Scientific advances are predicated upon the principle that experiments and conclusions drawn from published information can be repeated and further advanced by others. Therefore, a condition of publication in mSystems® is that authors make data fully available, without restriction, except in rare circumstances.
The minimum data set for which authors are required to provide access includes all data, metadata, and methods used to reach the conclusions in the submitted paper and any additional data required to replicate the study findings. New software and/or algorithms essential to the conclusions of the submitted manuscript are included under this data availability policy. Acceptable data-sharing methods are provided below.
Should restrictions to data access become apparent, the matter will be referred to the journal's Editor in Chief and ethics panel for consideration and may result in the rejection of a submitted manuscript, issuance of a correction or retraction, and/or notification of the authors' funding institution.
Data Availability and Peer Review
Data availability will be confirmed prior to publication and must be provided during the modification stage, if not before. Furthermore, data must be made available, upon request, for peer review. The preferred method for sharing is through deposition of the data in a public repository. Should authors have concerns about making their data public prior to publication, they may wish to consider a repository with the option for confidential hosting of data with anonymous access available to peer reviewers. While these repositories coordinate the public release of the data with the publication date of the manuscript, it is the authors' responsibility to communicate with the repository to ensure public release concurrent with online publication of the final article. An alternative is for authors to provide data for peer review as Supplemental Material Not for Publication at the time of submission.
Data Availability Paragraph
Authors should provide the following in a Data Availability paragraph at the end of the materials and methods section of their submitted manuscript: data description, name(s) of the repositories, and digital object identifiers (DOIs) or accession numbers. For some public repositories, the DOIs or accession numbers are not provided until the manuscript has been accepted; this should be noted in the cover letter. In these cases, authors are responsible for providing the DOIs or accession numbers at the proof stage.
Acceptable Data-Sharing Methods
We recommend that you make the data available for sharing through a suitable public repository, examples of which are mentioned below. ASM encourages authors to select the repository most appropriate for their research. While ASM does not dictate repository selection, authors are expected to comply with field-specific standards. Submission to a field-endorsed public repository is mandated for some data sets. Examples, with suitable repositories, include: nucleotide and amino acid sequences [GenBank, EMBL Nucleotide Sequence Data Base (ENA), DNA DataBank of Japan (DDBJ)]; microarray, next-generation sequencing, and other high-throughput functional genomics data [Gene Expression Omnibus (GEO), ArrayExpress, Center for Information Biology gene EXpression database (CIBEX)]; macromolecular structures as determined by X-ray crystallography or cryo-electron microscopy [Worldwide Protein Data Bank (wwPDB)]; and scientific names of new fungi, key nomenclature, and descriptive material (MycoBank Database). Authors are encouraged to comply with community metadata standards, such as the "Minimal Information about any (X) Sequence" (MIxS) checklist, when submitting to GenBank, ENA, or DDBJ.
Updated lists of field-specific repositories are provided by re3data.org, in collaboration with DataCite. Microbiology-related databases can be found in this minireview by Igor Zhulin, published in the Journal of Bacteriology.
For new software and/or computer algorithms, authors must deposit the associated source code, documentation for running and installing software, and a test data set with control parameter settings in an appropriate repository. Such repositories should have a proven track record for hosting similar projects, preferably for a number of years. Examples include: CRAN, SourceForge, Bioinformatics.org, and GitHub. Please refer to http://opensource.org/licenses for further guidance.
Unstructured repositories, such as Dryad and figshare, are suitable alternatives for the deposition of large data sets if no structured public repositories exist. Regardless of the field, authors are encouraged to select credible, trustworthy digital repositories with guarantees of long-term archiving of data. If the selected repositories have licensing policies, the policies should be no more restrictive than the Creative Commons Attribution (CC BY) license.
Data as Supplemental Material
Deposition of the data in a public repository is preferred. Alternatively, authors may upload data, particularly small data sets, as Supplemental Material at submission. This data will be made publicly available as part of the article upon publication. Authors should make every effort to make this information extractable in order to maximize accessibility and reusability. For example, tabulated data should be provided in spreadsheet, rather than PDF, format.
Exceptions to Data-Sharing Policy
Compliance with local and/or US government laws and regulations may prohibit or limit the sharing of data, especially for studies involving human subjects. Under no circumstances should adherence to ASM data policy breach patient confidentiality. Any such restrictions should be clearly described in the cover letter and will be evaluated by the editors on a case-by-case basis.
For controlled access to data (e.g., clinical trials), "data available on request" should be included in the materials and methods along with the group name, contact information to which requests should be submitted, and a specific explanation for the restrictions on public data deposition. It is not acceptable for the authors to be the sole named individuals responsible for ensuring data access. Similarly, if the conclusions of the submitted manuscript are based on primary data originally generated by someone other than the authors, it may be necessary to refer interested readers to a third party. For third-party data, please include "data available from (named source and contact information)"; full citation, if applicable; and the specific reason for the restriction on public deposition. Authors are responsible for providing the data to the editors and peer reviewers and for ensuring that data will be available from the data owner after publication.
Personal interests, including patents or potential future publications, are not acceptable reasons for restricting access to data. Furthermore, ASM will not consider manuscripts from which the conclusions depend solely on the analysis of proprietary data (i.e., data owned by commercial interests or copyrighted data), unless the authors include an analysis of public data that validates the conclusions of the manuscript.