Reporting standards and availability of data, materials, code and protocols (original) (raw)
An inherent principle of publication is that others should be able to replicate and build upon the authors' published claims. A condition of publication in a Nature Portfolio journal is that authors are required to make materials, data, code, and associated protocols promptly available to readers without undue qualifications. Any restrictions on the availability of materials or information must be disclosed to the editors at the time of submission. Any restrictions must also be disclosed in the submitted manuscript.
After publication, readers who encounter refusal by the authors to comply with these policies should contact the chief editor of the journal. In cases where editors are unable to resolve a complaint, the journal may refer the matter to the authors' funding institution and/or publish a formal statement of correction, attached online to the publication, stating that readers have been unable to obtain necessary materials to replicate the findings.
On this page
- Reporting requirements
- Availability of data
- Availability of materials
- Availability and peer review of computer code and algorithm
- Experimental protocols
- Pre-registration
- Replication studies
- Clinical trials
- Nature Portfolio journals' editorials
Reporting requirements
Nature Portfolio journals aim to improve the transparency of reporting and reproducibility of published results across all areas of science. Where relevant, manuscripts sent for review must include completed reporting summary documents.
Reporting requirements for research in the life sciences, behavioural & social sciences and ecology, evolution & environmental sciences
Authors of research articles in the life sciences, behavioural & social sciences and ecology, evolution & environmental sciences are required to provide details about elements of experimental and analytical design that are frequently poorly reported in a reporting summary that will be made available to editors and reviewers during manuscript assessment. The reporting summary will be published with all accepted manuscripts.
Reporting requirements for physical sciences research
For physical sciences, we require authors of research articles in some specific areas to provide details of characterization, or experimental and analytical design in a reporting summary, which will be made available to editors and reviewers during manuscript assessment and published with an accepted manuscript:
Reference copies
Please note: because of advanced features used in these forms, you must use Adobe Reader to open the documents and fill them out. If you would like to quickly view the forms or would like to reference the guidance text as you complete the template, please access a flat reference copy:
We support community efforts to increase transparency and quality of methods reporting. Thus, we have made these templates available for reuse and adaptation with attribution under a CC-BY license.
Guidance and resources related to the use and reporting of statistics are available here.
Reporting and materials availability requirements for geological, archaeological, and palaeontological research
Details of geological samples, archaeological materials and palaeontological specimens should include clear provenance information to ensure full transparency of the research methods. Samples should always be collected and exported in a responsible manner and in accordance with relevant permits and local laws. Any submission detailing new material from protected sites should include information regarding the requisite permission obtained. Palaeontological and type specimens should be deposited in a recognised museum or collection to permit free access by other researchers in perpetuity. Where applicable, accession codes should be provided for museum depositions, and we encourage deposition of 3-D scans of fossil specimens within a permanent, accessible repository to facilitate study by the scientific community.
Availability of data
Data availability: All published manuscripts reporting original research in Nature Portfolio journals must include a data availability statement. The data availability statement must make the conditions of access to the “minimum dataset” that are necessary to interpret, verify and extend the research in the article, transparent to readers. This minimum dataset may be provided through deposition in public community/discipline-specific repositories, custom proprietary repositories for certain types of datasets, or general repositories like Figshare, Zenodo and Dryad. Providing large datasets in supplementary information is strongly discouraged and the preferred approach is to make data available in repositories. Scientific Data, a Nature Portfolio journal, maintains a list of approved and recommended data repositories to support researchers seeking suitable repositories for their data. Please refer to our authorship policy for information about authors’ responsibilities for preserving and making available data, code and materials upon publication. Authors are responsible for obtaining all necessary permissions and ensuring compliance with local regulatory requirements for data sharing.
Mandatory deposition of data is required for certain data types; see table below with recommended repositories. Supporting data must be made available to editors and peer reviewers where requested at the time of submission for the purposes of evaluating the manuscript. Any restrictions on sharing must be discussed with the editor at submission who reserves the right to decline the study if these conditions are found to be unduly prohibitive.
Nature Portfolio journals' data availability policies are compatible with the standardised research data policies set out by Springer Nature. Authors who need help understanding our data sharing policies, finding a suitable data repository, or organising and sharing research data can access our Author Support portal for additional guidance.
