Status: Published
Version: 2.0
License: this recommendation document is licensed under CC BY-ND 2.0 UK
DOI: https://doi.org/10.3789/niso-rp-36-2020
ISBN: 978-1-950980-09-3
Provenance
Version 1.0 reworked by Melissa Harrison based on feedback and alignment with Data availability statements recommendation. This was then reviewed by the JATS4R Steering Committee.
Change history
Version 1.0 can be found here here.
Additional content:
- As per the JATS4R recommendation on Data availability statements, there are four options for capturing references to data. However, including the references within the main <ref-list> for the article is recommended by the Force11 Publishers Early Adopters Expert Group, and only those references are recognised by Google Scholar. See recommendation 2.
- Recommendations 7 onwards have been updated or added.
Context
<ref>, <mixed-citation>, <element-citation>, <person-group>, <data-title>, <source>, <year>, <pub-id>, <ext-link>, <version>
@publication-type, @person-group-type, @pub-id-type, @assigning-authority, @designator, @xlink:href
Description
This recommendation contains best practices for tagging citations to datasets in a reference list.
As per the JATS4R Recommendation on Data availability statements, there are four options for capturing references to data. However, including the references within the main <ref-list> for the article is recommended by the Force11 Publishers Early Adopters Expert Group, and only those references are recognised by Google Scholar.
- These recommendations only apply to JATS 1.1 and forward, because the tags needed to make data citations machine readable are only available from 1.1 onwards.
- The following recommendations are specifically about citations related to data and datasets. See JATS4R’s recommendations for Citations (general).
Additional reading
- Adapting JATS to support data citation
- Force 11 Joint Declaration of Data Citation Principles
- A data citation roadmap for scientific publishers
Recommendation
- @publication-type=”data” on <mixed-citation> or <element-citation>. Use “data” as the value of @publication-type to indicate that the citation is to a dataset, even if that dataset is the entire data repository.
[[Validator tool result: if @publication-type not “data” and <data-title> is present ERROR]]
- @specific-use on <element-citation> or <mixed-citation>. For publishers who elect to collect such granularity in their workflow, see the table below for four @specific-use attributes recommended for JATS XML. For publishers who use the Relation Type method for Crossref deposits we’ve provided a mapping in the table.
| Data type (@specific-use) | Description | Map to this Crossref relationship type |
| “supporting” | Data that supports the study’s findings. Use this generic value if you do not wish to further distinguish whether the supporting data were generated or analyzed | “œreferences” |
| “generated” | Supporting data that were generated for the study | “isSupplementedBy” |
| “analyzed” | Supporting data that were analyzed (but not generated) for the study | “references” |
| “non-analyzed” | Referenced data that were neither generated nor analyzed for the study | “references” |
| – | Data type is not indicated (no @specific-use value is supplied) | “references” |
- [[Validator tool result: if a “Clean Value Test” on these strings in @specific-use fails. Example, warning if the value is “nonanalyzed” or “non-analysed” WARNING]]
- @person-group-type on <person-group>. As of version 1.1, the list of values for this attribute includes “curator”, specifically to support data citations. Use “curator” whenever appropriate.
- <data-title> / <source>. At least one of <data-title> or <source> must be present. <data-title> should hold the title of the dataset. <source> should contain the name of the holding repository. Both should be present if applicable.
[[Validator tool result: if @publication-type on (parent::mixed-citation or parent::element-citation) is “data” and one of <data-title> or <source> is not present ERROR]]
- <year>. This should contain the 4-digit year of publication. If the element contains anything other than a single 4-digit year (such as, for example, “2012”, “2005Q1”), then use the @iso-8601-date attribute to specify the 4-digit year.
[[Validator tool result: if the content is not a 4-digit year and there is no @iso-8601-date with content ERROR]]
- <pub-id>. This element should be used to hold the repository ID for the data. The repository ID should be a DOI or similar persistent identifier. The @pub-id-type attribute must be used — see the next recommendation for details.
- @pub-id-type on <pub-id>. In contrast to what is stated in the Tag Library (“Type of publication identifier or the organization or system that defined the identifier”) this attribute should only be used to state the type of identifier, and not to specify the organisation or system that defined the identifier.
[[Validator tool result: Defer result pending the discussion of the attribute value registry]] - @assigning-authority on <pub-id>. When the given type of identifier can be assigned by more than one organisation (e.g. DOIs minted by CrossRef or DataCite) and the organisation registering the identifier is known, include the @assigning-authority attribute on the <pub-id> element. For example, a DOI that is assigned by CrossRef should have “doi” as the @pub-id-type, and “crossref” as the @assigning-authority. For many types of identifiers, there is only one assigning authority. For example, PubMed IDs are always assigned by the National Library of Medicine. In these cases @assigning-authority is not necessary.
