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Omnisearch: A semantic search system based on the ontology for microrna target (OMIT) for microrna-target gene interaction data 期刊论文

编号：

1fd449ea-d191-43cf-adcc-5d459b1931b6
作者：

Huang, Jingshan[0];Gutiérrez, Fernando A.[1];Strachan, Harrison J.[2];Dou, Dejing[3];Huang, Weili[4];Smith, Barry[5];Blake, Judith A.[6];Eilbeck, Karen L.[7];Natale, Darren A.[8];Lin, Yu[9];Wu, Bin[10];De Silva, Nisansa H.Nisansa D.[11];Wang, Xiaowei[12];Liu, Zixing[13];Borchert, Glen M.[14];Tan, Ming[15];Ruttenberg, Alan[16];
地址：

University of South Alabama, Department of Computer Science,Mobile,United States[0];University of Oregon, Department of Computer and Information Science,Eugene,United States[1];University of South Alabama, School of Computing,Mobile,United States[2];University of Oregon, CIS Dept.,Eugene,United States[3];Miracle Query, Inc.,Eugene,United States[4];University at Buffalo, State University of New York, Department of Philosophy,Buffalo,United States[5];Jackson Laboratory,Bar Harbor,United States[6];University of Utah School of Medicine, Department of Human Genetics,Salt Lake City,United States[7];UniProt: EMBL-EBI,,United Kingdom[8];University of Michigan Medical School, Department of Microbiology and Immunology,Ann Arbor,United States[9];Kunming Medical University, Department of Microbiology and Immunology,Kunming,China[10];University of Oregon, Department of Computer and Information Science,Eugene,United States[11];Washington University in St. Louis, School of Medicine, Department of Radiation Oncology,St Louis,United States[12];University of South Alabama, Mitchell Cancer Institute,Mobile,United States[13];University of South Alabama, Department of Biology,Mobile,United States[14];University of South Alabama,Mobile,United States[15];University at Buffalo, State University of New York, School of Dental Medicine,Buffalo,United States[16];
语种：

英文
期刊：

Journal of Animal Science and Biotechnology ISSN：1674-9782 2016 年 7 卷 1 期
收录：
关键词：

Biomedical ontology Data annotation Data integration MicroRNA Non-coding RNA Ontology development Semantic search SPARQL query Target gene
摘要：

As a special class of non-coding RNAs (ncRNAs), microRNAs (miRNAs) perform important roles in numerous biological and pathological processes. The realization of miRNA functions depends largely on how miRNAs regulate specific target genes. It is therefore critical to identify, analyze, and cross-reference miRNA-target interactions to better explore and delineate miRNA functions. Semantic technologies can help in this regard. 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 search in the miRNA field. 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 data. Important changes in the current version OMIT are summarized as: (1) following a modularized ontology design (with 2559 terms imported from the NCRO ontology); (2) encoding all 1884 human miRNAs (vs. 300 in previous versions); and (3) setting up a GitHub project site along with an issue tracker for more effective community collaboration on the ontology development. The OMIT ontology is free and open to all users, accessible at: http://purl.obolibrary.org/obo/omit.owl. The OmniSearch system is also free and open to all users, accessible at: http://omnisearch.soc.southalabama.edu/index.php/Software. ? 2016 Huang et al.
推荐引用方式
GB/T 7714：

Huang Jingshan[0],Gutiérrez Fernando A.[1],Strachan Harrison J.[2], et al. Omnisearch: A semantic search system based on the ontology for microrna target (OMIT) for microrna-target gene interaction data [J].Journal of Animal Science and Biotechnology,2016,7(1).
APA：

Huang Jingshan[0],Gutiérrez Fernando A.[1],Strachan Harrison J.[2],Dou Dejing[3],&Ruttenberg Alan[16].(2016).Omnisearch: A semantic search system based on the ontology for microrna target (OMIT) for microrna-target gene interaction data .Journal of Animal Science and Biotechnology,7(1).
MLA：

Huang Jingshan[0], et al. "Omnisearch: A semantic search system based on the ontology for microrna target (OMIT) for microrna-target gene interaction data" .Journal of Animal Science and Biotechnology 7,1(2016).

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