Data availability statements should include information where relevant on the following aspects:
- Information about access to primary datasets (generated during the study) and referenced datasets (datasets analyzed in the study) must be provided. Where data are publicly available, accession codes or other unique identifiers if relevant must be provided.
- Clinical trial data: data availability statements for manuscripts reporting clinical trial data should follow the standards set out in the ICMJE recommendations on clinical trial data sharing and provide the following information:
- whether individual de-identified participant data (including data dictionaries) will be shared (“undecided” is not an acceptable answer);
- what data in particular will be shared;
- whether additional, related documents will be available (e.g., study protocol, statistical analysis plan, etc.);
- when the data will become available and for how long;
- by what access criteria data will be shared (including with whom, for what types of analyses, and by what mechanism).
- Data availability subject to controlled access: the data availability statement should include the following information: reasons for controlled access (eg., privacy, ethical/legal issues), conditions of access must be described precisely including contact details for access requests, timeframe for response to requests, restrictions imposed on data use via data use agreements. A copy or link to the data use agreement should be provided if requested by editors. Restrictions on controlled access datasets including restrictions on downstream data reuse or authorship requirements must be clearly described in manuscript and to editors at the time of submission. Editors may decline further consideration of the manuscript after evaluation if restrictions are found to be unduly prohibitive.
- Third party data: when data obtained from third parties cannot be made available, the restrictions should be clearly stated in the data availability statement. Authors must make data available for purposes of peer review, if requested by reviewers, within the terms of a data use agreement and if compliant with ethical and legal requirements.
· Proprietary data: Authors are responsible for ensuring and obtaining agreement with the third party data provider that dataset (s) used in the study will be available under conditions specified in the data availability statement (including whether the dataset will be available for a fee) so as to ensure post-publication availability for replication and verification purposes. Availability for this purpose must be clearly stated in the data availability statement.
· Administrative data (including data held by governments, local authorities and international organizations): Social science and other studies using administrative data must ensure that the data are used in compliance with local regulatory and legal frameworks that govern data use.
· Identity of third party provider: the identity of the third party data provider must be made known to the editors at time of submission and peer review. We expect that the data availability statement will state the identity of the third party data source; exceptions may be made for studies where the identity of the data provider is not relevant to the study and/or public release pose a reputational or commercial risk to the data provider. See published examples here and here.
Researchers should provide information in the manuscript on their data collection methods sufficient to support peer review. If data processing steps were performed by the third-party, out of the control of the authors, this should be clearly stated in the methods. Editors reserve the right to decline consideration if a manuscript fails to provide sufficient information regarding data collection approach.
Data citation: Datasets that have been deposited in repositories should be included as formal citations in the article reference list. This includes datasets generated during the study as well as existing datasets analyzed during the study. Citations of datasets should include the minimum information recommended by DataCite and follow Nature Portfolio style including: author(s), title, publisher (repository name), and identifier.
Dataset identifiers including DOIs should be expressed as full URLs. For example: Hao, Z., AghaKouchak, A., Nakhjiri, N. & Farahmand, A. Global Integrated Drought Monitoring and Prediction System (GIDMaPS) Data sets. figshare http://dx.doi.org/10.6084/m9.figshare.853801 (2014)
More information about writing data availability statements and data citation is available through the Springer Nature Research Data policy page.
Mandates for specific datasets
For the following types of data set, submission to a community-endorsed, public repository is mandatory. Accession numbers must be provided in the paper. Examples of appropriate public repositories are listed below and here.
*From January 2019, where community repositories are available, we will require data sharing through such repositories for papers in the Earth, space and environmental sciences published in Nature, Nature Geoscience , Communications Earth & Environment and Communications Sustainability. Where such repositories are not available, datasets may be hosted in general data repositories such as Figshare, Dryad or Zenodo. See our editorial for more details.
Special considerations
DNA and protein sequences: When publishing reference genomes, the assembly must be made available in addition to the sequence reads. Sequence must be deposited even for short stretches of novel sequence information such as epitopes, functional domains, genetic markers, or haplotypes. Short novel sequences must include surrounding sequence information to provide context. The sequences of all small RNA probes central to the conclusions of the paper must be provided.
