Open Data policy

• Open Data policy

• Minimum data requirements

• Choosing your repository

• Recommended repositories

• Acknowledgement of data in your article

• FAQs

The Microbiology Society supports Open Data and the FAIR principles and strongly encourages all authors, regardless of policy on the journal or platform, to make their supporting data open by depositing it with recognised and publicly archiving repositories such as Figshare, Dryad, Zenodo and CodeOcean.
 
We encourage authors to employ Open Data practices, to ensure that researchers can reuse and reanalyse the data – in an effort to increase reproducibility in the scientific literature, and maintain transparency wherever possible. It ensures authors get credit for conducting the research and collecting the data first, and can generate further citations as the datasets are iterated upon in future work. To read how both researchers and science as a whole benefit from Open Data practices, read our Microbe Post blog.

We have partnered with Figshare to support our authors in making their research as open as possible. If you would like to deposit your data in our Figshare account, please contact the Editorial Office using the relevant journal email address and they will assist you.

Open Data policy

Microbial Genomics and Access Microbiology have mandatory Open Data policies. This means that authors are required to deposit and provide access to all generated and supporting data, code or software, which have led to the conclusions drawn in their article and allow the procedure described in the article to be repeated. 

We require authors to either deposit their supporting data in publicly available repositories (where available and appropriate) or present them in the main manuscript or additional supplementary material whenever possible. All DOIs and accession numbers will be checked for validity by the Editorial Office, and all data will be reviewed for relevance as part of the peer review process.

Microbial Genomics: all sequencing data must be deposited and be publicly available at submission, however all other supporting data can be made privately available at point of submission for peer review, and then must be made publicly available at acceptance.

Access Microbiology: owing to the preprint stage of the platform, all supporting data must be deposited and be publicly available at time of submission. 

In studies with human subjects, underlying data should be made available where possible (without compromising participant privacy or legal requirements), including the minimum data or reference to work required to reproduce the results presented in the associated article. All files generated by your research constitute relevant data. These may be raw or processed data. Examples include, but are not limited to:

• Individual-level deidentified patient data. Please exclude direct identifiers such as patient IDs, names, identifying images and videos; ensure there are 2 or less indirect identifiers such as gender, age, location of treatment, rare disease and socioeconomic data.
• Survey results
• Interview transcripts
• Statistical code
• Code
• Images
• Videos
• Spreadsheets
• Audio files
• Text files
• Imaging and scan files

Microbial Genomics and Access Microbiology will not accept articles that do not provide supporting data for personal reasons or that request an embargo period.

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Minimum data requirements

Sequences

Microbial Genomics, Access Microbiology and International Journal of Systematic and Evolutionary Microbiology require that all sequence data be deposited and made publicly available prior to submission. This is to ensure longevity of the data and to maximise it re-use.

Articles reporting new sequence data must include an accession number from one of the recognised public databases (GenBank, EMBL, DDBJ or PIR) and you must adhere to the relevant deposition criteria for the database. Individual accessions should be provided for each sequence (not simply the BioProject accession), and it should be clear from the manuscript how the strain identifiers used in the paper link to the individual BioSample accessions in the public database. Raw sequence reads (fastq files) should be deposited, not just assembled genome sequences, as assemblies are an inference from the raw data. Where assemblies are analysed in the paper, assemblies should also be deposited so that the analyses described in the manuscript can be reproduced. 

MLST analyses

If your article reports on MLST analyses, the MLST gene sequence data for all samples presented in the article must be available.

Insertion sequences

If your article reports on insertion sequences, whether stand-alone or as part of larger sequencing projects, you should deposit the relevant information in the ISfinder Database and provide the attribution number as part of your submitted article.

Microarray and other genome-wide studies

Data from microarray gene expression studies must comply with the MIAME guidelines. If your conclusions explicitly or implicitly depend on genome-wide profiling you should deposit the relevant complete data sets in a public online database such as GEO before submission, with password protection if appropriate, and provide the accession number and password with their submitted article.

Ongoing sequencing projects

If you are making use of data from ongoing sequencing projects, you must follow the guidelines set by the project and give appropriate acknowledgement of the data source. You should show evidence that you have discussed your findings with the scientists responsible for the sequencing programme and that the organisation has approved what is being submitted.

Third-party data

Genomic data may have restrictions imposed on use in third-party publications even if the data is available on a public repository. If you are using sequence data from public repositories, you should adhere to the principles on fair use laid out in the Fort Lauderdale and Toronto agreements; and for pathogen sequence data, the WHO Code of Conduct for open and timely sharing of pathogen genetic sequence data during outbreaks of infectious disease. This policy does not preclude analyses of aggregated public data, however detailed analyses of data from individual unpublished sources should adhere to fair use principles. The origin of third-party data should be clearly documented and appropriate credit given via citations or acknowledgements.

