Frequently asked questions

Commenting guidelines

What publications can be discussed? Any publication.

We encourage discussion and commenting about all publications in all fields. The only requirement is for the publication to have an ID that we recognize. Such IDs include the DOI and IDs for PubMed and the ArXiv. Note that failure of searches for DOIs often reflect problems with indexing by the journal or CrossRef.

What classes of comments can I make? Major, minor, negative or positive.

PubPeer accepts all types of comments about papers. Although many comments concern issues that are central to a paper’s conclusions, this is not an obligation. Comments about minor issues and details should be interpreted as such, although attention to detail is often important in science. We may draw the line at issues that have no significant bearing on the science, its interpretation or its presentation.

What can my comment contain? Facts, logic and publicly verifiable information.

By far the most important rule for commenting is to base your statements on publicly verifiable information. This will usually be the data published in the paper you are commenting on, but could also be another paper or some other source such as a book, newspaper or web site. Please cite your sources to allow easy verification. Conversely, comments based upon hearsay are unacceptable---you can’t say, "My friend used to work in the lab and said their glassware is dirty". If you wish to report personal knowledge, you must sign your comment.

Observation of this rule automatically focuses discussion on the facts and the science. It also greatly reduces the legal risks to PubPeer and to you. If comments only involve immediately verifiable facts there should be no difficulty in proving the truth of the statements. The truth is of course a strong defense in any defamation/libel case. However, our aim is not just to have a strong defense, but never to need one, since defending any case will cost money that maybe neither you nor we have. If your comment only contains the obvious truth, that should discourage unhappy authors from initiating any legal attack.

Please do not make allegations of misconduct on PubPeer. They are anyway unnecessary. Your audience on the site is mostly composed of highly intelligent researchers and scientists. They are quite capable of drawing their own conclusions if the facts are clearly presented.

Please also avoid speculation about researcher actions and motives. In some jurisdictions, if a statement is made along the lines of "X deliberately falsified the data", we could find ourselves in a defamation suit and having to prove each step of the falsification, specifically by X, but also of having to establish his deliberate state of mind at the time. The standard of proof can be very exacting and require information to which we would not have access---especially the private thoughts of the researcher! The British libel system is notorious in regard of the difficulty and cost of defending even totally meritless suits, but lawyers cost a lot of money everywhere.

What tone should I adopt? Polite and neutral.

Although we understand that frustration can easily build up, unnecessarily strong language just makes you and the site appear unreasonable, reducing the effectiveness of your comment and handing people a pretext to ignore your comment specifically and the site generally. Remember---your readers understand.

What makes a comment effective? Context, explanation and accuracy.

Although it is good to be concise, a minimum of context and explanation can be very helpful to readers, so please consider providing this even if it does require extra work.

Inclusion of images, diagrams, etc, can often strengthen a comment.

Please proof-read your comment carefully before posting it. A preview pane is provided when you prepare your comment. Comments submitted via an account (named or pseudonym) can be edited after submission, until another comment is submitted.

Do authors receive alerts? Yes.

Authors are automatically alerted when their paper is commented. Commenters will encounter dialogs for verifying author email information.

Can I post external links? Please do.

We encourage you to post links to external information relevant to articles or discussion about them. These might include other articles that confirm or contradict the reported results, blog posts and newspaper articles. However, we discourage and may limit indiscriminate bulk linking campaigns.

How does moderation work?

In order to keep discussion factual, of high quality and polite as well as to minimize legal risks for everybody, we reserve the right to remove or edit comments that do not conform to these guidelines. Please help us by reporting any comments you believe do not respect our guidelines (a button is provided on each comment).

Anonymous comments and those from “blacklisted” accounts only appear on the site after moderation, which can take up to a week.

PubPeer does not review comments scientifically and provides no warranty as to their veracity. All readers should evaluate comments for themselves.

Why doesn't PubPeer review comments scientifically?

PubPeer has grown as part of a reaction to the negative influence of editorial conflicts of interest, commercialism, errors and bias in the present system with its pre-publication review. We do not aim to reproduce it but to complement it with something different. Thus, PubPeer is designed around post-publication review and aims to facilitate open discussion. The philosophy driving the site is that authors should assume responsibility for assuring the quality, clarity, transparency and integrity of their publications. We make every effort to alert the authors to any comments and they are encouraged to respond. Such feedback can be extremely rapid and effective.

To implement scientific review on PubPeer would anyway be wholly impractical: PubPeer does not have the resources to address a quality-control problem that the planetary publishing industry has been unable to solve. Moreover, resolving many issues would require access to the original data, which are usually unavailable.

How can I ensure anonymity? Use Tor.

PubPeer gives users control of their anonymity and minimizes the user information held. Users who desire the strongest guarantee of anonymity should consider accessing the site via Tor (https://torproject.org) using the Tor browser bundle.

Why can’t I find the paper I want to comment on?

This usually occurs because the DOI has not been correctly indexed. These problems are more frequent for recent papers.

Authors

My paper has been commented! What can I do?

PubPeer offers you a permanent right of reply. We encourage you to respond on the site. There are special facilities for indicating author responses. We believe that honest, careful and competent authors should provide “after sales service” for their publications, by clarifying any points that readers find unclear.

Many questions can be resolved by showing your original data. We encourage you to do so. An increasing number of journals require you to give access to your data or even to publish it directly, so there is now nothing unusual in making your data public. Although some authors still prefer only to show their data to journal editors, in our experience an opaque editorial statement is much less convincing than sharing the data publicly. Low-volume image and tabular data can be posted directly on the site (although tables may be tedious to format). Larger data sets are better submitted to a specialist provider (such as Dryad http://datadryad.org/ or figshare https://figshare.com/) and then linked from a comment.

