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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. FAQ

1. Minimum Data Requirements

Microbial Genomics (MGen) 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 paper, or to allow the procedure described in the paper to be repeated.

MGen will not accept papers 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@sgm.ac.uk.

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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 paper, 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 Accession 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.

If supplementary data is better suited to PDF format (e.g. a text document for reading), rather than being deposited in an external database, please provide this as an additional file during submission, and state this in the Data Summary box of the submission template. All other bulk data from high-throughput experiments should be deposited in structured formats and appropriate repositories - see below.

Microbial Genomics (MGen) supports the development of open source software and if new software or a new algorithm is central to a submitted paper, 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.

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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, SGM is able to do this on your behalf. Please contact our Digital Platform Manager for further information before you submit your manuscript.
  3. Supplementary material better suited to PDF format should be uploaded as an additional file during submission. This is recommended only for reading material, since content within PDF files are not as easily discoverable, nor can the data be downloaded in an editable format. Further instructions on submitting supplementary data with a submission.
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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. FAQ

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

Microbial Genomics (MGen) 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 don’t want to or can’t make supporting data available?
MGen is a mandatory open data journal, and so not providing supporting data for personal reasons or other 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 acknowledgements.

For exceptional cases, or further guidance, please contact the editorial office (mgen@sgm.ac.uk).

Can I request an embargo period on supporting data?

MGen 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@sgm.ac.uk).

Will supplementary data be peer reviewed?

Some supplementary 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 supplementary 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).

Can I submit my supplementary data to the journal directly as an additional file?
Authors are permitted to upload supplementary data as an additional file; however we discourage this unless the supporting data is a text file for reading purposes only. Any such files will be published as provided in PDF format.

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