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ICBO 2016 Workshop #W02


OmniSearch and Beyond: ontology-based biomedical information integration and knowledge acquisition for miRNAs

Workshop type

Project Workshop (Tutorial, Project specific talks, Discussions)


Jingshan Huang, University of South Alabama

Co-organizer(s) Karen Eilbeck
Dejing Dou
Alan Ruttenberg
Website N/A
Workshop Abstract

To address an important research need, particularly in the realm of cancer research, we have developed a microRNA (miRNA) domain-specific application ontology: ‘Ontology for MIcroRNA Target’ (OMIT). The purpose of OMIT is to serve as a foundation for semantic annotation, data integration, and semantic queries in the miRNA field. In this proposed tutorial, we will describe our continuing effort to develop the OMIT, and will then demonstrate its use within a semantic search system, OmniSearch, designed to facilitate knowledge capture of miRNA-target interaction data. In particular, the software prototype of our OmniSearch system will be demonstrated and discussed during the tutorial. We will also discuss our recent efforts in developing the Non-Coding RNA Ontology (NCRO), aiming to provide a systematically structured and precisely defined controlled vocabulary for the extended domain of non-coding RNAs (ncRNAs). The NCRO will satisfy the urgent need for effective methodologies to bring together published discoveries from diverse segments of the ncRNA research community.

Note that techniques to be introduced and discussed in this tutorial are broadly applicable and can be customized to other bio domain areas. Also note that there will be no CFPs and we do not plan to publish papers out of this venue. Our tutorial will be a half-day session (or a two-hour one when deemed necessary by the main conference).


While the OMIT ontology has matured over several years, both the OmniSearch system and the NCRO ontology are in their infant phases. Therefore, we feel that it will be more appropriate to address these specific topics in the proposed tutorial rather than in the ICBO main conference. The topics proposed, OMIT, OmniSearch, and NCRO are all important, interesting topics to the bio-ontology community at large. The software tools developed for this project are relevant to a broad range of biomedical domain areas, where data integration over literature is required but complex. The tutorial will provide stimulating hands-on ontological querying and exploration. In addition, our research efforts, including the ontology development, visualization, data annotation, analysis, as well as real-world applications, have been funded by NIH/NCI. The new technology in the proposed tutorial is expected to encourage young researchers and also attract increased participation in the ICBO main conference.

Funding source (if any) NIH/NCI