- @xlink:href on <pub-id>. Optional. Including an @xlink:href with a fully resolved URI can improve the near term reusability of content. However, as identifying authorities can change their base URIs over time, omitting @xlink:href can improve the long term reusability of content. The decision to include @xlink:href should be evaluated by the interested parties on a case by case basis.
- <ext-link>. Use <ext-link> to provide a link directly to the data citation. If there is no pub-id, ext-link should be included.
[[Validator tool result: if no pub-id or ext-link ERROR]]
- <version>. Use this element to display the human-readable version number of the dataset.
- @designator on <version> (1.1 and above). Use this attribute to contain the machine-readable version number of the dataset. The element contents can be a more human-readable note (see the example).
[[Validator tool result: if <version> present and no @designator present ERROR]]
Examples
Example 1
<ref id="d1">
<element-citation publication-type="data" specific-use="analyzed">
<person-group person-group-type="author">
<collab>The Concerto Consortium</collab>
<name>
<surname>van Beethoven</surname>
<given-names>Ludwig</given-names>
</name>
<name>
<surname>Liszt</surname>
<given-names>F</given-names>
</name>
</person-group>
<person-group person-group-type="curator">
<name>
<surname>Bach</surname>
<given-names>JS</given-names>
</name>
</person-group>
<data-title>Title of dataset</data-title>
<year iso-8601-date="2014">2014</year>
<source>Repository Name</source>
<pub-id pub-id-type="doi" assigning-authority="datacite">10.1234/1234321</pub-id>
<version designator="16.2">16th version, second release</version>
</element-citation>
</ref>
Example 2: Some additional examples
<!--Data reference: Dryad dataset -->
<ref id="bib8">
<element-citation publication-type="data">
<person-group person-group-type="author">
<name>
<surname>Kok</surname>
<given-names>K</given-names>
</name>
<name>
<surname>Ay</surname>
<given-names>A</given-names>
</name>
<name>
<surname>Li</surname>
<given-names>L</given-names>
</name>
<name>
<surname>Arnosti</surname>
<given-names>DN</given-names>
</name>
</person-group>
<year iso-8601-date="2015">2015</year>
<data-title>Data from: Genome-wide errant targeting by Hairy</data-title>
<source>Dryad Digital Repository</source>
<pub-id pub-id-type="doi" >10.5061/dryad.cv323</pub-id>
</element-citation>
</ref>
<!--Data reference: RCSB Protein Data Bank -->
<ref id="bib9">
<element-citation publication-type="data">
<person-group person-group-type="author">
<name>
<surname>Du</surname>
<given-names>J</given-names>
</name>
<name>
<surname>Johnson</surname>
<given-names>LM</given-names>
</name>
<name>
<surname>Groth</surname>
<given-names>M</given-names>
</name>
<name>
<surname>Feng</surname>
<given-names>S</given-names>
</name>
<name>
<surname>Hale</surname>
<given-names>CJ</given-names>
</name>
<name>
<surname>Li</surname>
<given-names>S</given-names>
</name>
<name>
<surname>Vashisht</surname>
<given-names>AA</given-names>
</name>
<name>
<surname>Gallego-Bartolome</surname>
<given-names>J</given-names>
</name>
<name>
<surname>Wohlschlegel</surname>
<given-names>JA</given-names>
</name>
<name>
<surname>Patel</surname>
<given-names>DJ</given-names>
</name>
<name>
<surname>Jacobsen</surname>
<given-names>SE</given-names>
</name>
</person-group>
<year iso-8601-date="2014">2014</year>
<data-title>Crystal structure of KRYPTONITE in complex with mCHH DNA and
SAH</data-title>
<source>RCSB Protein Data Bank</source>
<pub-id pub-id-type="doi">10.2210/pdb4qen/pdb</pub-id>
</element-citation>
</ref>
<!--Data reference: ArrayExpress: pub-id-type="accession"-->
<ref id="bib11">
<element-citation publication-type="data">
<person-group person-group-type="author">
<name>
<surname>Radoshevich</surname>
<given-names>L</given-names>
</name>
<name>
<surname>Impens</surname>
<given-names>F</given-names>
</name>
<name>
<surname>Ribet</surname>
<given-names>D</given-names>
</name>
<name>
<surname>Quereda</surname>
<given-names>JJ</given-names>
</name>
<name>
<surname>Nam Tham</surname>
<given-names>T</given-names>
</name>
<name>
<surname>Nahori</surname>
<given-names>MA</given-names>
</name>
<name>
<surname>Bierne</surname>
<given-names>H</given-names>
</name>
<name>
<surname>Dussurget</surname>
<given-names>O</given-names>
</name>
<name>
<surname>Pizarro-Cerdá</surname>
<given-names>J</given-names>
</name>
<name>
