The development of non-coding RNA ontology

Jingshan Huang; Karen Eilbeck; Barry Smith; Judith A. Blake; Dejing Dou; Weili Huang; Darren A. Natale; Alan Ruttenberg; Jun Huan; Michael T. Zimmermann; Guoqian Jiang; Yu Lin; Bin Wu; Harrison J. Strachan; Nisansa De Silva; Mohan Vamsi Kasukurthi; Vikash Kumar Jha; Yongqun He; Shaojie Zhang; Xiaowei Wang; Zixing Liu; Glen M. Borchert; Ming Tan

doi:10.1504/IJDMB.2016.077072

The development of non-coding RNA ontology

Jingshan Huang, Karen Eilbeck, Barry Smith, Judith A. Blake, Dejing Dou, Weili Huang, Darren A. Natale, Alan Ruttenberg, Jun Huan, Michael T. Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Harrison J. Strachan, Nisansa De Silva, Mohan Vamsi Kasukurthi, Vikash Kumar Jha, Yongqun He, Shaojie Zhang, Xiaowei WangZixing Liu, Glen M. Borchert, Ming Tan

Division of Cancer Biology

Research output: Contribution to journal › Article › peer-review

9 Scopus citations

Abstract

Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic annotation of large amounts of ncRNA biological and clinical data.

Original language	English
Pages (from-to)	214-232
Number of pages	19
Journal	International Journal of Data Mining and Bioinformatics
Volume	15
Issue number	3
DOIs	https://doi.org/10.1504/IJDMB.2016.077072
State	Published - 2016

Keywords

Bio-ontologies
Domain ontology
Non-coding RNA
Ontology development
Reference ontology
Semantic data annotation

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10.1504/IJDMB.2016.077072

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Huang, J., Eilbeck, K., Smith, B., Blake, J. A., Dou, D., Huang, W., Natale, D. A., Ruttenberg, A., Huan, J., Zimmermann, M. T., Jiang, G., Lin, Y., Wu, B., Strachan, H. J., De Silva, N., Kasukurthi, M. V., Jha, V. K., He, Y., Zhang, S., ... Tan, M. (2016). The development of non-coding RNA ontology. International Journal of Data Mining and Bioinformatics, 15(3), 214-232. https://doi.org/10.1504/IJDMB.2016.077072

@article{a6bdafc5cc2045aba4cd51ae63f4b46c,

title = "The development of non-coding RNA ontology",

abstract = "Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic annotation of large amounts of ncRNA biological and clinical data.",

keywords = "Bio-ontologies, Domain ontology, Non-coding RNA, Ontology development, Reference ontology, Semantic data annotation",

author = "Jingshan Huang and Karen Eilbeck and Barry Smith and Blake, {Judith A.} and Dejing Dou and Weili Huang and Natale, {Darren A.} and Alan Ruttenberg and Jun Huan and Zimmermann, {Michael T.} and Guoqian Jiang and Yu Lin and Bin Wu and Strachan, {Harrison J.} and {De Silva}, Nisansa and Kasukurthi, {Mohan Vamsi} and Jha, {Vikash Kumar} and Yongqun He and Shaojie Zhang and Xiaowei Wang and Zixing Liu and Borchert, {Glen M.} and Ming Tan",

note = "Funding Information: Funding for J. Huang was provided in part by the National Cancer Institute (NCI) at the National Institutes of Health (NIH), under the Award Number U01CA180982. Funding for G.M. Borchert was provided in part by Natural Science Foundation (NSF) CAREER grant 1350064 (GMB) awarded by Division of Molecular and Cellular Biosciences (with co-funding provided by the NSF EPSCoR program) and in part by the Abraham A. Mitchell Cancer Research Fund. The views contained in this paper are solely the responsibility of the authors and do not represent the official views, either expressed or implied, of the NIH, NSF, the US Government, or the Abraham A. Mitchell Cancer Research Fund. Publisher Copyright: {\textcopyright} 2016 Inderscience Enterprises Ltd.",

year = "2016",

doi = "10.1504/IJDMB.2016.077072",

language = "English",

volume = "15",

pages = "214--232",

journal = "International Journal of Data Mining and Bioinformatics",

issn = "1748-5673",

number = "3",

}

Huang, J, Eilbeck, K, Smith, B, Blake, JA, Dou, D, Huang, W, Natale, DA, Ruttenberg, A, Huan, J, Zimmermann, MT, Jiang, G, Lin, Y, Wu, B, Strachan, HJ, De Silva, N, Kasukurthi, MV, Jha, VK, He, Y, Zhang, S, Wang, X, Liu, Z, Borchert, GM & Tan, M 2016, 'The development of non-coding RNA ontology', International Journal of Data Mining and Bioinformatics, vol. 15, no. 3, pp. 214-232. https://doi.org/10.1504/IJDMB.2016.077072

TY - JOUR

T1 - The development of non-coding RNA ontology

AU - Huang, Jingshan

AU - Eilbeck, Karen

AU - Smith, Barry

AU - Blake, Judith A.

AU - Dou, Dejing

AU - Huang, Weili

AU - Natale, Darren A.

AU - Ruttenberg, Alan

AU - Huan, Jun

AU - Zimmermann, Michael T.

AU - Jiang, Guoqian

AU - Lin, Yu

AU - Wu, Bin

AU - Strachan, Harrison J.

AU - De Silva, Nisansa

AU - Kasukurthi, Mohan Vamsi

AU - Jha, Vikash Kumar

AU - He, Yongqun

AU - Zhang, Shaojie

AU - Wang, Xiaowei

AU - Liu, Zixing

AU - Borchert, Glen M.

AU - Tan, Ming

N1 - Funding Information: Funding for J. Huang was provided in part by the National Cancer Institute (NCI) at the National Institutes of Health (NIH), under the Award Number U01CA180982. Funding for G.M. Borchert was provided in part by Natural Science Foundation (NSF) CAREER grant 1350064 (GMB) awarded by Division of Molecular and Cellular Biosciences (with co-funding provided by the NSF EPSCoR program) and in part by the Abraham A. Mitchell Cancer Research Fund. The views contained in this paper are solely the responsibility of the authors and do not represent the official views, either expressed or implied, of the NIH, NSF, the US Government, or the Abraham A. Mitchell Cancer Research Fund. Publisher Copyright: © 2016 Inderscience Enterprises Ltd.

PY - 2016

Y1 - 2016

N2 - Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic annotation of large amounts of ncRNA biological and clinical data.

AB - Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic annotation of large amounts of ncRNA biological and clinical data.

KW - Bio-ontologies

KW - Domain ontology

KW - Non-coding RNA

KW - Ontology development

KW - Reference ontology

KW - Semantic data annotation

UR - http://www.scopus.com/inward/record.url?scp=84975847387&partnerID=8YFLogxK

U2 - 10.1504/IJDMB.2016.077072

DO - 10.1504/IJDMB.2016.077072

M3 - Article

AN - SCOPUS:84975847387

SN - 1748-5673

VL - 15

SP - 214

EP - 232

JO - International Journal of Data Mining and Bioinformatics

JF - International Journal of Data Mining and Bioinformatics

IS - 3

ER -

The development of non-coding RNA ontology

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Keywords

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