Availability of supporting data

Submission of a manuscript to a BioMed Central journal implies that readily reproducible materials described in the manuscript, including all relevant raw data, will be freely available to any scientist wishing to use them for non-commercial purposes. Well established and widely supported databases exist for certain types of data such as nucleic acid sequences, protein sequences, and atomic coordinates; information on which can be found below and in journal instructions for authors and 'about' pages. An increasing number of research funding agencies also now support data sharing in the life sciences.

Some BioMed Central journals now additionally encourage or require authors, as a condition of publication, to include in some article types a section that provides a permanent link to the data supporting the results reported in the article. This section is called 'Availability of supporting data' and is only included in an article if supporting data are available in an open access repository or included in the additional files published with the article. The aim is to provide links in a consistent place within an article to supporting data - regardless of the location or format of the data - and to make it clear to readers when they can also access the data as well as the article.

The following format for the 'Availability of supporting data' section is required when data are available in an open access repository:

"The data set(s) supporting the results of this article is(are) available in the [repository name] repository, [unique persistent identifier and hyperlink to dataset(s) in http:// format]."

The following format is required when data are included as additional files:

"The data set(s) supporting the results of this article is(are) included within the article (and its additional file(s))"

We also recommend that the data set(s) be cited, where appropriate in the manuscript, and included in the reference list.

BioMed Central understands that it is not always possible or appropriate to openly share data, in some biomedical fields, so the 'Availability of supporting data' section is not required, or encouraged, in all journals; please see the journal's information for authors for specific manuscript formatting requirements. We recognize that the decision to mandate data deposition as a condition of publication is a decision best made by the scientific community a journal serves. The 'Availability of supporting data' section is a tool for editors, authors and scientific communities to, at the appropriate time, put data deposition policies into practice.

More information on BioMed Central's position on reproducible research, scientific data sharing and open data can be found in our open data statement.

What is the best repository for my data?

A growing number of domain and institution-specific repositories for scientific data relevant to BioMed Central's journals are now available. BioMed Central is collaborating with DataCite, the British Library, the Digital Curation Centre and the wider scientific community to develop and maintain a list of data repositories. The list can be found on the DataCite website.

Where no widely established or mandated repository or database (see below) exists for authors' data, we encourage authors to consult this list for suitable venues for their data so it can be permanently linked from their article. This list is a working document that will evolve over time.

Through a special arrangement with LabArchives, LLC, authors submitting manuscripts to BioMed Central journals can obtain a complimentary subscription to LabArchives with an allotment of 100MB of storage. LabArchives is an Electronic Laboratory Notebook which enables scientists to share and publish data files in situ; you can then link your article to these data. Data files published through LabArchives are assigned digital object identifiers (DOIs), facilitating data citation, and will remain available in perpetuity. Use of LabArchives’ software has no influence on the editorial decision to accept or reject a manuscript, and use of LabArchives or similar data publishing services does not replace preexisting community data deposition requirements set out below and in individual journals’ instructions for authors.

Information on databases and formats for specific types of scientific data already commonly used by our authors follows below.

Nucleotide sequences

Nucleotide sequences can be deposited with the DNA Data Bank of Japan (DDBJ), European Molecular Biology Laboratory (EMBL/EBI) Nucleotide Sequence Database, or GenBank (National Center for Biotechnology Information).

Protein sequences

Protein sequences can be deposited with SwissProt or the Protein Information Resource (PIR).

The accession numbers of any nucleic acid sequences, protein sequences or atomic coordinates cited in the manuscript should be provided, in square brackets with the corresponding database name; for example, [EMBL:AB026295, EMBL:AC137000, DDBJ:AE000812, GenBank:U49845, PDB:1BFM, Swiss-Prot:Q96KQ7, PIR:S66116].

The databases for which we can provide direct links are: EMBL Nucleotide Sequence Database (EMBL), DNA Data Bank of Japan (DDBJ), GenBank at the NCBI (GenBank), Protein Data Bank (PDB), Protein Information Resource (PIR) and the Swiss-Prot Protein Database (Swiss-Prot).

Mass spectrometry

Mass spectrometry data should be supplied in the mzML format recommended by the HUPO Protein Standards Initiative Mass Spectrometry Standards Working Group guidelines. We also recommend that the data is deposited in the ProteomeExchange though the PRIDE website, and protein interaction data can be submitted to members of the IMEx consortium.

