ArticleJournal of biomedical semantics2016
OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data.
Article in Journal of biomedical semantics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Representing dental restoration materials in the oral health and disease ontology.Journal of biomedical semantics · 2026Article
- SARS-Cov-2 small viral RNA suppresses gene expression via complementary binding to mRNA 3' UTR.microPublication biology · 2024Article
- Characterization of a novel sRNA contributing to biofilm formation inmicroPublication biology · 2023Article
- Dug: a semantic search engine leveraging peer-reviewed knowledge to query biomedical data repositories.Bioinformatics (Oxford, England) · 2022Article
- MetamORF: a repository of unique short open reading frames identified by both experimental and computational approaches for gene and metagene analyses.Database : the journal of biological databases and curation · 2021Article
- An integrative approach to investigate the association among high-sensitive C-reactive protein, body fat mass distribution, and other cardiometabolic risk factors in young healthy women.Methods (San Diego, Calif.) · 2018Article
- A semantics-oriented computational approach to investigate microRNA regulation on glucocorticoid resistance in pediatric acute lymphoblastic leukemia.BMC medical informatics and decision making · 2018Article
- Regulation of Pharmacogene Expression by microRNA in The Cancer Genome Atlas (TCGA) Research Network.Biomolecules & therapeutics · 2017Article
- 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.Methods (San Diego, Calif.) · 2017Article
- The development of non-coding RNA ontology.International journal of data mining and bioinformaticsArticle
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Authors and funding
17 authors.
Funding
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.
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