PeerJ Questions: a new way to never ‘Publish & Forget’ again

No time to read the details below? Head over to the questions to see what we’re talking about.

One of the disappointing aspects of publishing research today is that once an article is published, it is often “written in stone.” In reality, research continually evolves and new questions arise, thus leading to new papers. But what about the finer details within the already published manuscript? Readers often have nowhere to turn for answers as simple as “where can I purchase this reagent?” to more complex questions about specific methodologies or alternative conclusions – for example “how did you merge the data together?”. We shouldn’t just publish and then forget, but rather we should strive to enrich what is there, and ideally connect the thoughts that are rumbling around in our heads with that information.


One solution, today’s solution, is to email authors any questions. There are several obvious drawbacks to this: 1) delays in response, or no response at all; 2) authors may have to field the same questions again and again; 3) it could be a question that any domain expert could answer and not just the authors; and 4) answers change over time and others may not be able to access them. In the digital age it seems like we should be trying for more scalable solutions. This is why we have been planning PeerJ Questions since before we even started publishing. It might just be our greatest effort yet to bring something new to the format of academic publishing.

Whenever you visit an article on PeerJ each paragraph, figure and table is now enabled for “annotations” – open to anyone to use. Annotations are questions that can be trivial or deep. Anyone can answer a question, but once the question is live, authors are notified first in case they have the immediate answer. And better still, both the people who ask a question, and those that answer one, can receive academic contribution credit within the related article subject areas. This is done through a peer system of voting up and accepting ‘quality’ or ‘valuable’ answers.


That might be great, but without great discovery tools these questions would be far less useful. This is where the heat map comes in, which is activated in the left hand side, for any article with at least one question.


The heat map is like a bird’s eye view of the entire article that fits to the view of your screen to show where questions are being asked at the paragraph level (see a good example at our “Data reuse and the open data citation advantage” article). As you can see, you don’t need to scan the entire article to know where the most activity is occurring. You can also see questions side by side with the paragraph / figure / table to put them in better context than if they were placed at the end of the article. Each question also gets a unique URL to cite (and eventually DOIs). Lastly, we’ve integrated all questions and answers into the site-wide search and have plans to federate and open up the annotations to any system.

Two more things. Questions can also be asked on PrePrints, though in this case they are located at the end since only abstracts are shown for the online view of a PrePrint. And questions can be asked that are not attached to any article or PrePrint as well (available at

There’s a lot more of course, but we’ll leave the rest for you to discover. You can also learn more on the updated FAQ page for PeerJ Questions (

Head over to the questions and check it out. Remember it’s just getting started, so new questions are only just coming in.

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