The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology

Abstract

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users, accessible at: http://purl.obolibrary.org/obo/ncro.owl.

TrhOnt: building an ontology to assist rehabilitation processes

“…We can find in the literature many ontologies (e.g. [ 42 – 44 ]) that have been built with the purpose of supporting a precise and comprehensive semantic annotation of resources. However, TRHONT goes an step further and it also provides a framework where the reasoning process takes a relevant role.…”

A semantics-oriented computational approach to investigate microRNA regulation on glucocorticoid resistance in pediatric acute lymphoblastic leukemia

“…Being a semantic integration & search software system, OmniSearch was built upon Ontology for MicroRNA Target (OMIT) [ 20 ] and Non-Coding RNA Ontology (NCRO) [ 21 ]. Technical details of these two Basic Formal Ontology (BFO)-compliant bio-ontologies were included in our previously published work [ 20 , 21 ]. In this paper, we want to emphasize the well-structured MeSH terms defined in the OMIT ontology.…”

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

“…The OmniSearch analytical software was built upon semantic technologies (including semantic data annotation, semantic data integration, and semantic search) that are based on two domain ontologies, Ontology for MIcroRNA Targets (OMIT) [20–22] and Non-Coding RNA Ontology (NCRO) [17,18]. OmniSearch was developed to handle the significant challenge of effective miR data integration and knowledge acquisition.…”

“…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.…”