Challenges and opportunities for system biology standards and tools in medical research

Matthias König; Anika Oellrich; Dagmar Waltemath; Richard J B Dobson; Tim J P Hubbard; Olaf Wolkenhauer

Challenges and opportunities for system biology standards and tools in medical research

Matthias König, Anika Oellrich, Dagmar Waltemath^*, Richard J B Dobson, Tim J P Hubbard, Olaf Wolkenhauer

^*Corresponding author for this work

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

1 Citation (Scopus)

175 Downloads (Pure)

Abstract

Kinetic models are increasingly relevant in medical research. In systems biology, more than 10 years of experience with the development of standards and tools to construct and analyse kinetic models exists. This has supported the sharing of kinetic models, increased their reuse, and thereby has helped to reproduce and validate scientific results. Given this expertise, it seems natural to consider the application and development of standards and tools to meet the requirements of medical scientists. In this paper, we discuss challenges and opportunities for standards and tools from systems biology in medical research, and we suggest criteria for the safe use of simulations. We conclude that standards, tools and infrastructure need to be extended to ensure the quality, reliability and safety required when working with medical and patient data. This will foster the adaptation of modelling in the clinic, providing tools for improved diagnosis, prognosis and therapy.

Original language	English
Title of host publication	Proceedings of the 7th Workshop on Ontologies and Data in Life Sciences, organized by the GI Workgroup Ontologies in Biomedicine and Life Sciences
Publisher	CEUR-WS
Volume	1692
Publication status	Published - 29 Sept 2016
Event	7th Workshop on Ontologies and Data in Life Sciences, ODLS 2016 - Halle (Saale), Germany Duration: 29 Sept 2016 → 30 Sept 2016

Conference

Conference	7th Workshop on Ontologies and Data in Life Sciences, ODLS 2016
Country/Territory	Germany
City	Halle (Saale)
Period	29/09/2016 → 30/09/2016

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König, M., Oellrich, A., Waltemath, D., Dobson, R. J. B., Hubbard, T. J. P., & Wolkenhauer, O. (2016). Challenges and opportunities for system biology standards and tools in medical research. In Proceedings of the 7th Workshop on Ontologies and Data in Life Sciences, organized by the GI Workgroup Ontologies in Biomedicine and Life Sciences (Vol. 1692). CEUR-WS. http://ceur-ws.org/Vol-1692/paperC.pdf

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title = "Challenges and opportunities for system biology standards and tools in medical research",

abstract = "Kinetic models are increasingly relevant in medical research. In systems biology, more than 10 years of experience with the development of standards and tools to construct and analyse kinetic models exists. This has supported the sharing of kinetic models, increased their reuse, and thereby has helped to reproduce and validate scientific results. Given this expertise, it seems natural to consider the application and development of standards and tools to meet the requirements of medical scientists. In this paper, we discuss challenges and opportunities for standards and tools from systems biology in medical research, and we suggest criteria for the safe use of simulations. We conclude that standards, tools and infrastructure need to be extended to ensure the quality, reliability and safety required when working with medical and patient data. This will foster the adaptation of modelling in the clinic, providing tools for improved diagnosis, prognosis and therapy.",

author = "Matthias K{\"o}nig and Anika Oellrich and Dagmar Waltemath and Dobson, {Richard J B} and Hubbard, {Tim J P} and Olaf Wolkenhauer",

year = "2016",

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day = "29",

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volume = "1692",

booktitle = "Proceedings of the 7th Workshop on Ontologies and Data in Life Sciences, organized by the GI Workgroup Ontologies in Biomedicine and Life Sciences",

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König, M, Oellrich, A, Waltemath, D, Dobson, RJB , Hubbard, TJP & Wolkenhauer, O 2016, Challenges and opportunities for system biology standards and tools in medical research. in Proceedings of the 7th Workshop on Ontologies and Data in Life Sciences, organized by the GI Workgroup Ontologies in Biomedicine and Life Sciences. vol. 1692, CEUR-WS, 7th Workshop on Ontologies and Data in Life Sciences, ODLS 2016, Halle (Saale), Germany, 29/09/2016. <http://ceur-ws.org/Vol-1692/paperC.pdf>

Challenges and opportunities for system biology standards and tools in medical research. / König, Matthias; Oellrich, Anika; Waltemath, Dagmar et al.
Proceedings of the 7th Workshop on Ontologies and Data in Life Sciences, organized by the GI Workgroup Ontologies in Biomedicine and Life Sciences. Vol. 1692 CEUR-WS, 2016.

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

TY - CHAP

T1 - Challenges and opportunities for system biology standards and tools in medical research

AU - König, Matthias

AU - Oellrich, Anika

AU - Waltemath, Dagmar

AU - Dobson, Richard J B

AU - Hubbard, Tim J P

AU - Wolkenhauer, Olaf

PY - 2016/9/29

Y1 - 2016/9/29

N2 - Kinetic models are increasingly relevant in medical research. In systems biology, more than 10 years of experience with the development of standards and tools to construct and analyse kinetic models exists. This has supported the sharing of kinetic models, increased their reuse, and thereby has helped to reproduce and validate scientific results. Given this expertise, it seems natural to consider the application and development of standards and tools to meet the requirements of medical scientists. In this paper, we discuss challenges and opportunities for standards and tools from systems biology in medical research, and we suggest criteria for the safe use of simulations. We conclude that standards, tools and infrastructure need to be extended to ensure the quality, reliability and safety required when working with medical and patient data. This will foster the adaptation of modelling in the clinic, providing tools for improved diagnosis, prognosis and therapy.

AB - Kinetic models are increasingly relevant in medical research. In systems biology, more than 10 years of experience with the development of standards and tools to construct and analyse kinetic models exists. This has supported the sharing of kinetic models, increased their reuse, and thereby has helped to reproduce and validate scientific results. Given this expertise, it seems natural to consider the application and development of standards and tools to meet the requirements of medical scientists. In this paper, we discuss challenges and opportunities for standards and tools from systems biology in medical research, and we suggest criteria for the safe use of simulations. We conclude that standards, tools and infrastructure need to be extended to ensure the quality, reliability and safety required when working with medical and patient data. This will foster the adaptation of modelling in the clinic, providing tools for improved diagnosis, prognosis and therapy.

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M3 - Conference paper

AN - SCOPUS:84992416411

VL - 1692

BT - Proceedings of the 7th Workshop on Ontologies and Data in Life Sciences, organized by the GI Workgroup Ontologies in Biomedicine and Life Sciences

PB - CEUR-WS

T2 - 7th Workshop on Ontologies and Data in Life Sciences, ODLS 2016

Y2 - 29 September 2016 through 30 September 2016

ER -

Challenges and opportunities for system biology standards and tools in medical research

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