<surname>Knobeloch</surname>
<given-names>KP</given-names>
</name>
<name>
<surname>Cossart</surname>
<given-names>P</given-names>
</name>
</person-group>
<year iso-8601-date="2015">2015b</year>
<data-title>Transcription profiling by high throughput sequencing of LoVo
cells infected with Listeria for 24 hr compared to uninfected
cells</data-title>
<source>ArrayExpress</source>
<pub-id pub-id-type="accession"
xlink:href="https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3649/"
>E-MTAB-3649</pub-id>
</element-citation>
</ref>
<ref>
<mixed-citation publication-type="data" id="msb188202-cit-0063">
<person-group person-group-type="author">
<string-name>
<surname>Vaarala</surname>
<given-names>MH</given-names>
</string-name>, <string-name>
<surname>Hirvikoski</surname>
<given-names>P</given-names>
</string-name>, <string-name>
<surname>Kauppila</surname>
<given-names>S</given-names>
</string-name>, <string-name>
<surname>Vuoristo</surname>
<given-names>JT</given-names>
</string-name>, <string-name>
<surname>Paavonen</surname>
<given-names>TK</given-names>
</string-name>
</person-group>
(<year>2012</year>)
<data-title>Androgen regulated gene expression in human prostate</data-title>,
<source>Gene Expression Omnibus</source>, <pub-id pub-id-type="accession" xlink:href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32982">GSE32982</pub-id>.
</mixed-citation>
</ref>
<ref id="ref1">
<mixed-citation publication-type="data" id="data1" specific-use="analyzed">
<person-group person-group-type="author">
<string-name>
<surname>Traka</surname>
<given-names>M</given-names>
</string-name>, <string-name>
<surname>Gasper</surname>
<given-names>AV</given-names>
</string-name>, <string-name>
<surname>Melchini</surname>
<given-names>A</given-names>
</string-name>, <string-name>
<surname>Bacon</surname>
<given-names>JR</given-names>
</string-name>, <string-name>
<surname>Needs</surname>
<given-names>PW</given-names>
</string-name>, <string-name>
<surname>Frost</surname>
<given-names>V</given-names>
</string-name>, <string-name>
<surname>Chantry</surname>
<given-names>A</given-names>
</string-name>, <string-name>
<surname>Jones</surname>
<given-names>AM</given-names>
</string-name>, <string-name>
<surname>Ortori</surname>
<given-names>CA</given-names>
</string-name>, <string-name>
<surname>Barrett</surname>
<given-names>DA</given-names>
</string-name>, <string-name>
<surname>Ball</surname>
<given-names>RY</given-names>
</string-name>, <string-name>
<surname>Mills</surname>
<given-names>RD</given-names>
</string-name>, <string-name>
<surname>Mithen</surname>
<given-names>RF</given-names>
</string-name>
</person-group>
(<year>2008</year>)
<data-title>Transcription profiling by array of human prostate from patients with a previous diagnosis of Prostatic Intraepithelial Neoplasia and following consumption of high glucosinolate broccoli or peas to investigate interactions with the GSTM1 genotype</data-title>.
<source>ArrayExpress</source>.
<pub-id pub-id-type="accession" assigning-authority="EBI:arrayexpress">E?MEXP?1243</pub-id>
(<ext-link extlink-type="uri" xlink:href="https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-1243">https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-1243</ext-link>).
</mixed-citation>
</ref>
History
Working: September – October 2019
JATS4R Steering Committee review: November 2019 – April 29, 2020
Public review: April 29 – May 29, 2020
JATS4R Steering Committee review: May 30 – June 26, 2020
NISO Topic Committee approval: June 26 – July 26, 2020
Published: September 21, 2020
only becomes available in JATS 1.1 and later. Probably need to update to mention that. e.g.
(JATS v1.1 and forward).
/ . At least one of or must be present. should hold the title of the dataset. should contain the name of the holding repository. Both should be present if applicable.
(JATS v1.0 and earlier).
/ . At least one of or must be present. should hold the title of the dataset. should contain the name of the holding repository. Both should be present if applicable.
The validator tool will also need to account for this:
[[Validator tool result: (if JATS 1.1 and forward) @publication-type on (parent::mixed-citation or parent::element-citation) is “data” and one of or is not present ERROR]]
[[Validator tool result: (if JATS 1.0 and earlier) @publication-type on (parent::mixed-citation or parent::element-citation) is “data” and one of or is not present ERROR]]