Requirements for the formal representation of pathophysiology mechanisms by clinicians

Article


de Bono, B., Helvensteijn, M., Kokash, N., Martorelli, I., Sarwar, D., Islam, S., Grenon, P. and Hunter, P. 2016. Requirements for the formal representation of pathophysiology mechanisms by clinicians. Interface Focus. 6 (2), p. 20150075.
Authorsde Bono, B., Helvensteijn, M., Kokash, N., Martorelli, I., Sarwar, D., Islam, S., Grenon, P. and Hunter, P.
Abstract

Knowledge of multiscale mechanisms in pathophysiology is the bedrock of clinical practice. If quantitative methods, predicting patient-specific behaviour of these pathophysiology mechanisms, are to be brought to bear on clinical decision-making, the Human Physiome community and Clinical community must share a common computational blueprint for pathophysiology mechanisms. A number of obstacles stand in the way of this sharing—not least the technical and operational challenges that must be overcome to ensure that (i) the explicit biological meanings of the Physiome's quantitative methods to represent mechanisms are open to articulation, verification and study by clinicians, and that (ii) clinicians are given the tools and training to explicitly express disease manifestations in direct contribution to modelling. To this end, the Physiome and Clinical communities must co-develop a common computational toolkit, based on this blueprint, to bridge the representation of knowledge of pathophysiology mechanisms (a) that is implicitly depicted in electronic health records and the literature, with (b) that found in mathematical models explicitly describing mechanisms. In particular, this paper makes use of a step-wise description of a specific disease mechanism as a means to elicit the requirements of representing pathophysiological meaning explicitly. The computational blueprint developed from these requirements addresses the Clinical community goals to (i) organize and manage healthcare resources in terms of relevant disease-related knowledge of mechanisms and (ii) train the next generation of physicians in the application of quantitative methods relevant to their research and practice.

JournalInterface Focus
Journal citation6 (2), p. 20150075
ISSN2042-8898
2042-8901
Year2016
PublisherThe Royal Society
Accepted author manuscript
Digital Object Identifier (DOI)doi:10.1098/rsfs.2015.0099
Web address (URL)https://doi.org/10.1098/rsfs.2015.0099
Publication dates
Print19 Feb 2016
Publication process dates
Deposited02 Mar 2017
FunderInnovative Medicines Initiative (IMI)
Innovative Medicines Initiative (IMI)
European Union FP7
Innovative Medicines Initiative
Innovative Medicines Initiative
Seventh Framework Programme
Copyright information© 2016 The Authors. Published by the Royal Society. All rights reserved.
Permalink -

https://repository.uel.ac.uk/item/8524z

  • 8
    total views
  • 56
    total downloads
  • 2
    views this month
  • 2
    downloads this month

