A semantic approach for knowledge capture of MIcroRNA-Target gene interactions

Jingshan Huang; Fernando Gutierrez; Dejing Dou; Judith A. Blake; Karen Eilbeck; Darren A. Natale; Barry Smith; Yu Lin; Xiaowei Wang; Zixing Liu; Ming Tan; Alan Ruttenberg

doi:10.1109/BIBM.2015.7359816

A semantic approach for knowledge capture of MIcroRNA-Target gene interactions

Jingshan Huang, Fernando Gutierrez, Dejing Dou, Judith A. Blake, Karen Eilbeck, Darren A. Natale, Barry Smith, Yu Lin, Xiaowei Wang, Zixing Liu, Ming Tan, Alan Ruttenberg

Division of Cancer Biology

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

12 Scopus citations

Abstract

Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs' functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs' functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions.

Original language	English
Title of host publication	Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
Editors	lng. Matthieu Schapranow, Jiayu Zhou, Xiaohua Tony Hu, Bin Ma, Sanguthevar Rajasekaran, Satoru Miyano, Illhoi Yoo, Brian Pierce, Amarda Shehu, Vijay K. Gombar, Brian Chen, Vinay Pai, Jun Huan
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	975-982
Number of pages	8
ISBN (Electronic)	9781467367981
DOIs	https://doi.org/10.1109/BIBM.2015.7359816
State	Published - Dec 16 2015
Event	IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015 - Washington, United States Duration: Nov 9 2015 → Nov 12 2015

Publication series

Name	Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015

Conference

Conference	IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
Country/Territory	United States
City	Washington
Period	11/9/15 → 11/12/15

Keywords

SPARQL query
biomedical ontology
data annotation
data integration
microRNA
non-coding RNA
ontology development
semantic search
target gene

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10.1109/BIBM.2015.7359816

Cite this

Huang, J., Gutierrez, F., Dou, D., Blake, J. A., Eilbeck, K., Natale, D. A., Smith, B., Lin, Y., Wang, X., Liu, Z., Tan, M., & Ruttenberg, A. (2015). A semantic approach for knowledge capture of MIcroRNA-Target gene interactions. In L. M. Schapranow, J. Zhou, X. T. Hu, B. Ma, S. Rajasekaran, S. Miyano, I. Yoo, B. Pierce, A. Shehu, V. K. Gombar, B. Chen, V. Pai, & J. Huan (Eds.), Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015 (pp. 975-982). Article 7359816 (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2015.7359816

Huang, Jingshan ; Gutierrez, Fernando ; Dou, Dejing et al. / A semantic approach for knowledge capture of MIcroRNA-Target gene interactions. Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. editor / lng. Matthieu Schapranow ; Jiayu Zhou ; Xiaohua Tony Hu ; Bin Ma ; Sanguthevar Rajasekaran ; Satoru Miyano ; Illhoi Yoo ; Brian Pierce ; Amarda Shehu ; Vijay K. Gombar ; Brian Chen ; Vinay Pai ; Jun Huan. Institute of Electrical and Electronics Engineers Inc., 2015. pp. 975-982 (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015).

@inproceedings{19a4247dc21f4f13ae589a193609a03b,

title = "A semantic approach for knowledge capture of MIcroRNA-Target gene interactions",

abstract = "Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs' functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs' functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions.",

keywords = "SPARQL query, biomedical ontology, data annotation, data integration, microRNA, non-coding RNA, ontology development, semantic search, target gene",

author = "Jingshan Huang and Fernando Gutierrez and Dejing Dou and Blake, {Judith A.} and Karen Eilbeck and Natale, {Darren A.} and Barry Smith and Yu Lin and Xiaowei Wang and Zixing Liu and Ming Tan and Alan Ruttenberg",

note = "Funding Information: Research reported in this paper was partially supported by the National Cancer Institute (NCI) of the National Institutes of Health (NIH), under the Award Number UOICA180982. 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 or the U. S. Government. Publisher Copyright: {\textcopyright} 2015 IEEE.; IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015 ; Conference date: 09-11-2015 Through 12-11-2015",

