Open Data Policy

ASM Author Center / Ethics Resources and Policies

ASM thanks Microbial Genomics, published by the Society for General Microbiology, and PLOS for granting permission to adapt their open data policies.

Data Availability

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 any ASM Journal 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, except where noted below. Furthermore, data must be made available, upon request, for peer review.

Data must be provided earlier in the process, during submission and review, by Microbiology Resource Announcements (MRA) authors, because reviewers and editors need access to the data that underlie the conclusions reported in MRA manuscripts.

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 should consider a repository that offers 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.

Authors whose data does not already reside in a repository may provide a file(s) containing relevant data at the time of submission; in this case, authors should clearly indicate whether the file is intended for publication as supplemental material. An alternative is for authors to provide data for peer review as “Miscellaneous Files Not for Publication” at the time of submission.

Data Availability Paragraph

In a "Data availability" paragraph placed at the end of the Materials and Methods section of their submitted full-length article (or at the end of the text for shorter article types: e.g., announcements, short form papers, etc.), authors should include the following: data description, name(s) of the repositories, and digital object identifiers (DOIs) or accession numbers.

Acceptable Data-Sharing Methods

Public Repositories

ASM recommends that authors 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). For the case of amplicon, meta-'omic, and genomic nucleic acid data, raw sequence reads should be made available in the Sequence Read Archive. Authors are encouraged to comply with community metadata standards, such as the "Minimal Information about any (X) Sequence" (MIxS) checklist, when submitting to GenBank, SRA, ENA, or DDBJ.

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. Authors may 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.

Updated lists of field-specific repositories are provided by re3data.org, in collaboration with DataCite. A list of public data repositories is available on the ASM Journals’ Ethics Portal.

Data as Supplemental Material or Available on Request

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.

If an author does not make the data publicly available and instead states “data available on request,” an explanation must be included in the comment box within the Author Certification under the ASM Data Policy compliance question in the eJP submission system. ASM will consider explanations on a case-by-case basis.

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. Delays on data availability from clinical studies may be considered acceptable with appropriate justification, but in all cases, data must be made available 6 months after publication. 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.

Studies of commercial diagnostic test kits or systems may include limited materials and methods if the following criteria are met. To allow others to reproduce or build upon the work described, the kit or system must be sold or provided with complete and detailed instructions for use. The manuscript must include a description of the technology with enough detail for readers to assess the validity of the results. If the kit or system is an early (“beta”) version, it must be clear how it differs from the final version of the test. If these criteria are met, details such as primer or probe sequences may be omitted on a case-by-case basis at the discretion of the Editor. If such information is omitted, this should be stated in the author cover letter, with an explanation of why the omission is appropriate and how these criteria have been fulfilled.