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.

Word Vector Embeddings and Domain Specific Semantic based Semi-Supervised Ontology Instance Population

“…As defined by Thomas R. Gruber [2], 'ontologies are an explicit and formal specifications of the terms in the domain and the relations among them'. Ontologies have been expanding out from the realm of Artificial-Intelligence to domain specific tasks such as: Linguistics [4,5,9,21,22], Law [19], Medicine [10,11,13,14,16]. Ontologies have become common on the semantic iteration of the World-Wide Web [12].…”

“…Given an unlabelled instance Y, let Mensemble be a p x n matrix where n denotes the number of classes in the ontology and p denotes the number of basic models. Each column of the matrix corresponds to a class in the ontology and each row corresponds to a model while each mi,j is derived from Equation 13. (19) Here, S is the score vector of size n where element i in the vector denotes the total score for instance Y for the membership in Class Ci.…”

“…Due to the evolving ability of ontologies to overcome limitations in traditional natural language processing methods, the popularity of using ontologies in modern computation tasks are getting increased day by day. For an example, text classification [3], [4], word set expansions [5], linguistic information management [13], [14], and information extraction [15], [16] emphasize the growing popularity of the ontology based computations and processing.…”

Co-expression analysis among microRNAs, long non-coding RNAs, and messenger RNAs to understand the pathogenesis and progression of diabetic kidney disease at the genetic level

“…Bio-ontologies have been widely utilized nowadays, such as: Gene Ontology (GO) [16], the most successful and widely used bio-ontology with three independent sub-ontologies (biological processes, molecular functions, and cellular components); Non-Coding RNA Ontology (NCRO) [17,18], an Open Biological and Biomedical Ontologies (OBO) [19] candidate reference ontology in non-coding RNA (ncRNA) domain; and Ontology for MIcroRNA Target (OMIT) [20–22], an application ontology to provide the community with common data elements and data exchange standards in the miR research.…”

The development of non-coding RNA ontology

“…Ontology for MIcroRNA Target (OMIT): OMIT (Huang et al, 2011; Huang et al, 2014; Huang et al, 2015; Huang et al, 2016) is a miRNA domain ontology being developed as part of the NIH OmniSearch project. The purpose is to establish standard metadata in miRNA domain for more effective identification of miRNAs’ roles in various human diseases.…”