In eXtyles builds starting with 4550, Reference Processing parses references to preprints, but does not restructure them. (This is similar to how eXtyles handles conference proceedings.) Preprint references are tagged as <prpt>.

Why aren't preprint references restructured?

Because guidelines for citing preprints are still maturing, it’s safer to leave judgements about which elements to include and how to format them in the hands of experienced human editors. We’ve also found that the citation data submitted by authors varies widely, and we can’t always count on finding all the elements necessary to create a complete citation.

If your eXtyles configuration includes Crossref Linking and Correction, eXtyles queries Crossref to find DOIs for preprints, just as it does for other types of references. 

  • If Crossref returns a preprint DOI, eXtyles will insert it. 
  • If Crossref returns a DOI for the published version instead—which happens quite frequently—eXtyles will find and insert the DOI for the preprint if possible; however, this is possible only if the preprint metadata is correctly linked in Crossref. 
  • If the Crossref metadata indicates a final publication DOI for the preprint, eXtyles will also add a comment with the DOI and other publication for the journal article.

Reference lists exported from eXtyles to JATS comply with JATS4R recommendations for citing preprints.

Crossref linking and preprints

When you run Crossref Linking and Correction, you may see inconsistent results for preprints. eXtyles does its best, but the results depend on how Crossref resolves link queries. Unfortunately, Crossref query results are inconsistent, and sometimes Crossref does not have complete metadata.

Here’s an example. This input reference yields an “ideal” output: eXtyles adds the preprint DOI to the reference and adds a comment with information about the final publication as a journal article.


1. Dunham I. FORGE: A tool to discover cell specific enrichments of GWAS associated SNPs in regulatory regions. bioRxiv. 2014


In this case, eXtyles can provide both DOIs, because publishers have provided all the necessary metadata and Crossref has correctly cross-referenced the two DOIs. 

However, we also see cases like this one:


2. Lou B, Li T, Zheng S, et al. Serology characteristics of SARS-CoV-2 infection since the exposure and post symptoms onset. medRxiv. Preprint posted March 27, 2020.

Output A (final publication info missing)


Output B (preprint DOI missing)

Outputs A and B come from submitting exactly the same input to Crossref two different times, less than 1 minute apart. 

In Output A, eXtyles was able to find correct DOI for the preprint, but because the preprint and the published journal article aren’t linked in the Crossref database, there's no comment providing information about the published article. 

In Output B, eXtyles instead found the DOI for the published journal article in the Crossref database. eXtyles is smart enough to recognize that this isn’t the correct DOI, so it inserts a comment instead of just adding the DOI to the reference. But since the preprint and the final publication aren’t linked in the Crossref database, eXtyles can't add the preprint DOI.