• Marianne Calilhanna

JATS For Reuse Working Group - Preprint Citations

Updated: Apr 23

A guest blog by our friends at JATS4R and NISO


JATS4R (JATS for Reuse) is a working group devoted to optimizing the reusability of scholarly content by developing best-practice recommendations for tagging content in JATS XML. Public commenting on the JATS4R Preprint Citations recommendation is open.


You can add comments to the googledoc. The deadline for comments is Monday 4th May.

This recommendation document is licensed under CC BY-ND 2.0 UK


Description

In order to differentiate cited preprint articles from journal articles we recommend that a value of “preprint” is used to populate the @publication-type attribute when citing the article as it was published on the preprint server. 

Preprints have not been certified by journal-organized peer review. Most preprint servers apply some screening before a preprint is posted. Also, some preprints receive some form of review (e.g., Review Commons) and may have improved as a result, but the important difference is that the preprint version precedes journal acceptance. 

Note, F1000 and journals using the F1000 platform software, such as Wellcome Open Research, should not be treated as preprints (but as journal articles) because these articles are formally published from the outset and pass through peer review on the platform, whereas the current model for other preprint servers is that peer review is not managed on the preprint platform, a status change does not occur on the platform and this does not change its indexing status elsewhere, such as PubMed.

Note, JATS4R does not have a position on publishing practices; whether a journal updates preprint citations to journal citations should the article be subsequently published in a journal is up to the individual journal policy.


Context

<ref> and elements contained therein.


Recommendations

1.@publication-type=”preprint” on<mixed-citation> or <element-citation>. Use “preprint” as the value of @publication-type to indicate that the citation is a preprint.  

2. @person-group-type on <person-group> should be “author” by default [[Validator tool result:  Error if @person-group-type not present or not set to “author” and @publication-type=”preprint”]] 

3. <name> / <string-name> / <collab>. As per existing JATS4R recommendations on general citations, the <name> or <string-name> element should be used for an individual named author. Use <name> when the parent element is <element-citation>, and <string-name> when the parent is <mixed-citation>. When groups of authors (consortia) are cited under a group name or an institution is cited as the contributor, the <collab> element should be used.

4. <article-title>. This is used for the title of the preprint article.

[[Validator tool result:  Error if <article-title> not present and @publication-type=”preprint”]] 

5. <source>. This is used for the preprint platform name.

[[Validator tool result:  Error if <source> not present and @publication-type=”preprint”]] 

6. <pub-id>. Preprint articles should have a persistent identifier (PID). If there is no PID then the URL of the preprint article (see <ext-link> below) should be present.

[[Validator tool result:  Error if no <pub-id> or <ext-link> present ]] 

7. @pub-id-type on <pub-id> A typical id type will be “doi” or, for example “arxiv”

8. @assigning-authority on <pub-id>. It is not necessary to add this information but if the publisher choses to they must ensure the assigning-authority is correct. For example, not all DOIs are minted by Crossref, DataCite is another popular DOI provider.

9. <ext-link> This should be used to capture the URL of the cited preprint ONLY if no PID is provided. The @xmlns:xlink attribute should be used to capture the full URL without the use of entities. As per the JATS Tag Library, the @ext-link-type attribute should indicate the type of resource to which the link points. A list of commonly used values can be found in the PMC Tagging Guidelines.

[[Validator tool result: Error if <ext-link> and <pub-id> are both present ]]

10. <date date-type=”published”> . This is used for the published date of the preprint.

11. <year> is sufficient detail when providing a date for citations. It’s recommended that as much detail as possible is recorded in <date>

[[Validator tool result: Error if year is non-integer and and there is no @iso-8601-date. ]]

12. @iso-8601-date attribute on <date> is only required if the element content of <year> is non-integer. Otherwise it is recommended.

[[Validator tool result: Error if the year extracted from @iso-8601-date attribute does not match the numeric digits in the <year> element]]

13. <date-in-citation content-type=”access-date”>. It’s recommended that for preprint citations an access date be recorded with <year>, <month>, and <day>. If an access time is available it can be included in the @iso-8601-date.

. [[Validator tool result: Warning if date-in-citation[@content-type eq ‘access-date’] is absent. ]]


Examples

Preprint citation with DOI:

<ref id="bib3">
<element-citation publication-type="preprint">
<person-group person-group-type="author">
<name><surname>Bloss</surname><given-names>CS</given-names></name>
<name><surname>Wineinger</surname><given-names>NE</given-names></name>
<name><surname>Peters</surname><given-names>M</given-names></name>
<name><surname>Boeldt</surname><given-names>DL</given-names></name>
<name><surname>Ariniello</surname><given-names>L</given-names></name>
<name><surname>Kim</surname><given-names>JY</given-names></name>
<name><surname>Sheard</surname><given-names>J</given-names></name>
<name><surname>Komatireddy</surname><given-names>R</given-names></name>
<name><surname>Barrett</surname><given-names>P</given-names></name>
<name><surname>Topol</surname><given-names>EJ</given-names></name>
</person-group>
<year iso-8601-date="2016">2016</year>
<article-title>A prospective randomized trial examining health care utilization in individuals using multiple smartphone-enabled biosensors</article-title>
<source>bioRxiv</source>
<pub-id pub-id-type="doi">10.1101/029983</pub-id>
</element-citation>
 </ref>


