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 ontology files can be 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.

All files for the NCRO ontology can be found here.


References for OMIT:

1. 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, 9(7): 1-16, e100855, July 2014 (doi:10.1371/journal.pone.0100855).

2. J. Huang, F. Gutierrez, D. Dou, J.A. Blake, K. Eilbeck, D.A. Natale, B. Smith, Y. Lin, X. Wang, Z. Liu, M. Tan, and A. Ruttenberg, A semantic approach for knowledge capture of microRNA-target gene interactions, Proc. BHI Workshop at 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM-15), pp. 975-982, IEEE, Washington D.C., November 2015.


References for NCRO:

1. J. Huang, K. Eilbeck, J.A. Blake, D. Dou, D.A. Natale, A. Ruttenberg, B. Smith, M.T. Zimmermann, G. Jiang, Y. Lin, B. Wu, Y. He, S. Zhang, X. Wang, H. Zhang, Z. Liu, and M. Tan, A domain ontology for the non-coding RNA field, Proc. 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM-15), pp. 621-624, IEEE, Washington D.C., November 2015.