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

• Published in: Journal of biomedical semantics Vol. 7; no. 1; p. 25
• Main Authors: Huang, Jingshan, Gutierrez, Fernando, Strachan, Harrison J., Dou, Dejing, Huang, Weili, Smith, Barry, Blake, Judith A., Eilbeck, Karen, Natale, Darren A., Lin, Yu, Wu, Bin, Silva, Nisansa de, Wang, Xiaowei, Liu, Zixing, Borchert, Glen M., Tan, Ming, Ruttenberg, Alan
• Format: Journal Article
• Language: English
• Published: England BioMed Central 2016
• Subjects: Computational Biology - methods; Epistasis, Genetic - genetics; Gene Ontology; MicroRNAs - genetics; Semantics; User-Computer Interface; Data annotation; Semantic search; Ontology development; SPARQL query; Data integration; microRNA; Biomedical ontology; Non-coding RNA; Target gene
• ISSN: 2041-1480; 2041-1480
• DOI: 10.1186/s13326-016-0064-2

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.