Academic Publishing Wiki

There are two types of review articles in wiki publishing.

  1. Literature reviews are articles in which the author(s) review previously published ("formally published") articles.
  2. Peer review articles are critical evaluations of a single article.

This page contains instructions for peer review of articles in wiki format. If you perform a peer review of an article, you perform a critique of the style and intellectual content of the target article.

Peer Review Template

If you perform a peer review of an article that has been marked as a target for peer review, you report the results of your critique in the form of a wiki article. As soon as you begin to work on your peer review article, you should create a wiki page for your article and place the {{Peer Review Article}} template on your page.

Writing a peer review article is a serious commitment to the wiki publishing community. You are expected to complete your review in a timely manner. DO NOT even start to write a peer review article unless you are certain that you can complete it in a timely manner. Also, remember that your article will itself be subject to peer review by the wiki publishing community. If you publish a shoddy peer review, you can expect to suffer negative consequence including damage to your reputation as a reviewer and restriction of your freedom to publish in wiki journals.

Peer Review Outline

If you write a peer review article, you MUST make use of a peer review outline. In most cases, you should use the peer review outline that is required by the particular journal that the target article was submitted to.

There is a generic Peer review article outline that was created for articles submitted to a journal. If you wish to peer-review an article that has been submitted to Bioinformatics Journal, you MUST use this generic Peer review article outline. (Repeating: Bioinformatics Journal is currently using the generic peer review article outline for peer review of articles submitted to a journal.)

Peer Review

There are special rules for articles that are peer reviews of other articles. Authors can make modifications to their original articles while they are under peer review. For example, if a reviewer makes a good suggestion about how to improve an article, the author is free to modify the article in an attempt to improve the article and satisfy the reviewer. It is very important that reviewers make note of which version of an article is being reviewed. This information should be place in the "notes" section of your peer review article.

Authors are also free to either ignore a reviewer's suggestions or submit a rebuttal of a peer review article. If an author thinks a reviewer is wrong, a rebuttal can be given in the form of a new peer review article that is submitted as a critique of the peer review article that was targeted at the original article. Minor disputes and points of information can be exchanged between authors and reviewers by way of discussion pages; such resolution of issues should be attempted first. Note: there are only two steps in the peer review process.

  1. The reviews of an original article
  2. Author response to those reviews (optional)

If a reviewer wishes to formally respond to a rebuttal, the reviewer will do so in an appendix to their original peer review article.

Under the best of conditions, an article will be promptly reviewed by two reviewers and both will suggest that the reviewed article be published. If this happens, the article will qualify for "formal publishing" (see the next section, below).

Reviewers are expected to give detailed accounts of what they like and don't like about a reviewed article. Reviewers are also required to describe the scope of their review and give your article a ranking.

Scope of Reviews. The decision by Bioinformatics Journal about formally publishing an article requires at least two complete peer reviews of the article. Not all peer reviews are complete reviews. Some reviewers do not have competence or time to completely review your article, but they may be able to provide expert evaluation of parts of your article. Such partial reviews can be useful to the complete reviewers who will decide if an article should be formally published in Bioinformatics Journal.

Article rankings by peer reviewers. Peer review articles are expected to include a ranking of the reviewed article. Bioinformatics Journal uses a three value ranking system.

  1. Positive. If a reviewer gives a rank of "positive" this means that the reviewer wants the article to be formally published by Bioinformatics Journal. However, the reviewer can give an article a positive ranking while still requiring certain changes to the article. Generally such requirements must involve only minor alterations to the reviewed article.
  2. Neutral. A ranking of "neutral" means that the reviewer sees value in an article, but the reviewer is unable to recommend formal publication until the author of the reviewed article address concerns listed by the reviewer. Reviewer concerns might include questions that the authoer must answer in a rebuttal or changes that the author can simply make in the article. When the reviewer is informed that changes have been made in response to their request, if the changes satisfy the reviewer, the reviewer can change their ranking from "neural" to "positive".
  3. Negative. A ranking of "negative" means that the reviewer does not want to see the reviewed article formally published in Bioinformatics Journal. A reviewer who gives an article a negative ranking must explain what is wrong with the article. In the worst case, the reviewer may feel that the article is a complete disaster and may resent the fact that they wasted time reading it. Such a reviewer response can have serious implications if it is backed up by similar responses from other reviewers.