Example of a citation to a version of a preprint where the versions have separate DOIs:

<ref id="bib3">
<element-citation publication-type="preprint">
<person-group person-group-type="author">
<name><surname>Nyhan</surname><given-names>B</given-names></name>
<name><surname>Helmke</surname><given-names>G</given-names></name>
<name><surname>Sanders</surname><given-names>M</given-names></name>
<name><surname>Clayton</surname><given-names>K</given-names></name>
<name><surname>Carey</surname><given-names>J</given-names></name>
<name><surname>Stokes</surname><given-names>S</given-names></name>
</person-group>
<year iso-8601-date="2019">2019</year>
<article-title>Who Will Defend Democracy? Evaluating Tradeoffs in Candidate Support Among Partisan Donors and Voters</article-title>
<source>APSA Preprints</source>
<pub-id pub-id-type="doi">10.33774/apsa-2019-wjva3-v3</pub-id>
</element-citation>
</ref>

Example of a citation to a new version of a preprint where the versions do not have separate DOIs:

<ref id="bib3">
<element-citation publication-type="preprint">
<person-group person-group-type="author">
<name><surname>Ding</surname><given-names>SS</given-names></name>
<name><surname>Muhle</surname><given-names>LS</given-names></name>
<name><surname>Brown</surname><given-names>AEX</given-names></name>
<name><surname>Schumacher</surname><given-names>LJ</given-names></name>
<name><surname>Endres</surname><given-names>RG</given-names></name>
</person-group>
<year iso-8601-date="2019">2019</year>
<article-title>Comparison of solitary and collective foraging strategies of Caenorhabditis elegans in patchy food distributions</article-title>
<source>bioRxiv</source>
<pub-id pub-id-type="doi">10.1101/744649</pub-id>
<date-in-citation content-type=”access-date iso-8601-date="2020-02-03">February 3, 2020</date-in-citation>
</element-citation>
</ref>

Example of a citation to a preprint that does not have a DOI, but a PID:

<ref id="bib3">
<element-citation publication-type="preprint">
<person-group person-group-type="author">
<name><surname>Liu</surname><given-names>T</given-names></name>
<name><surname>Wang</surname><given-names>X</given-names></name>
<name><surname>Wang</surname><given-names>H</given-names></name>
<name><surname>Shi</surname><given-names>G</given-names></name>
<name><surname>Gao</surname><given-names>F</given-names></name>
<name><surname>Feng</surname><given-names>H</given-names></name>
<name><surname>Deng</surname><given-names>H</given-names></name>
<name><surname>Hu</surname><given-names>L</given-names></name>
<name><surname>Lochner</surname><given-names>E</given-names></name>
<name><surname>Schlottmann</surname><given-names>P</given-names></name>
<name><surname>von Molnár</surname><given-names>S</given-names></name>
<name><surname>Li</surname><given-names>Y</given-names></name>
<name><surname>Zhao</surname><given-names>J</given-names></name>
<name><surname>Xiong</surname><given-names>P</given-names></name>
</person-group>
<year iso-8601-date="2001">2001</year>
<article-title>Spin selectivity through chiral polyalanine monolayers on semiconductors</article-title>
<source>arXiv</source>
<pub-id pub-id-type="arxiv">2001.00097</pub-id>
</element-citation>
</ref>

Example of a preprint that does not have a PID:

<element-citation publication-type="preprint">
<person-group person-group-type="author">
<name><surname>Font Clos</surname><given-names>F</given-names></name>
<name><surname>Zapperi</surname><given-names>S</given-names></name>
<name><surname>La Porta</surname><given-names>C</given-names></name>
</person-group>
<year iso-8601-date="2020">2020</year>
<article-title>Blood Flow Contributions to Cancer Metastasis</article-title>
<source>iScience</source>
<ext-link ext-link-type="uri" xlink:href="https://ssrn.com/abstract=3533512">https://ssrn.com/abstract=3533512</ext-link>
</element-citation>
</ref>

Provenance

JATS4R sub-group. Subgroup members (listed alphabetically):

  • Brooke Begin

  • Lauren Fischer

  • Michael Jensen

  • August Muench

  • Stephen Laverick (Chair)

  • Wei Zhao

*ASAPio preprint working group members (Members: Hannah Hope, Wellcome; Richard Sever, bioRxiv; Michael Markie, F1000; Brooks Hanson, AGU; Jessica Polka, ASAPbio; Melissa Harrison, eLife; Emily Marchant, CUP)


History

Working: September 27, 2017 – Jan 3, 2020

Committee Review: January 3 – February 2, 2020

Additional Review*: February 2 – February 12, 2020 

Committee Review: February 13 – March 25, 2020

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