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

Journal: Journal of biomedical semantics
Published Date: Jan 1, 2016

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

  • Jingshan Huang
    School of Computing, College of Medicine, University of South Alabama, Mobile, AL, USA.
  • Fernando Gutierrez
    Computer and Information Science Department, University of Oregon, Eugene, Oregon, 97403-1202 USA.
  • Harrison J Strachan
    School of Computing, University of South Alabama, Mobile, Alabama, 36688-0002 USA.
  • Dejing Dou
    Computer and Information Science Department, University of Oregon, Eugene, Oregon, 97403-1202 USA.
  • Weili Huang
    Miracle Query, Inc., Eugene, Oregon, 97403-1202 USA.
  • Barry Smith
    Department of Philosophy, University at Buffalo, NY, USA.
  • Judith A Blake
    The Jackson Laboratory, Bar Harbor, ME, 04609, USA.
  • Karen Eilbeck
    Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah, 84112-5775 USA.
  • Darren A Natale
    Protein Information Resource, Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, D. C., United States of America.
  • Yu Lin
    Research School of Computer Science, Australian National University, Canberra, 2601, ACT, Australia.
  • Bin Wu
    Department of Psychiatry, Xi'an Mental Health Center, Xi'an, China.
  • Nisansa de Silva
    Computer and Information Science Department, University of Oregon, Eugene, Oregon, 97403-1202 USA.
  • Xiaowei Wang
    Beijing Centers for Preventive Medical Research, Beijing 100013, China.
  • Zixing Liu
    Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, 36604-1405 USA.
  • Glen M Borchert
    Department of Biology, University of South Alabama, Mobile, Alabama, 36688-0002 USA.
  • Ming Tan
    Graduate Institute of Biomedical Science, China Medical University, Taichung, Taiwan.
  • Alan Ruttenberg
    School of Dental Medicine, State University of New York at Buffalo, Buffalo, New York, United States of America.

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