Data availability statements

Status: PENDING DECISION

Pending Notice: This draft is pending the addition of the new <data-availability> element, submitted as a request to the JATS Standing Committee for inclusion in JATS 1.2. Submitted April 21, 2017: http://www.niso.org/apps/group_public/view_comment.php?comment_id=738&add_comment=1

 Context

<back>, <data-availability-statement>, <ref-list>

Description

There are three types of data that may be associated with an article:

  • Generated data: Included or referenced data that were generated for the study
  • Analysed data: Referenced data that were analysed for the study but were not generated for the study
  • Non-analysed Data: Referenced data that were neither generated nor analysed for the study

Full, structured citations should be provided for any referenced data; i.e., externally archived generated data, analysed data, and non-analysed data.
Recommended practice is to indicate the location(s) of any data that were generated or analysed for the study in a Data Availability statement (DAS). We recommend excluding non-analysed data from the DAS, and instead, only including it in the main reference list of the article. For any data that are not provided within the paper (i.e., as a table or a supplementary file/source data file), the DAS should provide access to the external data locations, either as direct links, or as links to the relevant reference included in the article’s reference list(s). If any generated or analysed data is not publicly available, the DAS should provide reasons for the omission.

Additional reading

Recommendations

  1. <back>. Contain the DAS in a <sec> element within <back> until such time as the <data-availability> element becomes available (see below)
  2. @sec-type=”data-availability” should be used on this <sec>
  3. <data-availability> {Pending approval by the JATS Standing Committee for JATS v1.2}. When this element is included in JATS, place it directly in <back> to contain the data availability information
  4. Use a <title> element to contain the title, and contain the substance of the text within <p>
  5. <ref-list> References for the data. There are three options for capturing references to data, as follows:
    • Contain references to data within a <ref-list> directly in the <data-availability> element; OR
    • Contain the references within the main <ref-list> for the article; OR
    •  Contain the data references within a sub-level <ref-list> at the end of the article
    • The recommendation from the Joint Declaration of Data Citation Principles is for option 2.
  6. <element-citation> or <mixed-citation>, @publication-type=”data”. Use this attribute on all <element-citation> or <mixed-citation> elements that contain references to data
  7. @specific-use. Publishers who use Method B (Relation Type) for Crossref deposits should use @specific-use on <element-citation> or <mixed-citation> to contain appropriate CrossRef inter_work_relation/@relationship-type values, as follows:

 

Type of data reference inter_work_relation/@relationship-type
Generated data that is externally archived “isSupplementedBy”
Analyzed data “references”
Non-analyzed data “references”

Examples

Example 1: Data files provided in the paper

 <back>
. . .
<data-availability>
<title>Data Availability</title>
<p> All data are provided within the paper and its supporting information.</p>
</data-availability>
<ref-list>
<title>References</title>
...
</ref-list>
</back>

Example 2: Data files provided in the paper – includes links to the specific internal data files

<back>
. . .
<data-availability>
<title>Data Availability</title>
<p> All data are provided in <xref ref-type="table" rid="table1">
Table 1</xref> and <xref ref-type="supplementary-material" rid="data1">Datasets S1</xref> and <xref ref-type="supplementary-material" rid="data2">S2</xref>.</p>
</data-availability>
<ref-list>
<title>References</title>
...
</ref-list>
</back>
Example 3: Data externally archived – links to full citations in main References (using Vancouver style - numbered references)
<back>
. . .
<data-availability>
<title>Data Availability</title>
<p>The data analysis file and all annotator data files are available in the Figshare repository, <ext-link ext-link-type="uri" xlink:href="https://doi.org/10.6084/m9.figshare.1285515">https://doi.org/10.6084/m9.figshare.1285515</ext-link> [<xref ref-type="bibr" rid="pone.0167292.ref032">32</xref>]. The measured and simulated Euler angles, and the simulation codes are available from the Dryad database, <ext-link ext-link-type="uri" xlink:href="https://doi.org/10.5061/dryad.cv323">https://doi.org/10.5061/dryad.cv323</ext-link> [<xref ref-type="bibr" rid="pone.0167292.ref033">33</xref>]. Microarray data are deposited in the Gene Expression Omnibus under accession number <ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70542>GSE70542</ext-link> [<xref ref-type="bibr" rid="pone.0167292.ref034">34</xref>].</p>
</data-availability>
<ref-list>
<title>References</title>
[Insert references here]
</ref-list>
</back>

Example 4: Data externally archived – full citations included as a ref list within the DAS