Linked phenotype and genotype data for human subjects: should be submitted to a public repository with appropriate access control (see above). Any restrictions on data access for sensitive data (for example electronic medical records, forensic data, and personal data from vulnerable populations) require an explanation of the nature of and reasons for the restrictions, and details of the conditions under which the data can be accessed or reused. (See the related Nature Genetics Editorial discussing privacy issues.)
Macromolecular structures: Official validation reports from the wwPDB are required for peer review. Atomic coordinates and related experimental data (structure factor amplitudes/intensities for crystal structures, or restraints for NMR structures) must be provided upon request. Electron microscopy-derived density maps and coordinate data must be deposited in EMDB. Accessibility in repositories must be designated "for immediate release on publication."
Crystallographic data for small molecules: Manuscript reporting new three-dimensional structures of small molecules from crystallographic analysis should include a .cif file and a structural figure with probability ellipsoids for publication as Supplementary Information. The structure factors for each structure should also be submitted. Both the structure factors and the structural output must have been checked using the IUCR CheckCIF routine, and a PDF copy of the output must be included at submission, together with a justification for any alerts reported.
Recommendations for other datasets
In addition to these mandates, the preferred way to share any data sets is via public repositories. Scientific Data, a sister publication to Nature Portfolio journals, maintains a list of approved and recommended data repositories organized by discipline. Please consult this list to identify an appropriate repository for your data sets.
When repositories do not exist for a particular data type, authors can deposit and share data via figshare or Dryad, two general-purpose scientific data repositories.
Availability of materials
A condition of publication in a Nature Portfolio journal is that authors are required to make unique materials promptly available to others without undue qualifications. It is acceptable to request reasonable payment to cover costs of distribution and reagents may be made available via commercial or non-commercial third party providers. Any restrictions on materials availability, including if materials are to be distributed by a for-profit company, must be clearly stated in the paper. As per our policy on authorship responsibilities, it is expected that the corresponding author (or relevant designated authors) will be responsible for materials availability unless otherwise stated.
Nature Portfolio supports the Resource Identification Initiative, with the aim of promoting unique, persistent identification and tracking of key biological resources, including antibodies, cell lines, model organisms and tools. We encourage authors to include unique identifiers provided by the Resource Identification Portal, (RRIDs; for example, Antibody: RRID:AB_2140114; Organism: RRID:MGI_MGI:3840442), in the manuscript. More information on how to include listed RRIDs or generate new RRIDs can be found on the Resource Identification Portal.
Authors reporting new chemical compounds integral to the conclusions of the paper must provide the chemical structure, synthesis and characterization of the compounds with sufficient experimental details to allow other researchers to reproduce the synthesis and characterization.
For biological materials such as mutant strains and cell lines the Nature Portfolio journals recommend authors use established public repositories when one exists (for example, Jackson Laboratory, the European Mouse Mutant Archive (EMMA), the European Conditional Mouse Mutagenesis Program (EUCOMM), the Knockout Mouse Project (KOMP), Addgene, RIKEN Bioresource Centre, the Mutant Mouse Regional Resource Centers, American Type Culture Collection, and provide accession numbers in the manuscript.
Cell lines: We strongly encourage deposition of new cell lines in repositories that will distribute them with certificates of authentication. Alternatively, we recommend that authors establish a profile of their new cell lines to allow future authentication. The distribution of human cell lines used in research should not be hindered by restrictions from donors. Researchers developing cell lines must investigate and disclose any restrictions associated with the tissue they are using (see this Nature Editorial for further explanation.) Cell line misidentification and cross-contamination is a common problem with serious consequences. Authors are asked to report on the source and authentication of their cell lines (relevant resources are listed under Further Reading)”.
Availability and peer review of computer code and algorithm
Authors must make available upon request, to editors and reviewers, any previously unreported custom computer code or algorithm used to generate results that are reported in the paper and central to its main claims. Any reason that would preclude the need for code or algorithm sharing will be evaluated by the editors who reserve the right to decline the paper if important code is unavailable.
For all studies using custom code or mathematical algorithm that is deemed central to the conclusions, a statement must be included under the heading "Code availability", indicating whether and how the code or algorithm can be accessed, including any restrictions to access. Code availability statements should be provided as a separate section after the data availability statement but before the references.