Related outputs

Functional Connectivity Evaluation for Infant EEG Signals based on Artificial Neural Network
Sharif, M., Naeem, U., Islam, S. and Karami, A. 2018. Functional Connectivity Evaluation for Infant EEG Signals based on Artificial Neural Network. in: Arai, Kohei, Kapoor, Supriya and Bhatia, Rahul (ed.) Intelligent Systems and Applications: Proceedings of the 2018 Intelligent Systems Conference (IntelliSys) Volume 2 Springer, Cham.
The Application of a Semantic-Based Process Mining Framework on a Learning Process Domain
Okoye, Kingsley, Islam, S., Naeem, U., Sharif, M., Azam, Muhammad Awais and Karami, A. 2018. The Application of a Semantic-Based Process Mining Framework on a Learning Process Domain. in: Arai, Kohei, Kapoor, Supriya and Bhatia, Rahul (ed.) Intelligent Systems and Applications: Proceedings of the 2018 Intelligent Systems Conference (IntelliSys) Volume 1 Springer, Cham.
Authentication of Smartphone Users Based on Activity Recognition and Mobile Sensing
Ehatisham-ul-Haq, Muhammad, Azam, Muhammad Awais, Loo, Jonathan, Shuang, Kai, Islam, S., Naeem, U. and Amin, Yasar 2017. Authentication of Smartphone Users Based on Activity Recognition and Mobile Sensing. Sensors. 17 (9), p. 2043.
Taskification – Gamification of Tasks
Naeem, U., Islam, S., Sharif, M., Sudakov, Sergey and Azam, Awais 2017. Taskification – Gamification of Tasks. in: Proceedings of the 2017 ACM International Joint Conference on Pervasive and Ubiquitous Computing and Proceedings of the 2017 ACM International Symposium on Wearable Computers ACM. pp. 631-634
SignalSense - Towards Quality Service
Islam, S., Sharif, M., Naeem, U. and Geehan, James 2017. SignalSense - Towards Quality Service. in: Proceedings of the 2017 ACM International Joint Conference on Pervasive and Ubiquitous Computing and Proceedings of the 2017 ACM International Symposium on Wearable Computers ACM. pp. 627-630
CrimeSafe - Helping you stay safe
Islam, S., Naeem, U., Sharif, M. and Dovnarovic, Arnold 2017. CrimeSafe - Helping you stay safe. in: Proceedings of the 2017 ACM International Joint Conference on Pervasive and Ubiquitous Computing and Proceedings of the 2017 ACM International Symposium on Wearable Computers ACM. pp. 642-645
gUML: Reasoning about Energy at Design Time by Extending UML Deployment Diagrams with Data Centre Contextual Information
Jebraeil, Nigar, Noureddine, A., Doyle, J., Islam, S. and Bashroush, R. 2017. gUML: Reasoning about Energy at Design Time by Extending UML Deployment Diagrams with Data Centre Contextual Information. in: 2017 IEEE World Congress on Services (SERVICES) Institute of Electrical and Electronics Engineers (IEEE). pp. In Press
Cloud Strife: Expanding the Horizons of Cloud Gaming Services
Doyle, J., Islam, S., Bashroush, R. and O'Mahony, Donal 2017. Cloud Strife: Expanding the Horizons of Cloud Gaming Services. in: 2017 IEEE World Congress on Services (SERVICES) Institute of Electrical and Electronics Engineers (IEEE).
Using semantic-based approach to manage perspectives of process mining: Application on improving learning process domain data
Kingsley, Okoye, Tawil, Abdel-Rahman H., Naeem, U., Islam, S. and Lamine, Elyes 2017. Using semantic-based approach to manage perspectives of process mining: Application on improving learning process domain data. in: 2016 IEEE International Conference on Big Data (Big Data) IEEE. pp. 3529-3538
Dependence Cluster Visualization
Islam, S., Krinke, Jens and Binkley, David 2010. Dependence Cluster Visualization. in: Proceedings of the 5th international symposium on Software visualization New York, NY, USA ACM. pp. 93-102
Less is more: Temporal fault predictive performance over multiple Hadoop releases
Harman, Mark, Islam, S., Jia, Yue, Minku, Leandro L., Sarro, Federica and Srivisut, Komsan 2014. Less is more: Temporal fault predictive performance over multiple Hadoop releases. in: Goues, Claire Le and Yoo, Shin (ed.) Search-Based Software Engineering Springer International Publishing.
ORBS: Language-Independent Program Slicing
Binkley, David, Gold, Nicolas, Harman, Mark, Islam, S., Krinke, Jens and Yoo, Shin 2014. ORBS: Language-Independent Program Slicing. in: Proceedings of the 22nd ACM SIGSOFT International Symposium on Foundations of Software Engineering New York, NY, USA ACM. pp. 109-120
Jolinar: Analysing the Energy Footprint of Software Applications (demo)
Noureddine, A., Islam, S. and Bashroush, R. 2016. Jolinar: Analysing the Energy Footprint of Software Applications (demo). in: Proceedings of the 25th International Symposium on Software Testing and Analysis New York, NY, USA ACM. pp. 445-448
Semantic-Based Model Analysis Towards Enhancing Information Values of Process Mining: Case Study of Learning Process Domain
Okoye, Kingsley, Tawila, Abdel-Rahman H., Naeem, U., Islam, S. and Lamine, Elyes 2017. Semantic-Based Model Analysis Towards Enhancing Information Values of Process Mining: Case Study of Learning Process Domain. in: Abraham, Ajith, Cherukuri, Aswani Kumar, Madureira, Ana Maria and Muda, Azah Kamilah (ed.) Proceedings of the Eighth International Conference on Soft Computing and Pattern Recognition (SoCPaR 2016) Springer, Cham.
Assessing the impact of global variables on program dependence and dependence clusters
Binkley, David, Harman, Mark, Hassoun, Youssef, Islam, S. and Li, Zheng 2009. Assessing the impact of global variables on program dependence and dependence clusters. Journal of Systems and Software. 83 (1), pp. 96-107.
An empirical study on dependence clusters for effort-aware fault-proneness prediction
Yang, Yibiao, Harman, Mark, Krinke, Jens, Islam, S., Binkley, David, Zhou, Yuming and Xu, Baowen 2016. An empirical study on dependence clusters for effort-aware fault-proneness prediction. in: Lo, David, Apel, Sven and Khurshid, Sarfraz (ed.) ASE’16 Proceedings of the 31st IEEE/ACM International Conference on Automated Software Engineering IEEE/ACM. pp. 296-307
Towards Cloud Security Monitoring: A Case Study
Ismail, Umar Mukhtar, Islam, S. and Islam, S. 2016. Towards Cloud Security Monitoring: A Case Study. in: 2016 Cybersecurity and Cyberforensics Conference (CCC) IEEE.
Measuring energy footprint of software features
Islam, S., Noureddine, A. and Bashroush, Rabih 2016. Measuring energy footprint of software features. in: 2016 IEEE 24th International Conference on Program Comprehension (ICPC) IEEE.
PORBS: A parallel observation-based slicer
Islam, S. and Binkley, David 2016. PORBS: A parallel observation-based slicer. in: 2016 IEEE 24th International Conference on Program Comprehension (ICPC) IEEE.
Efficient Identification of Linchpin Vertices in Dependence Clusters
Binkley, David, Gold, Nicolas, Harman, Mark, Islam, S., Krinke, Jens and Li, Zheng 2013. Efficient Identification of Linchpin Vertices in Dependence Clusters. ACM Transactions on Programming Languages and Systems. 35 (2), pp. 1-35.
ORBS and the limits of static slicing
Binkley, David, Gold, Nicolas, Harman, Mark, Islam, S., Krinke, Jens and Yoo, Shin 2015. ORBS and the limits of static slicing. in: 2015 IEEE 15th International Working Conference on Source Code Analysis and Manipulation (SCAM) IEEE. pp. 1-10
Coherent clusters in source code
Islam, S., Krinke, Jens, Binkley, David and Harman, Mark 2013. Coherent clusters in source code. Journal of Systems and Software. 88, pp. 1-24.
Uncovering Dependence Clusters and Linchpin Functions
Binkley, David, Beszédes, Árpád, Islam, S., Jász, Judit and Vancsics, Béla 2015. Uncovering Dependence Clusters and Linchpin Functions. in: 2015 IEEE 31st International Conference on Software Maintenance and Evolution (ICSME) IEEE. pp. 141-150