A domain ontology for the Non-Coding RNA field

Huang, Jingshan; Eilbeck, Karen; Blake, Judith A.; Dou, Dejing; Natale, Darren A.; Ruttenberg, Alan; Zimmermann, Michael T.; Jiang, Guoqian; Lin, Yuling; Wu, Bin; He, Yongqun; Zhang, Shaojie; Wang, Xiaowei; Zhang, He; Liu, Zixing; Tan, Ming

doi:10.1109/bibm.2015.7359755

Cited by 1 publication

(3 citation statements)

References 18 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“… As discussed earlier in “ Modularized ontology design ” Section, we have followed a modularized ontology design in this new version, which will significantly further facilitate the ontology maintenance and update. In particular, a total of 2559 terms in the updated OMIT have been imported from the NCRO ontology [ 32 ]. Because the NCRO is a comprehensive domain ontology in the ncRNA field, following the NCRO hierarchy will enhance the interoperability between the OMIT and future ontologies to be developed in other ncRNA sub-domains.…”

Section: Resultsmentioning

confidence: 99%

“… ro-imports.owl — Imports common relations (shared across different ontologies) from the Relation Ontology (RO) [ 31 ], for example, has participant and regulates . ncro.owl — Imports ncRNA-related terms and relations from the Non-coding RNA Ontology (NCRO) [ 32 ], for example, miRNA_target_gene and miRNA_gene_family . go-imports.owl — Imports gene product terms from the GO, for example, RNA binding and regulation of biological process .…”

Section: Omit Reconstructionmentioning

confidence: 99%

“…ncro.owl — Imports ncRNA-related terms and relations from the Non-coding RNA Ontology (NCRO) [ 32 ], for example, miRNA_target_gene and miRNA_gene_family .…”

Section: Omit Reconstructionmentioning

confidence: 99%

See 2 more Smart Citations

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

et al. 2016

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Section: Resultsmentioning

confidence: 99%