Upon publication, Nature Portfolio journals consider it best practice to release custom computer code in a way that allows readers to repeat the published results. Code should be deposited in a DOI-minting repository such as Zenodo or Code Ocean and cited in the reference list following the guidelines described here. Authors are encouraged to manage subsequent code versions and to use a license approved by the open source initiative. Full details about how the code can be accessed and any restrictions must be described in the Code Availability statement.
Peer review of code/algorithm/software: Nature journals undertake peer review of custom code or mathematical algorithm, and software, when it is central to the manuscript. For code/algorithm peer review, we require sharing of code/algorithm during the peer review process with editors and reviewers and inclusion of a Code Availability section in the manuscript upon publication. Journals offer an optional free service to support authors in sharing their code for peer review and publication via Code Ocean.
Experimental protocols
Nature Portfolio journals encourage authors to share their step-by-step experimental protocols on a protocol sharing platform of their choice. Where such protocols are available, please provide a DOI or other citation details in the paper. Springer Nature's protocols.io is a free-to-use and open resource for protocols; protocols deposited in protocols.io are citable and can be linked from the published article. More details can found at https://www.protocols.io/help/publish-articles.
Pre-registration
Nature Portfolio journals support study pre-registration (including clinical trials) and pre-registration of analysis plans in public repositories; details of pre-registration should be provided with submission.
Registered Reports, a research article format intended to reduce publication bias and increase methodological rigour is available at Nature Human Behaviour, Communications Psychology and for select disciplines at Nature Communications, Nature Methods, and Scientific Reports. Registered Reports involves a two-stage peer review approach where methods and analysis are pre-registered and peer reviewed before carrying out the intended research.
Replication studies
Nature Portfolio appreciates the value of replication of previous findings. We welcome submission of replication studies that provide new insights into previously published results and will evaluate these submissions with the same editorial standards we apply to other submissions.
Clinical Trials
Authors reporting phase II and phase III randomized controlled trials must refer to the CONSORT Statement for recommendations to facilitate the complete and transparent reporting of trial findings. Reports that do not conform to the CONSORT guidelines may need to be revised before formal review.
Authors reporting prognostic studies with tumor markers are encouraged to follow the REMARK guidelines for complete and transparent reporting.
Prospective clinical trials must be registered before the start of patient enrollment in www.clinicaltrials.gov or a similar public repository that matches the criteria established by ICMJE. Suitable publicly available registries are those listed on the ICMJE website as well as any of the primary registries that participate in the WHO International Clinical Trials Registry Platform, including the ISRCTN registry, which is administered and published by BMC (BMC is part of Springer Nature). The trial registration number must be reported in the paper.
For describing human biospecimens, we recommend referring to the BRISQ reporting guidelines (Biospecimen Reporting for Improved Study Quality) and ensuring at least Tier 1 characteristics are provided (doi: 10.1002/cncy.20147).
Nature Portfolio journals' editorials
Reporting requirements and reproducibility
- Nature authors say a reproducibility checklist is a step in the right direction, but more needs to be done. Nature. Checklists work to improve science, April 2018.
- Nature and the Nature Portfolio journals will publish more details on experiments described in life-sciences papers. Nature. Announcement: Towards greater reproducibility for life-sciences research in Nature, June 2017.
- Nature Editorial describing the initiatives taken on by Nature to improve research transparency: Transparency upgrade for Nature journals, March 2017
- Nature Special: Challenges in irreproducible research (updated November 2014) - collection of articles from Nature Portfolio journals addressing various aspects of irreproducibility.
- All Nature Portfolio journals publishing life sciences introduce measures to improve reporting standards. Nature. Announcement: Reducing our irreproducibility, April 2013.
- New rules for presentation of statistics. Nature Cell Biology. Reproducible methods and How robust are your data? June 2009.
- Nature Methods ushers in an Online Methods section, fully integrated with the paper, for all original research articles. Nature Methods. Methods section remake, May 2009.
- From now on, Nature Portfolio authors will be able to include more experimental details in their papers. Nature. Methods in full, February 2007.
Availability of data
- Nature backs the Enabling FAIR Data initiative and requires authors to deposit data in community repositories. Announcement: FAIR data in Earth science.
- As the research community embraces data sharing, academic journals can do their bit to help. Starting this month, all research papers accepted for publication in Nature and an initial 12 other Nature Portfolio titles will be required to include information on whether and how others can access the underlying data. Nature Announcement: where are the data? September 2016.
