FAIR Data Pipeline: provenance-driven data management for traceable scientific workflows

Mitchell, S. N. et al. (2022) FAIR Data Pipeline: provenance-driven data management for traceable scientific workflows. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 380(2233), 20210300. (doi: 10.1098/rsta.2021.0300) (PMID:35965468) (PMCID:PMC9376726)

Abstract

Modern epidemiological analyses to understand and combat the spread of disease depend critically on access to, and use of, data. Rapidly evolving data, such as data streams changing during a disease outbreak, are particularly challenging. Data management is further complicated by data being imprecisely identified when used. Public trust in policy decisions resulting from such analyses is easily damaged and is often low, with cynicism arising where claims of ‘following the science’ are made without accompanying evidence. Tracing the provenance of such decisions back through open software to primary data would clarify this evidence, enhancing the transparency of the decision-making process. Here, we demonstrate a Findable, Accessible, Interoperable and Reusable (FAIR) data pipeline. Although developed during the COVID-19 pandemic, it allows easy annotation of any data as they are consumed by analyses, or conversely traces the provenance of scientific outputs back through the analytical or modelling source code to primary data. Such a tool provides a mechanism for the public, and fellow scientists, to better assess scientific evidence by inspecting its provenance, while allowing scientists to support policymakers in openly justifying their decisions. We believe that such tools should be promoted for use across all areas of policy-facing research. This article is part of the theme issue ‘Technical challenges of modelling real-life epidemics and examples of overcoming these’.

• Item Type: Articles
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Mohr, Dr Sibylle and Bessell, Dr Paul and Archibald, Dr Blair and Harris, Miss Claire and Field, Mr Ryan and Reeve, Professor Richard and Brett, Mrs Alys and Mellor, Professor Dominic and Boden, Dr Lisa and Mitchell, Dr Sonia and Dundas, Professor Ruth and Enright, Dr Jessica and Matthews, Professor Louise and McMonagle, Ciaran and Turner, Dr Robert and Marion, Professor Glenn and McKendrick, Dr Iain
• Authors: Mitchell, S. N., Lahiff, A., Cummings, N., Hollocombe, J., Boskamp, B., Field, R., Reddyhoff, D., Zarębski, K., Wilson, A., Viola, B., Burke, M., Archibald, B., Bessell, P., Blackwell, R., Boden, L. A.,, Brett, A., Brett, S., Dundas, R., Enright, J., Gonzalez-Beltran, A., Harris, C., Hinder, I., Hughes, C. D., Knight, M., Mano, V., McMonagle, C., Mellor, D., Mohr, S., Marion, G., Matthews, L., McKendrick, I. J., Pooley, C. M., Porphyre, T., Reeves, A., Townsend, E., Turner, R., Walton, J., and Reeve, R.
• College/School: College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine; College of Medical Veterinary and Life Sciences > School of Health & Wellbeing > MRC/CSO SPHSU; College of Medical Veterinary and Life Sciences > School of Health & Wellbeing > Public Health; College of Science and Engineering > School of Computing Science
• Journal Name: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences
• Publisher: Royal Society
• ISSN: 1364-503X
• ISSN (Online): 1471-2962
• Published Online: 15 August 2022
• Copyright Holders: Copyright © 2022 The Authors
• First Published: First published in Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 380(2233): 20210300
• Publisher Policy: Reproduced under a Creative Commons License

Related URLs

• Research Data

Project Code	Award No	Project Name	Principal Investigator	Funder's Name	Funder Ref	Lead Dept
311856		Open Epidemiology for COVID-19: a transparent, traceable, open source pipeline for reproducible science	Richard Reeve	Science and Technology Facilities Council (STFC)	ST/V006126/1	Institute of Biodiversity, Animal Health and Comparative Medicine
190824		The BUG consortium Building Upon the Genome: using H. contortus genomic resources to develop novel interventions to control endemic GI parasites	Eileen Devaney	Biotechnology and Biological Sciences Research Council (BBSRC)	BB/M003949/1	Institute of Biodiversity, Animal Health and Comparative Medicine
302761		Tracking isometamidium resistance in livestock trypanaosomes	Michael Barrett	Biotechnology and Biological Sciences Research Council (BBSRC)	BB/S001034/1	SII - Parasitology
305944		Multilayer Algorithmics to Leverage Graph Structure	Kitty Meeks	Engineering and Physical Sciences Research Council (EPSRC)	EP/T004878/1	M&S - Statistics
304823002	1	Inequalities in health	Alastair Leyland	Medical Research Council (MRC)	MC_UU_00022/2	HW - MRC/CSO Social and Public Health Sciences Unit
307517		Landscape Decisions: Towards a new framework for using land assets programme	Richard Reeve	Natural Environment Research Council (NERC)	NE/T004193/1	M&S - Mathematics
309089		Simulating UK plant biodiversity under climate change to aid landscape decision making	Richard Reeve	Natural Environment Research Council (NERC)	NE/T010355/1	M&S - Mathematics
304823007	1	Inequalities in health	Alastair Leyland	Office of the Chief Scientific Adviser (CSO)	SPHSU17	HW - MRC/CSO Social and Public Health Sciences Unit