If you've looked at commenting systems on other journals you may have noticed that these 'annotations' tend to fall into a few different categories. In some instances, they are questions, and at other times (particularly in preprints) they are closer to being feedback. At PeerJ we want to distinguish between annotation types in order to provide different contextual support, tools, and structure.

Ultimately, by structuring annotations in this way, it becomes easier to find them and reuse them in the future. It also improves the literature over time by giving them dynamic narratives without impacting the original work, one of our goals at PeerJ. Finally, it makes it easier to give credit to annotators.

Q&A (or Questions & Answers) is available on both peer-reviewed articles and Preprints. Q&A is available at the paragraph, figure, and table level on peer-reviewed articles. On Preprints, questions can be asked at the bottom of the page. Questions can also be asked apart from any specific article or preprint.

It could quickly get confusing since questions can be asked on any paragraph or figure/table. The heat map is the solution to easily navigating to questions and understanding the amount of activity (and where most activity is happening) on a paper at a glance. Once at least one question is added it will appear on the left side of your screen.

Using: Hover on the heat map to see how many questions in that particular section and click on the heat map to open up that section.

Heat maps are only shown on peer-reviewed articles (i.e. not on Preprints) and are currently disabled on mobile devices due to the smaller screen size..

Three different ways - each with a different use case

1 - To the left of each paragraph, figure, and table on peer-reviewed articles you will see a faded comment icon that when hovered over will turn orange. Click it to reveal any questions and form for that section.

2 - Another way to add questions (example on Preprints) is to scroll to the bottom of the preprint or article and locate the "Ask a question" button. Not every section in an article is supported yet, for example supplemental files, so using the question form at the bottom of a paper makes sense in these situations.

3 - A final way to add a question is to go to the question index and ask a question that is unconnected to any article or preprint. This is useful for asking general questions. The search index is also accessible from the top navigation bar anywhere on the PeerJ site - locate the "Q&A " in the black navigation bar.

This is very important - anyone can ask a question or answer one. It doesn't have to be the author of a paper who answers, though that may be easier or make sense depending on the question.

Multiple answers can also be provided for each question, however individuals can only answer once per question.

You can edit your question, answer, or comment indefinitely. A history is started after a few minutes to give you time to correct any obvious typos, etc first.

We feel that allowing edits to improve a question or answer is critical if we want to create the best source of information about a subject. It makes sense then to keep a history in order to track changes. Keep in mind that votes can be removed if someone disagrees with a new edit.

Anyone can ask questions, give answers, or comment, but not everyone can vote. Voting privileges must be earned first. To give more credibility to the voting system, and thus the annotations, you must have at least 15 contribution points in at least one subject area.

If you've already authored an article in PeerJ or PeerJ Preprints then you've already received enough points to vote in any subject area. The same is true for academic editors or reviewers who elected to make their review open.

For everyone else, you can stil get points by contributing a question, answer, or comment and getting voted up by others. It only takes three up votes to get voting privileges. Or, someone can "accept" your answer. "Accepted" answers are given 15 points. There are other ways as well (see above for points available).

While anyone can ask a question or create an answer, only the original question author can accept an answer. When to accept is up to you, but only one answer can be accepted per question. If more than one answer is acceptable then you can still vote the others up and the answer author will receive contribution points for the vote.

Your user profile. You'll need to tick the "make profile visible" in your user settings first though. If your profile page is private, only your name, image if you uploaded one, and any articles published or edited will appear to other visitors.