- In our continued drive for reproducibility, Nature and the Nature Portfolio journals are strengthening our editorial links with the journal Scientific Data and enhancing our data-availability practices. Nature. Data-access practices strengthened, November 2014.
- Datasets can now be published, shared — and cited — in Scientific Data. Nature Physics. It’s good to share, July 2014.
- Data must be accessible to support the conclusions of scientific publications and for the research to have impact. Nature Genetics. It’s not about the data, February 2012.
- A recent report highlights the urgent issues regarding the preservation of large datasets. Nature Neuroscience. Ensuring data integrity, October 2009.
- Reference datasets should be accessible independently of scientific papers in a citable form, allowing attribution. Nature Cell Biology. Sharing data, November 2009.
- Datasets released to public databases in advance of (or with) research publications should be given digital object identifiers. Nature Genetics. Data producers deserve citation credit, October 2009.
- The scientific community needs to develop better incentives to encourage compliance and reward those who share. Nature Neuroscience. Got data? August 2007.
- Procedures for microattribution need to be established by journals and databases. Nature Genetics. Compete, collaborate, compel, August 2007.
- Online publishing should have made ‘data not shown’ largely a thing of the past. Nature Cell Biology. Nothing to hide (data not shown), June 2006.
Discipline-specific data sets
- Data from genome-wide association studies should be reported and deposited, even if the data does not reach genome-wide levels of significance. Nature Genetics. Asking for more, June 2012.
- Human exome sequencing data should ideally be archived in appropriate repositories before submission and authors must explain their data management plan before peer review. Nature Genetics. Capture and release, September 2011.
- Reference datasets should be accessible independently of scientific papers in a citable form, allowing attribution. Nature Cell Biology. Sharing data, November 2009.
- Proposes a universal tagging system that connects databases with authors. Nature Biotechnology. Credit where credit is overdue, July 2009.
- Genetically modified mouse strains must be made available. Nature. The sharing principle, June 2009.
- Deposition of proteomics data. Nature Methods. Thou shalt share your data, March 2008.
- Describing the Nature Portfolio journals' Creative Commons license for genome sequences. Nature. Shared genomes, December 2007.
- Scientists coin new terms, or neologisms, at a tremendous pace, but name choice can have unforeseen results. Nature Structural & Molecular Biology. Name that gene! August 2007.
- Raw proteomics and molecular interaction data should be deposited in repositories at submission Democratizing proteomics data (March 2007), and researchers should embrace minimum information reporting guidelines. Time for leadership (August 2007). Nature Biotechnology.
- The tools for genome-wide association studies are now available. Here we present the journal's current criteria for manuscripts in this area of research. Nature Genetics. Framework for a fully powered risk engine, November 2005.
- Biological research must provide the data necessary for replication. Nature Medicine. Structural Integrity, February 2005.
- How to discuss ancestry and ethnicity. Nature Genetics. The unexamined 'Caucasian', June 2004.
- Clarifying the Nature Portfolio journals' policy on data deposition for chemical structures. Nature. Crystal Clear, June 2005.
- Required controls for studies involving RNAi. Nature Cell Biology. Whither RNAi? June 2003.
- Controls for studies involving microarrays. Nature Immunology. Microarray policy, February 2003.
- Data requirements for studies involving microarrays. Nature Cell Biology. Microarray data standards, November 2002.
- The microarray community has issued guidelines that will make their data much more useful and accessible. Nature. Microarray standards at last, September 2002.
- Any paper containing new structural data will not be accepted without an accession number from the Brookhaven Protein Data Bank. Nature. New policy for structural data, July 1998.
- Statements by presidents of countries and societies highlight the concern that human genome data be publicly accessible, and quickly. Nature. Rules of genome access, March 1990.
Availability of materials
- There must be no restrictions on the redistribution of patient-derived cell lines or other tissue. Nature. Common consent, 20 August 2009.
- Nature Chemical Biology is committed to enhancing interdisciplinary communication and features online content to increase the accessibility of chemical information for our readers. Nature Chemical Biology. A new look for chemical information, June 2007.
- Note to biologists: submissions to Nature Portfolio should contain complete descriptions of materials and reagents used. Nature. Illuminating the black box, 16 July 2006.
- Pragmatically adapting our sharing-of-materials policy. Nature Cell Biology. Sharing science, May 2006.
