Availability of Materials and Data

Ethics / Ethical Guidelines

Availability of data and materials By publishing in the journal, the authors agree that, subject to requirements or limitations imposed by local and/or U.S. Government laws and regulations, any materials and data that are reasonably requested by others are available from a publicly accessible collection or will be made available in a timely fashion, at reasonable cost, and in limited quantities to members of the scientific community for noncommercial purposes. Newly determined nucleotide and amino acid sequences and/or structural determinations must be deposited into the appropriate data-specific repository. New scientific names of fungi along with key nomenclatural and descriptive material must be deposited in MycoBank. These new accession numbers must be included in the manuscript no later than the modification stage of the review process. It is expected that this data will be released to the public no later than the publication (online posting) date of the accepted manuscript. Similarly, the authors agree to make available computer programs and/or code, originating in the authors’ laboratory, that is the only means of confirming the conclusions reported in the article but that is not available commercially. The program(s) and suitable documentation regarding its (their) use may be provided by any of the following means: (i) as a program transmitted via the Internet, (ii) as an Internet server-based tool, or (iii) as a compiled or assembled form on a suitable medium. The authors guarantee that they have the authority to comply with this policy either directly or by means of material transfer agreements through the owner. ASM asks authors to assert this in a “Data availability” paragraph, which should appear at the end of the Materials and Methods section (or at the end of the text) of their submitted manuscript.

Accessibility of mass spectrometry data. Proteomics, metabolomics, or imaging mass spectrometry and related data must be accessible through hyperlinks so that reviewers can rapidly assess accessibility. Currently accepted data repositories are MassIVE, which is a part of ProteomeXchange, at http://massive.ucsd.edu/ProteoSAFe/static/massive.jsp (proteomics), GNPS at http://gnps.ucsd.edu (metabolomics, natural products, and imaging mass spectrometry data), MetaboLights at https://www.ebi.ac.uk/metabolights/, and OpenMSI at https://openmsi.nersc.gov/openmsi/client/ (imaging mass spectrometry data). For reference spectra, we encourage deposition into GNPS at http://gnps.ucsd.edu, European MassBank at https://massbank.eu/MassBank/, or MassBank of North America at http://mona.fiehnlab.ucdavis.edu. Other available data repositories may be acceptable, and we encourage database repository administrators or authors of papers to contact the journal for additional appropriate databases that should be listed. Only databases that make all the data accessible via hyperlinks and permit their download, including reference libraries, are considered acceptable repositories.

Data citation statement. To promote reproducibility, ASM expects researchers to identify and cite data sets and/or code used in their experiments and studies. These may be large or complex data sets that can include, but are not limited to, data from microarray, genomic, structural, proteomic, or video imaging analyses. Authors should cite both the data set repository and the published article in which the data set and/or code was originally described. Citations of data should be included in the reference list with persistent unique identifiers (e.g., active DOIs, accession numbers, etc.). If computer code or software was created to generate results or interpret data, then a statement to that effect should be included in the “Data availability” paragraph. In cases where the software is publicly available (e.g., FigTree to generate phylogenetic trees), the URL of the software informational page should be provided. It is preferred that authors use established, publicly available data type-specific repositories. If there is no appropriate repository available, general publicly available repositories should be used (e.g., Dryad, figshare, etc.). Below is an overview of the elements that should appear in a data citation, as well as examples of complete data citations. Please note that similar information is available in the References section of the Instructions to Authors of each journal.

Culture deposition. ASM expects authors to deposit important strains in publicly accessible culture collections and to refer to the collections and strain numbers in the text. Since the authenticity of subcultures of culture collection specimens that are distributed by individuals cannot be ensured, authors should indicate laboratory strain designations and donor sources as well as original culture collection identification numbers.

Authentication of cell lines. Cell line misidentification or contamination can adversely impact the validity of research findings. Authors should describe the source along with the date and method used for authentication of any cell lines used in manuscripts. Cell lines used less than 6 months after receipt from a cell bank that performs authentication do not require reauthentication, but the source and method of authentication should be reported in the Materials and Methods section of a manuscript.

The components of a complete data citation include the following:

  • Responsible party (senior author, collector, agency),
  • Publication year,
  • Complete name of a data set, including the name of the database or repository and its URL, or the name of the analysis software (if appropriate), including the version and project,
  • Publisher (if appropriate), and
  • Persistent unique identifier(s) (e.g., URL[s] or accession number[s]).

The following templates may be helpful.

Author. Year. Description of study topic. Retrieved from Database URL (accession no. ••••••). {Unpublished raw data.}
Author. Year. Description or title of software (version). Repository URL. Retrieved day month year. {Software or code.}

Examples follow.

Christian SL, McDonough J, Liu C-Y, Shaikh S, Vlamakis V, Badner JA, Chakravarti A, Gershon ES. 2002. Data from “An evaluation of the assembly of an approximately 15-Mb region on human chromosome 13q32-q33 linked to bipolar disorder and schizophrenia.” GenBank https://www.ncbi.nlm.nih.gov/nuccore/AF339794 (accession no. AF339794). {Accession number.}
Sun Z. 2013. Reprocessed: in-depth membrane proteomic study of breast cancer tissues. ProteomeXchange http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=RPXD000665 (accession number requested). {Unassigned accession number.}
Hogle S. 2015. Supplemental material for Hogle et al. 2015 mBio. figshare https://doi.org/10.6084/m9.figshare.1533034.v1. Retrieved 16 March 2017. {Code and/or software.}
Nesbitt HK, Moore JW. 2016. Data from “Species and population diversity in Pacific salmon fisheries underpin indigenous food security.” Dryad Digital Repository https://doi.org/10.5061/dryad.ng8pf. {Data set in repository.}

Manuscript submissions that have appeared in preprint archives should cite the preprint in References, and the fact that a paper has appeared online before should be mentioned parenthetically at the end of the introductory section: (This article was submitted to an online preprint archive [1].) The reference should take the form noted above in the reference below.

Wang Y, Rozen D. 2016. Colonization and transmission of the gut microbiota of the burying beetle, Nicrophorus vespilloides, through development. bioRxiv https://doi.org/10.1101/091702.

For more information, please see ASM editorials regarding availability of materials/data. If an author wishes to transfer a manuscript to (or from) mBio, mSphere, or mSystems, please be mindful of the data policy guidelines and resources:

 

UPDATED December 2018