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Guide for GigaScience reviewers
Thank you for agreeing to review a manuscript submitted to GigaScience. Our aim with GigaScience is to champion high standards of documentation, testing, and reproducibility of the creation and analyses of large-scale data. GigaScience therefore has strict requirements on data availability, licensing, documentation and testing. To achieve this, as a referee we will ask you to review manuscripts that present novel datasets with a specific eye toward making certain that the minimum standards for the field are fulfilled and that all appropriate testing of data accuracy has been carried out. However, we also recognize that reviewing data is challenging and time-consuming; therefore, we will also have all data-generation manuscripts assessed by a Data Reviewer who will focus specifically on these aspects as opposed to making an assessment of whether the biological analyses done are reasonable and accurate. We do, still, ask every reviewer, where appropriate, to satisfy themselves that the authors have followed the data guidelines of their field.
Open Peer-Review Policy. To further increase review transparency, GigaScience promotes open (non-anonymous) peer-review. As a default, we will pass a reviewer's name on to the authors along with the comments. However, if reviewers do not wish to have their name revealed, we will honor that request. Reviewers are also asked to declare any competing interests and to agree to Open Peer Review, which works on two levels: the authors receive the signed report (unless the referee specifically opts out) and, if the manuscript is published, the same report will be made available to the readers. The pre-publication history (initial submission, reviews and revisions - see, for example, pre-publication history) will also be posted on the web with the published article. For further information please see our editorial.
Reviewers are reminded of the importance of timely reviews. GigaScience aims for a rapid review process where the suitability of a paper for publication will be assessed primarily on criteria of scientific excellence and rigor. The editors' goal is to give authors a decision following peer review within four weeks of an article's submission. To achieve this, we rely on our reviewers to contact the editors (firstname.lastname@example.org) should they encounter or foresee any problems meeting the deadline for a report.
Confidentiality. Any manuscript sent for peer review is a confidential document and should remain so until it is formally published. Exceptions: As we are promoting and encouraging more transparent review and the use of pre-print servers, if the authors and reviewers consent then we do allow open discussion of the work prior to publication.
Reviewing of the manuscript. Suitability of research for publication in GigaScience is dependent primarily on the data quality and utility and on the soundness of the biological conclusions from all data analyses, rather than on a subjective assessment of its immediate impact. Note, that although GigaScience will not make general interest level the primary criterion for publication, it aims to provide its readership with the highest quality large-scale data, data analyses tools, and analyses that will have significant usability and utility for the community.
As a referee we ask that you assess the paper on its own merits. The following list of potential issues may be helpful.
- Is the rationale for collecting and analyzing the data well defined?
Is the work carried out on a dataset that can be described as "large-scale" within the context of its field? Does it clearly describe the dataset and provide sufficient context for the reader to understand its potential uses? Does it properly describe previous work?
- Is it clear how data was collected and curated?
Credit should be given for transparency and provision of all supporting information.
- Is it clear - and was a statement provided - on how data and analyses tools used in the study can be accessed?
While we make every effort to make sure this information is available, we appreciate reviewers providing an extra eye to make absolutely certain that this information is clearly stated and properly available. Data availability and access to tools are essential for reproducibility and provide the best means for reuse.
- Are accession numbers given or links provided for data that, as a standard, should be submitted to a community approved public repository?
Following community standards for data sharing is a requirement of the journal. Additionally, data sharing in the broadest possible manner expands the ways in which data and tools can be accessed and used.
- Is the data available in the public domain under a Creative Commons license?
Note, that unless otherwise stated, data hosted in our database (GigaDB) is available under a CC0 waiver. Additionally, did the authors indicate where the software tools and relevant source code are available, preferably under an appropriate Open Source Initiative compliant license? If data is currently not in a hosted repository we can help authors copy it over to our own GitHub page.
- Are the data sound and well controlled?
If you feel that inappropriate controls have been used please say so, indicating the reasons for your concerns, and suggesting alternative controls where appropriate. If you feel that further experimental/clinical evidence is required for obtaining solid biological conclusions and substantiating the results, please provide details.
- Is the interpretation (Analysis and Discussion) well balanced and supported by the data?
The interpretation should discuss the relevance of all the results in an unbiased manner. Are the interpretations overly positive or negative? Note that the authors may include opinions and speculations in an optional 'Potential Implications' section of the manuscript; thus, if there is material in other parts of the manuscript that you feel would be better suited in such a section, please state that. Conclusions drawn from the study should be valid and result directly from the data shown, with reference to other relevant work as applicable. Have the authors provided references wherever necessary?
- Are the methods appropriate, well described, and include sufficient details and supporting information to allow others to evaluate and replicate the work?
Please remark on the suitability of the methods for the study.
If statistical analyses have been carried out, please indicate if you feel they need to be assessed specifically by an additional reviewer with statistical expertise.
- What are the strengths and weaknesses of the methods?
Please comment on any improvements that could be made to the study design to enhance the quality of the results. If any additional experiments are required, please give details. If novel experimental techniques were used please pay special attention to their reliability and validity.
- Have the authors followed best-practices in reporting standards?
This is an essential component as ease of reproducibility and usability are key criteria for manuscript publication. Have the authors followed and used reporting checklists recommended by the Biosharing network and if the methods are amenable, have the authors used workflow management systems such as Galaxy, Taverna or one of the many related systems listed on MyExperiment? We can also host these in our Giga-Galaxy server if they currently do not have a home.
- Can the writing, organization, tables and figures be improved?
Although the editorial team may also assess the quality of the written English, please do comment if you consider the standard is below that expected for a scientific publication.
If the manuscript is organized in such a manner that it is illogical or not easily accessible to the reader please suggest improvements. Please provide feedback on whether the data are presented in the most appropriate manner; for example, is a table being used where a graph would give increased clarity? Are the figures of a high enough quality to be published in their present form?
- When revisions are requested.
Reviewers may recommend revisions for any or all of the following reasons: the data require additional testing to ensure their quality, additional data are required to support the authors' conclusions; better justification is needed for the arguments based on existing data; or the clarity and/or coherence of the paper needs to be improved.
- Are there any ethical or competing interests issues you would like to raise?
The study should adhere to ethical standards of scientific/medical research and the authors should declare that they have received ethics approval and or patient consent for the study, where appropriate.
Whilst we do not expect reviewers to delve into authors' competing interests, if you are aware of any issues that you do not think have been adequately addressed, please inform the Editorial office.
Portability of peer review
To support efficient and thorough peer review, we aim to reduce the number of times a manuscript is reviewed, thereby speeding up the publication process and reducing the burden on peer reviewers. Therefore, please note that, if a manuscript is not accepted for publication in GigaScience and the authors choose to submit a revised version to another BioMed Central published journal, we will pass the reviews on to the other journal's editors at the authors’ request. We will reveal the reviewers' names to the handling editor for editorial purposes unless reviewers let us know when they return their report that they do not wish us to share their report with another BioMed Central published journal and/or that they do not wish to participate further in the peer review of this manuscript.
Reviewers are asked to bear the editorial standards of GigaScience in mind and alert the editors if authors have not fully adhered to them. GigaScience is a member of the Committee on Publication Ethics (COPE).
Standards of reporting
GigaScience supports initiatives aimed at improving the reporting of research. Reviewers can find more details on this at Standards of Reporting in 'About GigaScience'.