- There is a great need for community standards for sharing data, materials and information between chemists and biologists. Nature Chemical Biology. Molecular cross-fertilization, February 2006.
- On sharing materials to foster reproducible research. Nature Cell Biology. Policy update, March 2005.
- On sharing materials to foster reproducible research. Nature Genetics. 'Good citizenship' or good business?, October 2004.
Resources on cell line identity
To help curb the inadvertent use of cross-contaminated or otherwise misidentified cell lines, authors are asked to check their reagents against the list of known misidentified cell lines maintained by the International Cell Line Authentication Committee (ICLAC) and also accessible through the NCBI BioSample database. If using a cell line that is on this list, authors should provide a scientific justification and state the identity issue in the Methods section. Editors reserve the right to demand that the data be removed from the paper if the justification is deemed unsatisfactory. In addition, authors must identify the source of cell lines (with catalog number if obtained from vendor or cell bank) and report whether the cell lines have been authenticated. They should include the method used, the results and when authentication testing was last performed for that cell line. Authentication test results must be provided upon request. Mycoplasma contamination testing status must also be reported. As of May 2015, these requirements are particularly emphasized for cancer research where the issue of cell line misidentification has been well documented, but authors in all disciplines are strongly encouraged to comply with these reporting criteria. It is good practice to obtain cell lines from reputable repositories, to routinely authenticate cell line stocks and test them for mycoplasma contamination. Resources on cell line authentication follow.
- Authentication of Human Cell Lines: Standardization of STR profiling (American National Standards Institute)
- Yu M. et al. A resource for cell line authentication, annotation, and quality control. Nature, 520, 307–311, doi:10.1038/nature14397 (April 2015).
- Capes-Davis, A. et al. Match criteria for human cell line authentication: Where do we draw the line? Int J of Cancer, doi:10.1002/ijc.27931 (2012).
STR profiles and misidentified cell lines databases:
- Database of Cross-contaminated or Misidentified Cell Lines (International Cell Line Authentication Committee)
- BioSample Database (NCBI/NIH)
- COSMIC Cell Line Project
- ATCC STR Profile database
- DSMZ STR Profile Verification database
Background and guidance:
- Announcement: Time to tackle cells' mistaken identity. Nature 520, 264, doi:10.1038/520264a (16 April 2015).
- Geraghty R. J. et al. Guidelines for the use of cell lines in biomedical research. British J of Cancer 111, 1021–1046, doi:10.1038/bjc.2014.166 (2014).
- Lorsch J. R., Collins F. S., Lippincot-Schwartz J. Fixing problems with cell lines. Science 346, 1452-1453, doi:10.1126/science.1259110 (2014).
- Dirks, W.G. and Drexler, H.G. STR DNA typing of human cell lines: detection of intra- and interspecies cross-contamination. Methods Mol Biol 946, 27-38, doi: 10.1007/978-1-62703-128-8_3 (2013).
- Masters, J. R. Cell-line authentication: End the scandal of false cell lines. Nature 492, 186, doi:10.1038/492186a (2012).
- Cell line misidentification: the beginning of the end. Nat Rev Cancer 10, 441-448, doi:10.1038/nrc2852 (2010).
- Identity crisis. Nature 457, 935-936, doi:10.1038/457935b (2009).
- The websites of the International Cell Line Authentication Committee and ATCC provide useful additional information.
Availability of computer code
- Nature journals encourage researchers who submit papers that rely on bespoke software to provide the programs for peer review. Nature Does your code stand up to scrutiny? March 2018.
- Sharing data is key for efficient scientific progress. More open code would be beneficial too. Nature Geoscience. Towards transparency, November 2014.
- Papers in Nature Portfolio journals should make computer code accessible where possible. Nature. Code share, October 2014.
- The usefulness of computational methods can be improved by releasing code and designing software that supports reproducible research. Nature Methods. Software with impact, March 2014. (See also this comment)
- Review, replication, reuse and recognition are all incentives to provide code. Nature Genetics. Credit for code, January 2014.
- Improving the integration of computational analysis into biology will require better documentation, validation and accessibility of software associated with papers. Nature Biotech. In need of an upgrade, October 2013.
- Software that is custom-developed as part of novel methods must be made available to readers upon publication. Nature Methods. Social software, March 2007.