Question on new DOI Changes

I was really excited to see that DOIs can now be included for references.

"For most reference types Paperpile lets the citation style control how to display DOIs and URLs. However, for print articles Paperpile does not show DOIs or URLs by default. More precisely, citations of types “Journal article” and “News article” with the field “pages” set will not include DOIs or URLs. To override this behavior activate the option “Always include DOI and URLs”.

My question is this. Where you do you set the override indicated above?

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It’s at the bottom of the citation style dialog.

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Does this only work for new documents or also for existing/ongoing documents?

If you checkmark the “Alway include DOIs and URLs …” box and reformat the references, nothing really changes. Maybe I am missing something? I checked whether all the papers have DOIs and they do.

It also works for old documents. However, you need to make sure the style you choose actually shows DOIs. Some styles never show DOIs and Paperpile does not override that.

It’s a surprisingly complex topic how to include DOIs and URLs in citations. We tried to explain it in our help pages ( but we should point this out more clearly there.

Thanks for your answer! I agree it’s very tricky. The problem is that some styles (such as mBio) do not need a DOI for most citation types. However, they do require the DOI if the citation is from an online-only publication and/or the page/volume numbers are not in the standard format. I am not sure if the citation style file has these exceptions coded in, though.

That is exactly the problem! Some CSL files have these exceptions coded in and some do not. The CSL file you mentioned (“journal-of-molecular-biology.csl”) for example, has a conditional on the “volume”. If the volume is not present, it will display the DOI otherwise not. It does, however, not check for the “pages”.

If you select the option “Always include DOIs and URLs”, it does not necessarily mean that all the formatted references will have a DOI at the end. It still depends on the implementation of the particular CSL file if the DOI or URL will be displayed. From our side “Always include DOIs and URLs” means that we will provide DOIs and URLs to the CSL Processor (citeproc-js) and then the particular CSL file setting will decide if the DOI or URL will be displayed.

Personally, I find the approach to define a journal as an online-only journal solely on the presence/absence of volume or pages a bit tricky. PLoS ONE is the classic online-only journal, but each article gets a volume and a page number assigned. Based on these rules, PLoS ONE articles will however not receive a DOI when formatted with this style.

There is no easy solution to this problem. And finding one that fits everyone’s needs is even more tricky.

I feel your pain and I am sorry to be hovering around this topic. However, I am now inserting DOIs into everything by hand. (Super painful as well…)

Could the option “include DOI” perhaps override every and all CSL file rules and show the DOI after the CSL Processor step? Is this very hard?

No, we definitely can’t do that.

For this kind of scenario we actually have the option to upload your own CSL style. The easiest would be to start with your style and use the style editor here to add DOIs:

I wonder why do you need DOIs? If the journal wants it chances are that the CSL style is not correct anyway and you could contribute your changes back to the repository.

More general note: Don’t read instructions to authors. If you don’t care about DOIs and only the journal requires it, just ignore it. If it is an open access journal they get thousands of dollars and that should be enough to figure it out themselves. If it’s a closed access journal they make billions a year and I don’t think you should worry too much making their job easier printing your paper.

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