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Open data policy

Contents

  1. Minimum data requirements
  2. Submission of data
    • 2.1. Acknowledgement of data
    • 2.2. Data sharing
    • 2.3. Recommended depositories
  3. FAQs

1. Minimum data requirements

Microbial Genomics is a mandatory open data journal. Authors are required to provide access to all supporting data, which have either led to the conclusions drawn in their article, or to allow the procedure described in the article to be repeated.

We require authors to ensure that their datasets are either deposited in publicly available repositories (where available and appropriate) or presented in the main manuscript or additional supplementary material whenever possible.

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

If you have difficulty submitting large data files please contact the Editorial Office mgen@microbiologysociety.org.

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2. Submission of data

2.1 Acknowledgement of data

Authors are expected to provide a data availability statement in accordance with the journal’s Open Data Policy, and to detail relevant DOI(s) and/or accession numbers through the Data Summary section of the submission template. A Data Bibliography should be provided at the end of the article, in the following format: Last name1, Initial1 and Last name2, Initial2. Depository full name. Accession number or 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.

All DOIs and acccession numbers will be checked for validity prior to peer review, and all data will be reviewed for relevance as part of the peer review process.

Microbial Genomics supports 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 depository 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 http://opensource.org/licenses for further guidance.

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.

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2.2 Data sharing

Authors should make an informed decision about where to submit their data to ensure it is held in a relevant depository, which is credible and guarantees the long term archiving of such work. Data should be openly accessible under a relevant creative commons licence (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 recommend authors publish their data in established subject-specific depositories such as GenBank and EMBL-EBI and/or established general depositories such as Dryad. See our full list of recommendations.
  2. Where possible, authors are encouraged to submit their data to the Society’s publishing partner, figshare. figshare will provide each data file associated with an individual manuscript, with a citable DOI, and on acceptance 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. As the society has a relationship with figshare authors will not be charged hosting fees. If you would like to publish your data with figshare, the Microbiology Society is able to do this on your behalf. Please contact the journal team for further information before you submit your manuscript.
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2.3 Recommended depositories

Type of data
Suggested depositories
DNA and RNA sequences
Genbank; EMBL Nucleotide Sequence Database (ENA); NCBI Trace Archive; NCBI Sequence Read Archive (SRA)
Protein sequences
Uniprot, PRIDE
Linked genotype and phenotype data
dbGAP, The European Genome-phenome Archive (EGA)
Open source software
CRAN, SourceForge, Bioinformatics.Org, Open Bioinformatics Foundation (O|B|F), Google Code, Savannah, GitHub and the Codehaus
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3. 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 not essential to its understanding.

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

Microbial Genomics is a mandatory open data journal, 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. Delaying availability of this data to a later date during the submission process would delay the journal’s submission to publication times.

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

Microbial Genomics is a mandatory open data journal, and so not providing supporting data for personal or other reasons does not comply with the journal’s policies and may result in your paper being rejected.

If the statement ‘data available on request’ is provided, authors must also state the group or committee that should be contacted for such requests.

We recognise that for clinical data involving human hosts, ethical guidelines might preclude the release of certain metadata. Please state as such in the data availability statement.

For exceptional cases, or further guidance, please contact the Editorial Office (mgen@microbiologysociety.org).

Can I request an embargo period on supporting data?

Microbial Genomics does not accept requests for an embargo period on the publication and availability of supporting data and such requests do not comply with the journal’s policies and may result in your paper being rejected. For exceptional cases, please contact the Editorial Office (mgen@microbiologysociety.org).

Will supporting data be peer reviewed?

Some supporting data may be peer reviewed on occasion, however in most cases only checks for relevance of content and validity of DOI(s) and or accession number(s) will be performed.

Under what licence should supporting data be published?

This will depend on the open access policy of the depository you choose to submit your data, however the journal requests that you select a depository with a relevant creative commons licence (at the very least as open as CC-BY).


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