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 Wang

Zixing Liu, Glen M. Borchert, Ming Tan

Division of Cancer Biology

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

10 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 = "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",

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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

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 - https://www.scopus.com/pages/publications/84975847387

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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