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

Jingshan Huang,Shaojie Zhang,Darren A Natale,Michael T Zimmermann,Dejing Dou,Barry Smith,Alan Ruttenberg,Jun Huan,Guoqian Jiang,Harrison J Strachan,Yongqun He,Judith A Blake,Glen M Borchert,Ming Tan,Zixing Liu,Xiaowei Wang,Bin Wu,Karen Eilbeck,Yuling Lin ,Hu Wei-Li

doi:10.1186/s13326-016-0066-0

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.

Highlights

It is known that non-coding RNAs, a special class of functional RNA molecules, will not be translated into proteins
The Non-Coding RNA Ontology (NCRO) ontology can serve as a resource for annotating and integrating ncRNA data produced by diverse communities, thereby significantly enhancing integrative and comparative analysis of the myriad resources currently housed in disparate sources
Terms break down as follows: 82.68 % were defined in the NCRO ontology itself, and the rest were imported from extant ontologies: Basic Formal Ontology (BFO) (1.14 %), Gene Ontology (GO) (8.67 %), Sequence Ontology (SO) (6.50 %), PRotein Ontology (PRO) (0.10 %), CHEBI (0.29 %), OBI (0.13 %), Information Artifact Ontology (IAO) (0.06 %), DOID (0.13 %), CLO (0.06 %), and UBERON (0.16 %)

Summary

Introduction

It is known that non-coding RNAs (ncRNAs), a special class of functional RNA molecules, will not be translated into proteins. The BioPortal, too, contains, no comprehensive ncRNA ontologies These observations indicate that there is an important gap that needs to be filled — the Non-Coding RNA Ontology (NCRO) project. Domain-specific ontology in the ncRNA field, the NCRO ontology aims to supply a systematically structured, precisely defined controlled vocabulary for the ncRNA domain, consisting of a set of common, standardized terms and relations that will facilitate the discovery, curation, analysis, exchange, and reasoning of data about the structures, functions, and molecular, cellular, organismal, therapeutic, or biotechnological uses of ncRNAs. The NCRO ontology can serve as a resource for annotating and integrating ncRNA data produced by diverse communities, thereby significantly enhancing integrative and comparative analysis of the myriad resources currently housed in disparate sources. Section ‘Related work’ summarizes state-of-the-art research in ncRNAs and bio-ontologies; Section ‘Ontology scope’ gives an overview of the scope covered by the NCRO ontology; Section ‘Ontology development’ introduces NCRO development principles and procedure; Section ‘NCRO terms, relations, and reasoning’ describes NCRO terms and relations, as well as ontology reasoning; Section ‘Examples in NCRO annotations’ presents two examples to demonstrate how NCRO annotations and ontology reasoning can be performed to facilitate knowledge capture; Section ‘Conclusions’ concludes with future research directions

Related work

Findings

Conclusions