<back>
. . .
<data-availability>
<title>Data Availability</title>
<p>The following datasets were generated or analyzed for this study:</p>
<ref-list>
<ref id="pone.0167830.data001">
<label>D1</label>
<element-citation publication-type="data" specific-use=”isSupplementedBy”>
<name><surname>Read</surname><given-names>K</given-names></name>
<data-title>Sizing the Problem of Improving Discovery and Access to NIH-funded Data: A Preliminary Study (Datasets)</data-title>
<source>Figshare</source>
<year>2015</year>
<pub-id pub-id-type="doi" assigning-authority="figshare" xlink:href="https://doi.org/10.6084/m9.figshare.1285515">https://doi.org/10.6084/m9.figshare.1285515</pub-id>
</element-citation>
</ref>
<ref id="pone.0167830.data002">
<label>D2</label>
<element-citation publication-type="data" specific-use=”references”>
<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>
<data-title>Genome-wide errant targeting by Hairy</data-title>
<source>Dryad Digital Repository</source>
<year>2015</year>
<pub-id pub-id-type="doi" assigning-authority="dryad" xlink:href="https://doi.org/10.5061/dryad.cv323">https://doi.org/10.5061/dryad.cv323</pub-id>
</element-citation>
</ref>
<ref id="pone.0167830.data003">
<label>D3</label>
<element-citation publication-type="data" specific-use=”references”>
<name><surname>Hoang</surname><given-names>C</given-names></name>
<name><surname>Swift</surname><given-names>GH</given-names></name>
<name><surname>Azevedo-Pouly</surname><given-names>A</given-names></name>
<name><surname>MacDonald</surname><given-names>RJ</given-names></name>
<data-title>Effects on the transcriptome of adult mouse pancreas (principally acinar cells) by the inactivation of the Ptf1a gene in vivo</data-title>
<source>NCBI Gene Expression Omnibus</source>
<year>2015</year>
<pub-id pub-id-type="accession" assigning-authority="NCBI" xlink:href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70542">GSE70542</pub-id>
</element-citation>
</ref>
</ref-list>
</data-availability>
<ref-list>
<title>References</title>
...
</ref-list>
</back>

Example 5: Data files provided in the paper – includes links to the specific internal data files

<back>
. . .
<data-availability>
<title>Data Availability</title>
<p>The data analysis file and all annotator data files are available in the Figshare repository:
<element-citation publication-type="data" specific-use="isSupplementedBy">
<name><surname>Read</surname><given-names>K</given-names></name>
<data-title>Sizing the Problem of Improving Discovery and Access to NIH-funded Data: A Preliminary Study (Datasets)</data-title>
<source>Figshare</source>
<year>2015</year>
<pub-id pub-id-type="doi" assigning-authority="figshare" xlink:href="https://doi.org/10.6084/m9.figshare.1285515">https://doi.org/10.6084/m9.figshare.1285515</pub-id>
</element-citation></p>
<p>The measured and simulated Euler angles, and the simulation codes are available from the Dryad database:
<element-citation publication-type="data" specific-use="references">
<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>
<data-title>Genome-wide errant targeting by Hairy</data-title>
<source>Dryad Digital Repository</source>
<year>2015</year>
<pub-id pub-id-type="doi" assigning-authority="dryad" xlink:href="https://doi.org/10.5061/dryad.cv323">https://doi.org/10.5061/dryad.cv323</pub-id>
</element-citation>
</p>
<p> Microarray data are deposited in the Gene Expression Omnibus under accession number GSE70542:
<element-citation publication-type="data" specific-use="references">
<name><surname>Hoang</surname><given-names>C</given-names></name>
<name><surname>Swift</surname><given-names>GH</given-names></name>
<name><surname>Azevedo-Pouly</surname><given-names>A</given-names></name>
<name><surname>MacDonald</surname><given-names>RJ</given-names></name>
<data-title>Effects on the transcriptome of adult mouse pancreas (principally acinar cells) by the inactivation of the Ptf1a gene in vivo</data-title>
<source>NCBI Gene Expression Omnibus</source>
<year>2015</year>
<pub-id pub-id-type="accession" assigning-authority="NCBI" xlink:href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70542">GSE70542</pub-id>
</element-citation>
</p>
</data-availability>
<ref-list>
<title>References</title>
….
</ref-list>
</back>

Example 6: Data externally archived – links to full citations in a separate section for Data References (ref links have an alternative labeling scheme)

<back>
. . .
<data-availability>
<title>Data Availability</title>
<p>The data analysis file and all annotator data files are available in the Figshare repository, <ext-link ext-link-type="uri" xlink:href="https://doi.org/10.6084/m9.figshare.1285515">https://doi.org/10.6084/m9.figshare.1285515</ext-link> [<xref ref-type="bibr" rid="pone.0167292.data001">D1</xref>]. The measured and simulated Euler angles, and the simulation codes are available from the Dryad database, <ext-link ext-link-type="uri" xlink:href="https://doi.org/10.5061/dryad.cv323">https://doi.org/10.5061/dryad.cv323</ext-link> [<xref ref-type="bibr" rid="pone.0167292.data002">D2</xref>]. Microarray data are deposited in the Gene Expression Omnibus under accession number <ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70542>GSE70542</ext-link> [<xref ref-type="bibr" rid="pone.0167292.data003">D3</xref>].</p>
</data-availability>
<ref-list>
<title>References</title>
….
</ref-list>
<ref-list>
<title>Data References</title>
[Insert references here]
</ref-list>
</back>

Example 7: Data cannot be made publicly available

<back>
. . .
<data-availability>
<title>Data Availability</title>
<p> Ethical restrictions according to the Japanese Ethical Guidelines for Human Genome/Gene Analysis Research (http://www.lifescience.mext.go.jp/files/pdf/n796_00.pdf, page 33) prevent public sharing of individual genotype data. All summarized data are available upon request. Data requests may be sent to the UMIN IRB (irb@xxxxxxxx.jp)..</p>
</data-availability>
<ref-list>
<title>References</title>
...
</ref-list>
</back>

Example 8: No data was generated [This seems unlikely, but it’s possible, e.g., for theoretical works]

<back>
. . .
<data-availability>
<title>Data Availability</title>
<p> During the course of this research no data was analysed, reused or generated.</p>
</data-availability>
<ref-list>
<title>References</title>
...
</ref-list>
</back>