title: OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data.
abstract: 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.
authors.affiliation: School of Computing, University of South Alabama, Mobile, Alabama, 36688-0002 USA.
authors.forename: Jingshan
authors.initials: J
authors.lastname: Huang
authors.affiliation: Computer and Information Science Department, University of Oregon, Eugene, Oregon, 97403-1202 USA.
authors.forename: Fernando
authors.initials: F
authors.lastname: Gutierrez
authors.affiliation: School of Computing, University of South Alabama, Mobile, Alabama, 36688-0002 USA.
authors.forename: Harrison J
authors.initials: HJ
authors.lastname: Strachan
authors.affiliation: Computer and Information Science Department, University of Oregon, Eugene, Oregon, 97403-1202 USA.
authors.forename: Dejing
authors.initials: D
authors.lastname: Dou
authors.affiliation: Miracle Query, Inc., Eugene, Oregon, 97403-1202 USA.
authors.forename: Weili
authors.initials: W
authors.lastname: Huang
authors.affiliation: Department of Philosophy, University at Buffalo, Buffalo, New York, 14260-4150 USA.
authors.forename: Barry
authors.initials: B
authors.lastname: Smith
authors.affiliation: Genome Informatics, The Jackson Laboratory, Bar Harbor, Maine, 04609-1523 USA.
authors.forename: Judith A
authors.initials: JA
authors.lastname: Blake
authors.affiliation: Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah, 84112-5775 USA.
authors.forename: Karen
authors.initials: K
authors.lastname: Eilbeck
authors.affiliation: Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington D.C., 20007-1485 USA.
authors.forename: Darren A
authors.initials: DA
authors.lastname: Natale
authors.affiliation: Center for Computational Science, University of Miami, Miami, Florida, 33146-2960 U.S.A.
authors.forename: Yu
authors.initials: Y
authors.lastname: Lin
authors.affiliation: Department of Microbiology and Immunology, First Affiliated Hospital, Kunming Medical University, Kunming, Yunnan, 650032 China.
authors.forename: Bin
authors.initials: B
authors.lastname: Wu
authors.affiliation: Computer and Information Science Department, University of Oregon, Eugene, Oregon, 97403-1202 USA.
authors.forename: Nisansa de
authors.initials: Nd
authors.lastname: Silva
authors.affiliation: Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, 63110-0001 USA.
authors.forename: Xiaowei
authors.initials: X
authors.lastname: Wang
authors.affiliation: Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, 36604-1405 USA.
authors.forename: Zixing
authors.initials: Z
authors.lastname: Liu
authors.affiliation: Department of Biology, University of South Alabama, Mobile, Alabama, 36688-0002 USA.
authors.forename: Glen M
authors.initials: GM
authors.lastname: Borchert
authors.affiliation: Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, 36604-1405 USA.
authors.forename: Ming
authors.initials: M
authors.lastname: Tan
authors.affiliation: School of Dental Medicine, University at Buffalo, Buffalo, New York, 14214-8006 USA.
authors.forename: Alan
authors.initials: A
authors.lastname: Ruttenberg
mesh_terms: D019295:Computational Biology / Q000379:methods*; D004843:Epistasis, Genetic / Q000235:genetics*; D063990:Gene Ontology; D035683:MicroRNAs / Q000235:genetics*; D012660:Semantics; D014584:User-Computer Interface
chemical_list: D035683:MicroRNAs
keywords: Biomedical ontology; Data annotation; Data integration; Non-coding RNA; Ontology development; SPARQL query; Semantic search; Target gene; microRNA