Software

Microbial Genomics and Access Microbiology support the development of open-source software and if new software or a new algorithm is central to a submitted article, the authors must deposit the associated source code, documentation for running and installing software, and a test dataset with control parameter settings. Authors are requested to select a repository that has been in existence for a number of years and already hosts a number of such projects, for example: CRAN, SourceForge, Bioinformatics.Org, Open Bioinformatics Foundation (O|B|F), Google Code, Savannah, GitHub and the Codehaus. Please refer to opensource.org/licenses for further guidance. If authors wish to submit a Software Article, please refer to the Article Types page for more information on what should be included. 

Microbial Genomics has partnered with Microreact, a free data visualisation and sharing platform that allows scientists and health professionals worldwide to better collaborate to understand disease outbreaks. The journal is encouraging authors to upload their data files to Microreact, which can then provide interactive querying of the data via trees, maps, timelines and tables, and will be published in Microbial Genomics via a permanent web link. 

If you have difficulty submitting large data files please contact the Editorial Office at [email protected] or [email protected].

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Choosing your repository

Authors should make an informed decision about where to submit their data to ensure it is held in a relevant repository, which is credible and guarantees the long-term archiving of such work. Data should be openly accessible under a relevant Creative Commons license (at the very least CC-BY). Authors are requested to comply with field-specific standards for the preparation and reporting of data.

Our recommendations:

1. We ask authors to publish their sequencing data in established subject-specific repositories such as GenBank and EMBL-EBI. See our full list of recommendations.
   
2. Where possible, authors are encouraged to submit their non-sequencing, supporting data to the Society’s publishing partner, Figshare. The deposited data associated with an individual manuscript is assigned a citable DOI, and the supporting data will be viewable on the Figshare website with a link to the published paper, and vice versa. Additionally, the data will also be hosted on the journal’s Figshare portal, allowing for greater discovery of content. Authors will not be charged hosting fees. If you would like to publish your data with Figshare please contact the Editorial Office who will assist you.
   1. We recommend authors, where possible, to include the full suite of gels and blots in their supporting data, and in some cases Editors may ask for these to be included for a more thorough evaluation of the study design.

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Recommended repositories

The following are recognised repositories, each specialising in a different form or structure of data. Please see the individual guidelines for each repository for guidance on how to submit and structure your data and metadata.  

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Acknowledgment of data in your article

Authors should provide a ‘Data Summary’ section of the manuscript (see submission template as an example) that describes any data, software or code that has either been generated in the research or that has been previously published and reused in the research. Authors should include the DOI(s) and/or accession numbers. Where possible, this should also be included as a reference at the end of the article, in the following format: 

Author name(s). Title or description of data. Repository name. Accession number or full, hyperlinked DOI. (YYYY).

Where a large project includes multiple samples, accession number(s) and/or DOI(s) must be provided for each individual sample such that the analyses can be reproduced. 

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FAQs

What is the difference between supplementary material and supporting data?

Supplementary material is information integral to a full understanding of the article whereas supporting data provides additional, relevant, and useful expansion of the article, but is not essential to its understanding.

Can I submit supporting data at revision stage or following acceptance?

Microbial Genomics and Access Microbiology have mandatory Open Data policies and so availability and access to supporting data is a prerequisite of initial submission. Checks on supporting data, including relevance and validity of links are performed prior to peer review. 

What if I do not want to or cannot make supporting data available? 

Microbial Genomics and Access Microbiology have mandatory Open Data policies, and so not providing supporting data for personal or other reasons does not comply with this policy and may result in your paper being rejected. 

We recognise that for clinical data involving human hosts, ethical guidelines might preclude the release of certain metadata. Additionally, patented and proprietary data may also have limits imposed on public availability. Please state as such in the Data Summary section of the article, and work with your institution or organisation to ensure reviewers at least can access the underlying data. We can provide support to deposit data privately, in circumstances that warrant it.

For exceptional cases, or further guidance on private deposition of data, please contact the Editorial Office.

Can I request an embargo period on supporting data? 

Microbial Genomics and Access Microbiology do not accept requests for an embargo period on the publication of supporting data, such requests do not comply with the Open Data policy. For exceptional cases, please contact the Editorial Office ([email protected] or [email protected]).

For Microbial Genomics, all sequencing data must be deposited and publicly available at submission, however all other supporting data can be made privately available for peer review and then must be made available at acceptance.

For Access Microbiology, owing to the preprint stage of the platform, will require all supporting data to be publicly available at time of submission.

Will supporting data be peer reviewed? 

Reviewers are expected to review all supplementary and supporting materials related to an article. 

Under what license should supporting data be published?

This will depend on the Open Access policy of the repository you choose to submit your data, however we request that you select a repository with a relevant Creative Commons licence (at the very least as open as CC-BY).

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