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OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data

Jingshan Huang, Fernando Gutierrez, Harrison J. Strachan, Dejing Dou, Weili Huang, Barry Smith, Judith A. Blake, Karen Eilbeck, Darren A. Natale, Yu Lin, Bin Wu, Nisansa de Silva (+5 others)
2016 Journal of Biomedical Semantics  
We previously developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), whose goal was to serve as a foundation for semantic annotation, data integration, and semantic  ...  In this paper we describe our continuing effort to develop the OMIT, and demonstrate its use within a semantic search system, OmniSearch, designed to facilitate knowledge capture of miRNA-target interaction  ...  Acknowledgements Funding for Huang, J was provided in part by the National Cancer Institute  ... 
doi:10.1186/s13326-016-0064-2 pmid:27175225 pmcid:PMC4863347 fatcat:wgowilvzsjcj7kvabm3wcrk6te

Co-expression analysis among microRNAs, long non-coding RNAs, and messenger RNAs to understand the pathogenesis and progression of diabetic kidney disease at the genetic level

Lihua Zhang, Rong Li, Junyi He, Qiuping Yang, Yanan Wu, Jingshan Huang, Bin Wu
2017 Methods  
There is a desperate need to explore novel biomarkers to further facilitate the early diagnosis and effective treatment in DKD patients, thus preventing them from developing endstage renal disease (ESRD  ...  Diabetic kidney disease (DKD) is a serious disease that presents a major health problem worldwide.  ...  Acknowledgments Research reported in this paper was partially supported by: The National Natural Science Foundation of China (NSFC  ... 
doi:10.1016/j.ymeth.2017.05.023 pmid:28577935 pmcid:PMC5540768 fatcat:oq5oesxkljbj5ihxn6zc67k5we

The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology

Jingshan Huang, Karen Eilbeck, Barry Smith, Judith A. Blake, Dejing Dou, Weili Huang, Darren A. Natale, Alan Ruttenberg, Jun Huan, Michael T. Zimmermann, Guoqian Jiang, Yu Lin (+8 others)
2016 Journal of Biomedical Semantics  
Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs.  ...  (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal.  ...  EPSCoR program) and in part by the Abraham A.  ... 
doi:10.1186/s13326-016-0066-0 pmid:27152146 pmcid:PMC4857245 fatcat:i4jghl5vfncdjhbt5rxvmnnlfe