DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining
Authors
Salhi, AdilEssack, Magbubah
Alam, Tanvir
Bajić, Vladan P.
Ma, Lina
Radovanovic, Aleksandar
Marchand, Benoit
Schmeier, Sebastian
Zhang, Zhang
Bajić, Vladimir B.
Article (Published version)
Metadata
Show full item recordAbstract
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.
Keywords:
Noncoding RNA / microRNA / long noncoding RNA / knowledgebase / literature-mining / text-mining / data-mining / information integration / bioinformatics / Alzheimer diseaseSource:
RNA Biology, 2017, 14, 7, 963-971Funding / projects:
- Cell Cycle Aberrations and the Impact of Oxidative Stress in Neurodegenerative Processes and Malignant Transformation of the Cell (RS-MESTD-Basic Research (BR or ON)-173034)
- Strategic Priority Research Program of the Chinese Academy of Sciences [XDB13040500]
- International Partnership Program of the Chinese Academy of Sciences [153F11KYSB20160008]
- National Programs for High Technology Research and Development [2015AA020108]
- 100 Talent Program of the Chinese Academy of Sciences
DOI: 10.1080/15476286.2017.1312243
ISSN: 1547-6286; 1555-8584
PubMed: 28387604
WoS: 000407258600016
Scopus: 2-s2.0-85019759452
Institution/Community
VinčaTY - JOUR AU - Salhi, Adil AU - Essack, Magbubah AU - Alam, Tanvir AU - Bajić, Vladan P. AU - Ma, Lina AU - Radovanovic, Aleksandar AU - Marchand, Benoit AU - Schmeier, Sebastian AU - Zhang, Zhang AU - Bajić, Vladimir B. PY - 2017 UR - https://vinar.vin.bg.ac.rs/handle/123456789/1675 AB - 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. T2 - RNA Biology T1 - DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining VL - 14 IS - 7 SP - 963 EP - 971 DO - 10.1080/15476286.2017.1312243 ER -
@article{ author = "Salhi, Adil and Essack, Magbubah and Alam, Tanvir and Bajić, Vladan P. and Ma, Lina and Radovanovic, Aleksandar and Marchand, Benoit and Schmeier, Sebastian and Zhang, Zhang and Bajić, Vladimir B.", year = "2017", 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.", journal = "RNA Biology", title = "DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining", volume = "14", number = "7", pages = "963-971", doi = "10.1080/15476286.2017.1312243" }
Salhi, A., Essack, M., Alam, T., Bajić, V. P., Ma, L., Radovanovic, A., Marchand, B., Schmeier, S., Zhang, Z.,& Bajić, V. B.. (2017). DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining. in RNA Biology, 14(7), 963-971. https://doi.org/10.1080/15476286.2017.1312243
Salhi A, Essack M, Alam T, Bajić VP, Ma L, Radovanovic A, Marchand B, Schmeier S, Zhang Z, Bajić VB. DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining. in RNA Biology. 2017;14(7):963-971. doi:10.1080/15476286.2017.1312243 .
Salhi, Adil, Essack, Magbubah, Alam, Tanvir, Bajić, Vladan P., Ma, Lina, Radovanovic, Aleksandar, Marchand, Benoit, Schmeier, Sebastian, Zhang, Zhang, Bajić, Vladimir B., "DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining" in RNA Biology, 14, no. 7 (2017):963-971, https://doi.org/10.1080/15476286.2017.1312243 . .