectMicroRNAen
dc.subjectText-miningen
dc.subjectKnowledgebaseen
dc.subjectLong Noncoding Rnaen
dc.subjectInformation Integrationen
dc.subjectData-miningen
dc.subjectLiterature-miningen
dc.titleDES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-miningen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalRNA Biologyen
dc.eprint.versionPost-printen
dc.contributor.institutionVINCA Institute of Nuclear Sciences , Belgrade 11001 , Republic of Serbia.en
dc.contributor.institutionCAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics , Chinese Academy of Sciences (CAS) , Beijing 100101 , China.en
dc.contributor.institutionNew York University , Abu Dhabi , UAE.en
dc.contributor.institutionMassey University Auckland, Institute of Natural and Mathematical Sciences , Albany, Auckland 0632 , New Zealand.en
dc.contributor.institutionCollaborative Innovation Center of Genetics and Development, Fudan University , Shanghai 200438 , China.en
kaust.authorSalhi, Adilen
kaust.authorEssack, Magbubahen
kaust.authorAlam, Tanviren
kaust.authorRadovanovic, Aleksandaren
kaust.authorBajic, Vladimir B.en
kaust.grant.numberBAS/1/1606-01-01en
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