title: DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining.
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 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.
authors.affiliation: a King Abdullah University of Science and Technology (KAUST) , Computational Bioscience Research Center (CBRC) , Thuwal , Kingdom of Saudi Arabia.
authors.forename: Adil
authors.initials: A
authors.lastname: Salhi
authors.affiliation: a King Abdullah University of Science and Technology (KAUST) , Computational Bioscience Research Center (CBRC) , Thuwal , Kingdom of Saudi Arabia.
authors.forename: Magbubah
authors.initials: M
authors.lastname: Essack
authors.affiliation: a King Abdullah University of Science and Technology (KAUST) , Computational Bioscience Research Center (CBRC) , Thuwal , Kingdom of Saudi Arabia.
authors.forename: Tanvir
authors.initials: T
authors.lastname: Alam
authors.affiliation: b VINCA Institute of Nuclear Sciences , Belgrade , Republic of Serbia.
authors.forename: Vladan P
authors.initials: VP
authors.lastname: Bajic
authors.affiliation: c BIG Data Center, Beijing Institute of Genomics (BIG) , Chinese Academy of Sciences , Beijing , China.|d CAS Key Laboratory of Genome Sciences and Information , Beijing Institute of Genomics, Chinese Academy of Sciences (CAS) , Beijing , China.
authors.forename: Lina
authors.initials: L
authors.lastname: Ma
authors.affiliation: a King Abdullah University of Science and Technology (KAUST) , Computational Bioscience Research Center (CBRC) , Thuwal , Kingdom of Saudi Arabia.
authors.forename: Aleksandar
authors.initials: A
authors.lastname: Radovanovic
authors.affiliation: e New York University , Abu Dhabi , UAE.
authors.forename: Benoit
authors.initials: B
authors.lastname: Marchand
authors.affiliation: f Massey University Auckland, Institute of Natural and Mathematical Sciences , Albany , Auckland , New Zealand.
authors.forename: Sebastian
authors.identifier: 0000-0002-3947-8226
authors.initials: S
authors.lastname: Schmeier
authors.affiliation: c BIG Data Center, Beijing Institute of Genomics (BIG) , Chinese Academy of Sciences , Beijing , China.|d CAS Key Laboratory of Genome Sciences and Information , Beijing Institute of Genomics, Chinese Academy of Sciences (CAS) , Beijing , China.|g University of Chinese Academy of Sciences , Beijing , China.|h Collaborative Innovation Center of Genetics and Development , Fudan University , Shanghai , China.
authors.forename: Zhang
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: a King Abdullah University of Science and Technology (KAUST) , Computational Bioscience Research Center (CBRC) , Thuwal , Kingdom of Saudi Arabia.
authors.forename: Vladimir B
authors.initials: VB
authors.lastname: Bajic
mesh_terms: D019307:1-(5-Isoquinolinesulfonyl)-2-Methylpiperazine / Q000031:analogs & derivatives / Q000627:therapeutic use; D000544:Alzheimer Disease / Q000188:drug therapy / Q000235:genetics; D057225:Data Mining; D004014:Dictionaries as Topic; D018450:Disease Progression; D063990:Gene Ontology; D006801:Humans; D051188:Knowledge Bases; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000378:metabolism; D012984:Software
chemical_list: D035683:MicroRNAs; D062085:RNA, Long Noncoding; D019307:1-(5-Isoquinolinesulfonyl)-2-Methylpiperazine; C049347:fasudil
keywords: Alzheimer disease; Noncoding RNA; bioinformatics; data-mining; information integration; knowledgebase; literature-mining; long noncoding RNA; microRNA; text-mining