A text mining application for linking functionally stressed-proteins to their post-translational modifications

Oliver Bonham-Carter, Dhundy R. Bastola

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

Abstract

In the proteome, stresses may work against optimal protein function and PTMs play roles in protein stress responses. Many peer-reviewed articles are available to bioinformatics research in the literature, however, the details of stress, protein and their PTM interactions have been scattered throughout the literature and these concepts are mentioned amongst the other details of respective studies. In each publication, for instance, there are many small pieces of knowledge which could be combined to build a better understanding. Since it is impossible to harvest all of its available knowledge using manual means, text mining methods are an attractive approach to assemble ideas from articles where these concepts may not have been a main focus. We present a text mining method to harvest and assemble a knowledge base relating to the relationships of stresses, proteins and PTMs from the literature. Although we also studied the stresses, proteins and PTMs which were associated with apoptosis, diabetes and Parkinson's diseases in the literature, to introduce our method, we address these concepts as they are related to Alzheimer's disease. We use the results from our text mining tool to process article abstracts to build networks which suggest how functional proteins may be linked to environmental stresses and their PTMs. We discuss how networks of biologically relevant keywords may eventually be used to describe directions in research which could be further explored to forecast new trends of studies. We also show how our method may help to predict stress, protein and PTM associations which may be included in these future studies.

Original languageEnglish (US)
Title of host publicationProceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
Editorslng. 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
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages611-614
Number of pages4
ISBN (Electronic)9781467367981
DOIs
StatePublished - Dec 16 2015
EventIEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015 - Washington, United States
Duration: Nov 9 2015Nov 12 2015

Publication series

NameProceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015

Other

OtherIEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
CountryUnited States
CityWashington
Period11/9/1511/12/15

Fingerprint

Data Mining
Pulse time modulation
Post Translational Protein Processing
Heat-Shock Proteins
Proteins
Knowledge Bases
Proteome
Computational Biology
Research
Parkinson Disease
Publications
Alzheimer Disease
Apoptosis
Cell death
Bioinformatics
Medical problems

ASJC Scopus subject areas

  • Software
  • Artificial Intelligence
  • Health Informatics
  • Biomedical Engineering

Cite this

Bonham-Carter, O., & Bastola, D. R. (2015). A text mining application for linking functionally stressed-proteins to their post-translational modifications. 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. 611-614). [7359753] (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2015.7359753

A text mining application for linking functionally stressed-proteins to their post-translational modifications. / Bonham-Carter, Oliver; Bastola, Dhundy R.

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. 611-614 7359753 (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Bonham-Carter, O & Bastola, DR 2015, A text mining application for linking functionally stressed-proteins to their post-translational modifications. 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., 7359753, Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015, Institute of Electrical and Electronics Engineers Inc., pp. 611-614, IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015, Washington, United States, 11/9/15. https://doi.org/10.1109/BIBM.2015.7359753
Bonham-Carter O, Bastola DR. A text mining application for linking functionally stressed-proteins to their post-translational modifications. 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. 611-614. 7359753. (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015). https://doi.org/10.1109/BIBM.2015.7359753
Bonham-Carter, Oliver ; Bastola, Dhundy R. / A text mining application for linking functionally stressed-proteins to their post-translational modifications. 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. 611-614 (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015).
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