Data Citations

Protein Data Bank in Europe sample:

...
<ref>
 <mixed-citation publication-type="data"><person-group
  ><string-name>Kollman JM</string-name>, 
  <string-name>Charles EJ</string-name>, <string-name
  >Hansen JM</string-name></person-group>, 
  <year iso-8601-date="2014">2014</year>, <data-title>Cryo-EM structure of 
  the CTP synthetase filament</data-title>, <ext-link ext-link-type="uri" 
  xlink:href="http://www.ebi.ac.uk/pdbe/entry/EMD-2700">
  http://www.ebi.ac.uk/pdbe/entry/EMD-2700</ext-link>, Publicly available 
  from <source>The Electron Microscopy Data Bank (EMDB)</source>.</mixed-citation>
</ref>
...

GigaScience sample:

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<ref>
 <mixed-citation publication-type="data">Zheng LY, 
  Guo XS, He B, Sun LJ, Pi CM, Jing H-C: Genome data from 
  [<ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/100012">
  http://dx.doi.org/10.5524/100012</ext-link>] <source>GigaScience</source> 
  <year iso-8601-date="2011">2011</year>.</mixed-citation>
</ref>
...

Data in figshare, referenced through a DOI:

...
<ref>
 <mixed-citation publication-type="data">Di Stefano B, Collombet S, 
  Graf T. <source>Figshare</source> <ext-link ext-link-type="doi" 
  assigning-authority="figshare" 
  xlink:href="http://dx.doi.org/10.6084/m9.figshare.939408">
  http://dx.doi.org/10.6084/m9.figshare.939408</ext-link> 
  (<year iso-8601-date="2014">2014</year>).</mixed-citation>
</ref>
...

Dryad Digital Repository, referenced through a DOI:

...
<ref>
 <mixed-citation publication-type="data"><person-group person-group-type="authors"
  ><string-name>Dubuis JO</string-name>, <string-name>Samanta R</string-name>, 
  <string-name>Gregor T</string-name></person-group> 
  (<year iso-8601-date="2013">2013</year>).  Data from: 
  <data-title>Accurate measurements of dynamics and reproducibility 
  in small genetic networks</data-title>. <source>Dryad Digital 
  Repository</source> doi:<pub-id pub-id-type="doi">10.5061/dryad.35h8v</pub-id>
 </mixed-citation>
</ref>
...

GenBank Protein sample:

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<ref>
 <mixed-citation publication-type="data">
  <data-title>Homo sapiens cAMP responsive element binding protein 1 
  (CREB1), transcript variant A, mRNA</data-title>. <source>GenBank</source> 
  <ext-link ext-link-type="genbank" xlink:href="NM_004379.3">NM_004379.3</ext-link>.
 </mixed-citation>
</ref>
...

RNA Sequence sample:

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<ref>
 <mixed-citation publication-type="data">Xu, J. <etal/> 
  <data-title>Cross-platform ultradeep transcriptomic profiling 
  of human reference RNA samples by RNA-Seq</data-title>. 
  <source>Sci. Data</source> <volume>1</volume>:<elocation-id>140020</elocation-id>.  
  doi: <pub-id pub-id-type="doi">10.1038/sdata.2014.20</pub-id> 
  (<year iso-8601-date="2014">2014</year>).</mixed-citation>
</ref>
...

Element Citation: Analyzed data sources are mentioned in the Data Availability Statement section, and then the data sources are referenced in the References List within that section.

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<back>
...
<sec sec-type="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 iso-8601-date="2015">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 iso-8601-date="2015">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 iso-8601-date="2015">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>
</sec>
</back>
...

Mixed Citation: Analyzed data are mentioned in the Data Availability Statement section, and then the data are referenced in the References List within that section.

...
<back>
...
<sec sec-type="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>
  <mixed-citation publication-type="data" 
    specific-use="isSupplementedBy">
   <string-name><surname>Read</surname> <given-names>K</given-names></string-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 iso-8601-date="2015">2015</year>. 
   <pub-id pub-id-type="doi" assigning-authority="figshare"
     xlink:href="https://doi.org/10.6084/m9.figshare.1285515">View Data</pub-id>
  </mixed-citation>
</ref>
    
<ref id="pone.0167830.data002">
  <label>D2</label>
  <mixed-citation publication-type="data" 
    specific-use="references">
   <string-name><surname>Kok</surname> <given-names>K</given-names></string-name>, 
   <string-name><surname>Ay</surname> <given-names>A</given-names></string-name>, 
   <string-name><surname>Li</surname> <given-names>L</given-names></string-name>.
   <data-title>Genome-wide errant targeting by Hairy</data-title>. 
   <source>Dryad Digital Repository</source>. <year iso-8601-date="2015">2015</year>. 
   <pub-id pub-id-type="doi" assigning-authority="dryad"
     xlink:href="https://doi.org/10.5061/dryad.cv323">View Data</pub-id>
  </mixed-citation>
</ref>
    
<ref id="pone.0167830.data003">
  <label>D3</label>
  <mixed-citation publication-type="data" 
    specific-use="references">
   <string-name><surname>Hoang</surname> <given-names>C</given-names></string-name>,
   <string-name><surname>Swift</surname> <given-names>GH</given-names></string-name>,
   <string-name><surname>Azevedo-Pouly</surname> <given-names>A</given-names></string-name>,
   <string-name><surname>MacDonald</surname> <given-names>RJ</given-names></string-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 iso-8601-date="2015">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"
   >View Data</pub-id>
  </mixed-citation>
</ref>
</ref-list>
</sec>
</back>
...