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doi = "10.1109/BIBM.2015.7359816",

language = "English",

series = "Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015",

publisher = "Institute of Electrical and Electronics Engineers Inc.",

pages = "975--982",

editor = "Schapranow, {lng. Matthieu} and Jiayu Zhou and Hu, {Xiaohua Tony} and Bin Ma and Sanguthevar Rajasekaran and Satoru Miyano and Illhoi Yoo and Brian Pierce and Amarda Shehu and Gombar, {Vijay K.} and Brian Chen and Vinay Pai and Jun Huan",

booktitle = "Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015",

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Huang, J, Gutierrez, F, Dou, D, Blake, JA, Eilbeck, K, Natale, DA, Smith, B, Lin, Y, Wang, X, Liu, Z, Tan, M & Ruttenberg, A 2015, A semantic approach for knowledge capture of MIcroRNA-Target gene interactions. in LM Schapranow, J Zhou, XT Hu, B Ma, S Rajasekaran, S Miyano, I Yoo, B Pierce, A Shehu, VK Gombar, B Chen, V Pai & J Huan (eds), Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015., 7359816, Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015, Institute of Electrical and Electronics Engineers Inc., pp. 975-982, IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015, Washington, United States, 11/9/15. https://doi.org/10.1109/BIBM.2015.7359816

A semantic approach for knowledge capture of MIcroRNA-Target gene interactions. / Huang, Jingshan; Gutierrez, Fernando; Dou, Dejing et al.
Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. ed. / lng. Matthieu Schapranow; Jiayu Zhou; Xiaohua Tony Hu; Bin Ma; Sanguthevar Rajasekaran; Satoru Miyano; Illhoi Yoo; Brian Pierce; Amarda Shehu; Vijay K. Gombar; Brian Chen; Vinay Pai; Jun Huan. Institute of Electrical and Electronics Engineers Inc., 2015. p. 975-982 7359816 (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

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AU - Huang, Jingshan

AU - Gutierrez, Fernando

AU - Dou, Dejing

AU - Blake, Judith A.

AU - Eilbeck, Karen

AU - Natale, Darren A.

AU - Smith, Barry

AU - Lin, Yu

AU - Wang, Xiaowei

AU - Liu, Zixing

AU - Tan, Ming

AU - Ruttenberg, Alan

N1 - Funding Information: Research reported in this paper was partially supported by the National Cancer Institute (NCI) of the National Institutes of Health (NIH), under the Award Number UOICA180982. 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 or the U. S. Government. Publisher Copyright: © 2015 IEEE.

PY - 2015/12/16

Y1 - 2015/12/16

N2 - Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs' functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs' functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions.

AB - Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs' functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs' functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions.

KW - SPARQL query

KW - biomedical ontology

KW - data annotation

KW - data integration

KW - microRNA

KW - non-coding RNA

KW - ontology development

KW - semantic search

KW - target gene

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DO - 10.1109/BIBM.2015.7359816

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BT - Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015

A2 - Schapranow, lng. Matthieu

A2 - Zhou, Jiayu

A2 - Hu, Xiaohua Tony

A2 - Ma, Bin

A2 - Rajasekaran, Sanguthevar

A2 - Miyano, Satoru

A2 - Yoo, Illhoi

A2 - Pierce, Brian

A2 - Shehu, Amarda

A2 - Gombar, Vijay K.

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PB - Institute of Electrical and Electronics Engineers Inc.

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Huang J, Gutierrez F, Dou D, Blake JA, Eilbeck K, Natale DA et al. A semantic approach for knowledge capture of MIcroRNA-Target gene interactions. In Schapranow LM, Zhou J, Hu XT, Ma B, Rajasekaran S, Miyano S, Yoo I, Pierce B, Shehu A, Gombar VK, Chen B, Pai V, Huan J, editors, Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. Institute of Electrical and Electronics Engineers Inc. 2015. p. 975-982. 7359816. (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015). doi: 10.1109/BIBM.2015.7359816

A semantic approach for knowledge capture of MIcroRNA-Target gene interactions

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