Open research: it’s more than open access

Issue: Metabolism, Health and Disease

07 May 2019 article

In the last issue of Microbiology Today we wrote about open access (OA), copyright, and author rights. In this article we discuss the wider world of open research, also known as open science and open scholarship.

Open research has developed over the last twenty years in response to a combination of factors, including the open access movement, funders’ need to map the returns on their research investments, concerns about research reproducibility and research waste, and a desire to properly recognise researchers for all their efforts rather than simply their published output. It covers many aspects of research, from laboratory notebooks and data, to collaboration through scholarly social networks, to citizen science.

Much like open access, open research carries with it benefits for the whole scholarly community. Open methods and open data, in particular, can reduce research waste and aid reproducibility by clearly identifying the precise protocols used in a given lab, and the results associated with that protocol. For individual researchers the increased visibility and engagement associated with open methods, data and code can lead to new collaborations and drive the creation of new research questions. Many organisations and funders are now giving researchers credit for their open research objects, as well as journal articles.

FAIR principles for open research

One of the biggest challenges in open research is good data management, which facilitates discovery and knowledge exchange for both humans and machines. Standing for ‘Findable’, ‘Accessible’, ‘Interoperable’ and ‘Reusable’, the FAIR principles were launched in 2016 in response to this challenge. Many people assume FAIR applies only to data, but the same principles guide many other aspects of open research, such as open protocols and methodologies, and open source code.

Rich metadata describing research outputs is key in making them ‘findable’: including items such as keywords, author names, funding data and an abstract will make sure that search engines and other machines will be able to find the research object. ‘Accessibility’ relies on standard protocols for retrieving research objects – from a researcher’s perspective the key to accessibility is to use a compliant repository or platform, such as those described below. For research outputs to be ‘interoperable’ they need to use community agreed standards and contain links to related information using persistent identifiers like digital object identifiers (DOIs), which allow machines to navigate easily between research objects. Lastly, clear usage licences (such as the Creative Commons licence described in the February issue of Microbiology Today: help researchers and machines understand the ways in which they can ‘reuse’ the research objects.

Making your research open

The Society’s journals work with several FAIR-compliant open research initiatives* and we encourage you to make use of them. They all offer free services, and every research object in these initiatives has a DOI, so they are easily citable and are usually counted in research evaluation exercises.

First up is, a browser-based tool for open methods which meets the FAIR principles. We all know that optimising protocols is time-consuming and that the information is often locked in lab notebooks. One of the things we love about is that researchers can follow experiments step-by-step in real time and record their changes, keeping an accurate record of their method and making it easy to write up for publication.

We also work with data repositories such as figshare, Dryad, and Zenodo, as well as Microreact for genomic epidemiology. These services allow researchers to upload large data sets; being FAIR, these are vastly superior to the older ‘supplementary data files’ associated with journal articles.

We recommend CodeOcean for sharing code. Unlike most other services, CodeOcean gives researchers the ability to execute published code without installing anything on their computers – you can even change parameters, modify the code and upload data to see how results change, without needing specialist software.

*We do not receive revenue from these initiatives and are promoting them only because our team truly believes they are useful tools for our members.

Publishing for the community


Journal of General Virology

Journal of Medical Microbiology

Microbial Genomics

International Journal of Systematic and Evolutionary Microbiology

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