Ontology

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The OMIT ontology in the OmniSearch project was developed in both the OWL and OBO formats.

The most up-to-date OMIT ontology files and other documentation are accessible here. Besides, the OMIT ontology is also included in both the OBO Library and the NCBO BioPortal.

In this project, a reference ontology, NCRO, is also under development. NCRO stands for Non-Coding RNA Ontology (pronounced as an-ke-row). The NCRO ontology aims to provide a common set of terms and relations that will facilitate the curation, analysis, exchange, sharing, and management of ncRNA data. If research groups around the world utilize the NCRO to perform annotations on their ncRNA data, it will significantly enhance comparative analysis of the wealth of information from disparate sources. 

The most up-to-date NCRO ontology files and other documentation are accessible here. Besides, the NCRO ontology is also included in both the OBO Library and the NCBO BioPortal.




References for OMIT:

1. J. Huang,  F. Gutierrez, H.J. Strachan, D. Dou, W. Huang, B. Smith, J.A. Blake, K. Eilbeck, D.A. Natale, Y. Lin, B. Wu, N. de Silva, X. Wang, Z. Liu, G.M. Borchert, M. Tan, and A. Ruttenberg, “OmniSearch: A semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data,” J Biomed Semantics., 2016 May 10;7:25. doi: 10.1186/s13326-016-0064-2. eCollection 2016. PubMed PMID: 27175225; PubMed Central PMCID: PMC4863347.PDF Link in Journal of Biomedical Semantics
2. J. Huang, J. Dang, G.M. Borchert, K. Eilbeck, H. Zhang, M. Xiong, W. Jiang, H. Wu, J.A. Blake, D.A. Natale, and M. Tan, “OMIT: Dynamic, Semi-Automated Ontology Development for the microRNA Domain,” PLOS ONE, 2014 Jul 15;9(7):e100855. doi: 10.1371/journal.pone.0100855. eCollection 2014. PubMed PMID: 25025130; PubMed Central PMCID: PMC4099014.PDF Link in PLOS ONE

References for NCRO:

1. J. Huang, K. Eilbeck, B. Smith, J.A. Blake, D. Dou, W. Huang, D.A. Natale, A. Ruttenberg, J. Huan, M.T. Zimmermann, G. Jiang, Y. Lin, B. Wu, H.J. Strachan, Y. He, S. Zhang, X. Wang, Z. Liu, G.M. Borchert, and M. Tan, “The Non-Coding RNA Ontology (NCRO): A comprehensive resource for the unification of non-coding RNA biology,” J Biomed Semantics., 2016 May 4;7:24. doi: 10.1186/s13326-016-0066-0. eCollection 2016. PubMed PMID: 27152146; PubMed Central PMCID: PMC4857245.PDF Link in Journal of Biomedical Semantics
2. J. Huang, K. Eilbeck, B. Smith, J.A. Blake, D. Dou, W. Huang, D.A. Natale, A. Ruttenberg, J. Huan, M.T. Zimmermann, G. Jiang, Y. Lin, B. Wu, H.J. Strachan, N. de Silva, M. Kasukurthi, V. Jha, Y. He, S. Zhang, X. Wang, Z. Liu, G.M. Borchert, and M. Tan, “The Development of Non-Coding RNA Ontology,” Int. J. Data Mining and Bioinformatics, 15(3):214-232, June 2016. doi: 10.1504/IJDMB.2016.077072. PubMed Central PMCID: PMC5156483; NIHMSID: NIHMS795655.PDF Link in NCBI PMC