机构：[1]School of Computing, University of South Alabama, Mobile, Alabama36688-0002, USA[2]Computer and Information Science Department, Universityof Oregon, Eugene, Oregon 97403-1202, USA[3]Miracle Query, Inc., Eugene,Oregon 97403-1202, USA[4]Department of Philosophy, University at Buffalo,Buffalo, New York 14260-4150, USA[5]Genome Informatics, The JacksonLaboratory, Bar Harbor, Maine 04609-1523, USA[6]Department of BiomedicalInformatics, University of Utah, Salt Lake City, Utah 84112-5775, USA[7]Department of Biochemistry and Molecular and Cellular Biology, GeorgetownUniversity Medical Center, Washington D.C. 20007-1485, USA[8]Center for Computational Science, University of Miami, Miami, Florida 33146-2960, U.S.A[9]Department of Microbiology and Immunology, First Affiliated Hospital,Kunming Medical University, Kunming, Yunnan 650032, China昆明医科大学附属第一医院[10]Departmentof Radiation Oncology, Washington University School of Medicine, St. Louis,Missouri 63110-0001, USA[11]Mitchell Cancer Institute, University of SouthAlabama, Mobile, Alabama 36604-1405, USA[12]Department of Biology,University of South Alabama, Mobile, Alabama 36688-0002, USA[13]School ofDental Medicine, University at Buffalo, Buffalo, New York 14214-8006, USA.
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.
基金：
National Cancer Institute (NCI) at the National Institutes of Health (NIH)United States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Cancer Institute (NCI) [U01CA180982]; Natural Science Foundation (NSF) CAREER grant - Division of Molecular and Cellular Biosciences [1350064]; NSF EPSCoR program; Abraham A. Mitchell Cancer Research Fund
第一作者机构：[1]School of Computing, University of South Alabama, Mobile, Alabama36688-0002, USA
通讯作者：
推荐引用方式(GB/T 7714)：
Huang Jingshan,Gutierrez Fernando,Strachan Harrison J.,et al.OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data[J].JOURNAL OF BIOMEDICAL SEMANTICS.2016,7:doi:10.1186/s13326-016-0064-2.
APA：
Huang, Jingshan,Gutierrez, Fernando,Strachan, Harrison J.,Dou, Dejing,Huang, Weili...&Ruttenberg, Alan.(2016).OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data.JOURNAL OF BIOMEDICAL SEMANTICS,7,
MLA：
Huang, Jingshan,et al."OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data".JOURNAL OF BIOMEDICAL SEMANTICS 7.(2016)