Structures

Protein structures can be deposited with one of the members of the Worldwide Protein Data Bank. Nucleic Acids structures can be deposited with the Nucleic Acid Database at Rutgers. Crystal structures of organic compounds can be deposited with the Cambridge Crystallographic Data Centre.

Chemical structures and assays

Structures of chemical substances can be deposited with PubChem Substance. Bioactivity screens of chemical substances can be deposited with PubChem BioAssay.

Microarray data

Where appropriate, authors should adhere to the standards proposed by the Microarray Gene Expression Data Society and must deposit microarray data in MIAME-compliant format in one of the public repositories, such as ArrayExpress, Gene Expression Omnibus (GEO) or the Center for Information Biology Gene Expression Database (CIBEX).

Computational modeling

We encourage authors to prepare models of biochemical reaction networks using the Systems Biology Markup Language and to deposit the model with the BioModels database, as well as submitting it as an additional file with the manuscript.

Plasmids

We encourage authors to deposit copies of their plasmids as DNA or bacterial stocks with Addgene, a non-profit repository, or PlasmID, the Plasmid Information Database at Harvard.

What is the right format for my data?

To help maximize potential for data reuse and increase the efficiency of science, shared data should where possible be made available in formats that are widely agreed by the relevant scientific field - data standards. Journals that include the 'Availability of supporting data' article section encourage authors to comply with available field-specific standards for the preparation and recording of data. We recommend authors review the BioSharing website, and a special article series published in BMC Research Notes, for information on best practice in their field for sharing of data, with particular attention to maintaining patient confidentiality.

How do I cite data?

To help facilitate the earning of academic credit for data sharing and publication we recommend that published datasets referred to in submitted manuscripts be cited in reference lists. Datasets supporting the results reported in submitted manuscripts should be included in an 'Availability of supporting data' article section and cited in the reference list. When citing datasets we recommend the format agreed by DataCite, where persistent identifiers, such as digital object identifier (DOI) names, are displayed as linkable, permanent URLs. For example:

Zheng, L-Y; Guo, X-S; He, B; Sun, L-J; Peng, Y; Dong, S-S; Liu, T-F; Jiang, S; Ramachandran, S; Liu, C-M; Jing, H-C (2011): Genome data from sweet and grain sorghum (Sorghum bicolor). GigaScience Database. http://dx.doi.org/10.5524/100012.

More information on citing data can be found in the Digital Curation Centre's guide on How to Cite Datasets and Link to Publications.

Journals requiring or encouraging the inclusion of the 'Availability of supporting data' section

A list of BioMed Central journals that encourage or require authors to include this section can be found in the table below.

Search for articles published in BioMed Central journals which have supporting data available here.

Journals that include 'Availability of supporting data' section in their research articles
Journal Required or encouraged? Specific repository required? Applies to articles submitted from
Agriculture & Food Security Encouraged n/a November 2011
Annals of Clinical Microbiology and Antimicrobials Encouraged n/a November 2011
Biological Research Encouraged n/a November 2013
BMC Research Notes Encouraged n/a August 2011
BMC series biology journals Encouraged n/a October 2012
Cell & Bioscience Encouraged n/a December 2011
Cell Communication and Signaling Encouraged n/a January 2012
Cilia Encouraged n/a November 2012
Clinical Epigenetics Encouraged n/a December 2011
Extreme Physiology & Medicine Encouraged n/a January 2012
Flavour Encouraged n/a January 2012
Frontiers in Zoology Encouraged n/a December 2011
GigaScience Required GigaScience database (contact the editors) July 2011
Gut Pathogens Encouraged n/a November 2011
Implementation Science Encouraged n/a February 2012
Journal of Foot and Ankle Research Encouraged n/a December 2011
Journal of Molecular Signaling Encouraged n/a November 2012
Longevity & Healthspan Encouraged n/a January 2012
Mobile DNA Encouraged n/a December 2011
Open Network Biology Required Open Network Biology repository (contact the editors) July 2011
Orphanet Journal of Rare Diseases Encouraged n/a March 2012
Retrovirology Required n/a November 2011
Scoliosis Encouraged n/a December 2011
Silence Required n/a December 2011
Transplantation Research Encouraged n/a February 2012
Vascular Cell Encouraged n/a November 2012
Theoretical Biology and Medical Modelling Encouraged n/a July 2013
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