Did someone just accuse me of fraud?

Comments on PubPeer should not be automatically equated with allegations of misconduct, let alone credible ones. Numbers of comments should also be interpreted with great caution. Remember that comments can be about many different aspects of a paper: "major, minor, negative or positive". Every comment should be evaluated on its merits by the reader. Many comments concern research or presentation methods that users consider not to be best practice. A typical example would be differential splicing of gels or omission of loading their controls. This does not mean that the result is erroneous or that misconduct has occurred! However, it might reduce the faith that readers place in the work. Even for apparently serious issues, there can often be an innocent explanation, which is why authors are encouraged to clarify and defend their work, and to join in the community effort to define best practice.

Is someone out to get me?

Authors sometimes complain that they are the subject of a malicious and systematic campaign to denigrate them and all of their work. We and other readers have no way of evaluating the motivations or potential conflicts of interests of anonymous commenters. However, everybody can evaluate the substance of a comment, which we feel is more informative and fundamental. If a comment is correct and useful, does it matter who made it or why? Moderation ensures that comments are factual and verifiable. Authors can respond. Readers must perform their own scientific evaluation.

Who did this to me?

PubPeer will never willingly reveal information that might help identify a commenter. We have already been to court to defend the anonymity of our commenters. PubPeer discourages ad hominem arguments and encourages discussion about the scientific substance.

Why does PubPeer allow comments that I know are wrong?

PubPeer does not review comments scientifically (see above), so factual comments conforming to our guidelines may still be wrong, misguided or unconvincing. For this reason we insist that readers must always make up their own minds about comment content. If you believe a comment is wrong or based upon a misunderstanding, we encourage you to post a brief explanation to share your insight and help educate the community. Of course, those best placed to explain a publication are usually its authors, which is why we do everything we can to encourage and facilitate their responses.

I answered, so can you make the comment disappear?

Thank you for engaging. We believe good scientists distinguish themselves by responding effectively to questions about their work. In most cases we will not consider removing comments, even if the authors apparently provide a convincing reply or explanation. Our viewpoint is that other readers may have similar questions and that it is therefore beneficial for the comment thread to remain publicly accessible. More philosophically, it is rarely possible to make a definitive judgement and PubPeer is certainly not in a position to do so systematically. Note also that we won't modify or remove comment threads because of journal actions, such as publication of a correction. In addition to our policy of keeping the complete discussion history publicly available, many journal corrections are opaque, superficial and unsatisfactory.

The whole world can read this forever?

That’s the point. Authors who don’t want their work discussed should consider not publishing it.

How can I convince ungracious commenters?

Authors occasionally use the critical tone of some comments as a pretext for not responding on the site. This is a personal choice. However, even if a specific commenter proves hard to convince, it is important to consider the wider audience of readers, who will evaluate the comment for themselves.

Can I claim a copyright violation?

We provide a procedure for notification of copyright violations by copyright holders. We will vigorously oppose unfounded or vexatious takedown notices. Note however, that reproduction of figures and text for the purpose of “criticism” falls squarely under the Fair Use exception of copyright legislation in the US, where PubPeer is incorporated and where the site is hosted. Note also that we back up external images and can therefore usually replace any taken down by external sites.

Why did PubPeer send me a nasty email? (We didn’t.)

We regret that you received a nasty email, but it probably wasn’t from us. PubPeer controls the domains pubpeer.com, pubpeer.org and pubpeer.net. Emails from any other domains are definitely not from us, even if they contain the word “pubpeer”. It is unfortunately very easy to spoof the “From” and “Reply-to” fields in email headers, although this can often be revealed by examining the full headers and routing information in detail.

PubPeer does automatically send simple alerts from the above domains to authors whose papers are commented. Authors can opt out of these.

User accounts

I lost my anonymous access code. Can I recover it?

No. Your only option is to create a new account. Please be more careful next time.

Can I choose my own pseudonym?

No. These are assigned randomly from the tree of life.

Why hasn’t my comment appeared?

For anonymous and pseudonym comments, this is most likely because the comment is awaiting moderation. Comment status for pseudonym accounts can be examined by logging in, after which comments are visible but marked as awaiting moderation. New pseudonym accounts are systematically “blacklisted”, meaning that comments must be moderated. Accounts that make comments contravening our guidelines can be blacklisted at any time. Moderation can take up to a week.

Can I get an account without a suitable publication?

No problem. Just contact us directly (contact@pubpeer.org). In most cases we will be happy to create an account for you manually.

Plugins

What are the browser plugins?

As explained on the plugins page (http://blog.pubpeer.com/?p=143), the browser plugins highlight on any web page publications that have been discussed on PubPeer. In particular, this works on PubMed search results and journal web sites. Comment information is updated in the background and may take some time to propagate.

Where can I get the plugins?

Plugins for Firefox, Chrome and Safari are available via their respective software stores, linked from the plugin page (http://blog.pubpeer.com/?p=143). Once installed, they should update themselves automatically.

API

Can I access PubPeer data?

We (will soon) have an API. Contact us to request a key.

PubPeer Foundation and site

Who runs this site?

The site is operated by the PubPeer Foundation; see About.

Terms of service

What are the terms of use?

By using the site, commenters agree to abide by the terms of service detailed here

What is your privacy policy?

We collect only the information required for site operation. PubPeer will never willingly reveal and will never sell user information. Further information is available here.