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In the recently published seventh edition of the Publication Manual of the APA, a change was made to the citation style guidelines to allow authors to use shortened URLs in the References section, including shortDOIs. The change is discussed here with regard to shortened URLs, but shortDOIs are mentioned with only an explanation of what they are, not with guidelines on how to use them. The article does mention, however, that some journals may restrict use of shortened URLs.

Using a shortDOI seems like the best option in any case, since it occupies a fraction of the space of a full DOI. For example, https://doi.org/10.1016/j.chb.2019.03.032 becomes https://doi.org/ggcgpd. It's also far easier to enter the shortDOI into a web browser than the full DOI.

Is there any reason not to use the shortDOI service when creating a references list, either for a student paper or a manuscript for submission to a journal? Are there journals that give guidelines on when to use a shortDOI, since the APA manual simply states that it is optional when a DOI is "long or complex?" Are there other ways in which using a shortDOI might be problematic?

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The shortDOI service will work for referring your readers to the source, but is not widely used, and its use is even discouraged behind the scenes. As of July 2022 the shortDOI site states it was updated in April 2013, which gives some indication of its current status. The problem with shortDOI is that it just provides an alias for (i.e. link to) the actual DOI, that has to be created and maintained on top of the existing service, and then transformed whenever used. This made sense for its original purpose as a link shortener for, e.g., emails and mobile messaging, but with other uses it results in duplicate paper identifiers that cause extra work for anyone maintaining indices of papers, for example. And since shortDOIs never got that popular in the first place, not all APIs/services support them.

Journals and other publication venues are recommended to not use shortDOIs, but to make shorter regular DOIs. See this Twitter thread or Crossref's DOI display guidelines (emphasis mine):

The International DOI Foundation created the ShortDOI service as an open system that creates shortcuts to DOIs. DOIs can be long, so this service aimed to to the same thing as URL shortening services. For example, for the DOI https://doi.org/10.7774/cevr.2016.5.1.1, the short form is https://doi.org/bwfc. Only one ShortDOI is created for each DOI, and the ShortDOI returns exactly the same results as the DOI. ShortDOIs are not widely used and are not really actual DOIs themselves, which is confusing. We recommend simply creating shorter DOIs in the first place. Learn more about constructing your DOIs.

Given the above, I'd suggest it's generally better practice to use the regular DOI in bibliographies. This is especially the case if the DOI is only used as a hyperlink rather written out in the bibliography. That said, I am not aware of any journal publicly taking this position. Few journals seem to mention shortDOI at all, but there are some that make its use optional. For example, Workplace Health & Safety's author instructions state

When a DOI or URL is long or complex, you may use shortDOIs or shortened URLs if desired. Use the shortDOI service provided by the International DOI Foundation (http://shortdoi.org/) to create shortDOIs.

I was also able to find one journal that requests authors using shortDOIs: Cognitive Sustainability. Their Submission Preparation Checklist includes

Where available, URLs and DOIs for the references have been provided. Please use ShortDOI (http://shortdoi.org/).

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