If two reviewers agree that an article is a waste of time, the Bioinformatics Journal community may decide that any future article submissions from the author of the reviewed article require prescreening. In the worst case, the reviewers might both judge that the author is spamming the journal and the author might be told that future submissions are not welcome.

If only one of the first two complete reviewers of an article decides that the article should be published, then at least one more complete review might be required as a tie breaker. If neither of the first two reviewers gives the article a negative ranking, then the author has the option of withdrawing submission, trying to rebut the reviewers, or modifying the article in an attempt to satisfy the reviewers.

If one reviewer is positive or neutral but a second reviewer is negative, then the author of the reviewed article can try to rebut the negative reviewer. If a negative reviewer does not change their ranking of the article after reading a formal rebuttal from the author of the reviewed article, the author can wait for a third tie-breaking reviewer to critique the article or can withdraw the submission and try to publish in a different journal.

If there are more than two complete reviewers of an article and some reviewers rank the article as positive and others rank it as negative, then a cancellation rule goes into effect. One positive ranking cancels one negative ranking. A net ranking of two or more positives (after all negatives have been cancelled by additional positives) is required for formal publication in Bioinformatics Journal.

A net ranking of two or more negatives (after all positives have been canceled by additional negatives) is a rejection of the article. There is a chance that the author of a rejected article can successfully rebut the negative reviewers, or the author might decide to withdraw the submission and take the article to another journal.

Negative rankings of submitted articles are always a serious matter. This is true of articles that are themselves peer reviews. As mentioned above, authors who submit an article for peer review can in turn review the peer review articles that critique the originally submitted article. The same three-valued (positive, neutral, negative) ranking system is applied to peer review articles themselves. However, these rankings are used in different way than are the rankings of regular articles. Any member of the Bioinformatics Journal community can perform peer reviews. Peer review of peer review articles is important to the Bioinformatics Journal community. Peer review of peer review articles is a form of quality control for the peer reviewers themselves.

  1. Two negative rankings of a peer review article can cancel that peer review article's utility as part of a decision for formal publication of an article. For example, if two members of the Bioinformatics Journal community submit peer review articles that give negative rankings of an earlier peer review article, this can cancel the effect of that earlier peer review article. A negative ranking of another peer review article is a warning sign to the Bioinformatics Journal community that there may be a problem with a reviewer. A negative ranking of a peer review article must be accompanied by explicit description of error, bias, misconduct or poor judgment on the part of the original reviewer.
  2. Neutral rankings of a peer review article must be accompanied by specific suggestions for reconsideration on the part of the original reviewer. This is a form of questioning the judgment of another reviewer or bringing a new perspective to the attention of another reviewer.
  3. Positive rankings of a peer review article are a vote of confidence in favor of the original reviewer. One positive ranking of a peer review article can cancel the effect of one negative ranking. This can be important if the Bioinformatics Journal community is contemplating restrictions on a reviewer who has received negative rankings for past peer review articles.

Formal publishing

As described above, if the peer review process determines that there is a community consensus in favor of publication of an article, then formal publication becomes possible. In general, this means that there are two more positive reviewers of the article than negative reviewers. When the reviewers of an article agree that the author of the article has made adequate modifications in response to the requests of the reviewers, then a reviewer can mark the article with the Bioinformatics Journal Published Article template.

What happens after formal publishing?
Wiki journal does not generally accept articles that cite non-peer-reviewed sources. Once an article is formally published by Bioinformatics Journal, other authors can begin to make citations to that article. As discussed below, sometimes formally published wiki articles can change after publication, so citations to wiki journal articles should always explicitly cite the date of a specific version of the article that is cited.

After formal publishing, the first author of an article still has some control over the article. Some authors may decide to never allow future editing of a formally published article. Other authors may leave an article marked as open for Minor edits in order to allow the Bioinformatics Journal community to continue to correct minor errors in the article. For some articles, particularly literature review articles, authors may decide to periodically update the content of the article. In some cases, the first author may be open to adding new co-authors after formal publication who would assist in keeping the article updated and up to date as a review of the literature.

The Bioinformatics Journal also allows peer review to continue after formal publication of an article. This can be important for several reasons. Errors might be found in an article only after it has been formally published. Also, for articles that are updated by their author(s) after formal publication, new errors or problems might arise that warrant new critical evaluation by the Bioinformatics Journal community.