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Sample Citations for Archiving

This section contains samples of various types of citations tagged according to this Archiving Tag Set. Tagging citations is an editorial decision and an art, so these are not the only way the cited works could have been tagged. For many publishers, they will not even be Best practice, but they show one way and may help guide tagging use. Each sample that follows can be assumed to be inside a <ref>, which is inside a <ref-list>. The text will usually be shown twice, once tagged with the text-and-elements-style <mixed-citation> element and once with the element-style <element-citation> element.
Journal Citations
A Llanos De La Torre Quiralte citation, first in mixed-citation style and then in element-citation style. 
...
<ref id="G3">
 <mixed-citation publication-type="journal" publication-format="print">
  <string-name><surname>Llanos De La Torre Quiralte</surname>
  <given-names>M</given-names></string-name>,
  <string-name><surname>Garijo Ayestaran</surname>
  <given-names>M</given-names></string-name>,
  <string-name><surname>Poch Olive</surname>
  <given-names>ML</given-names></string-name>.
  <article-title xml:lang="es">Evolucion de la mortalidad
  infantil de La Rioja (1980-1998)</article-title>
  [<trans-title xml:lang="en">Evolution of the infant
  mortality rate in la Rioja in Spain (1980-1998)</trans-title>].
  <source>An Esp Pediatr</source>. <year iso-8601-date="2001-11">2001</year>
  <month>Nov</month>;<volume>55</volume>(<issue>5</issue>):
  <fpage>413</fpage>-<lpage>420</lpage>. Figura 3, Tendencia
  de mortalidad infantil [Figure 3, Trends in infant
  mortality]; p. 418. Spanish.</mixed-citation>
</ref>
...

...
<ref id="G3">
 <element-citation publication-type="journal" publication-format="print">
  <name><surname>Llanos De La Torre Quiralte</surname>
   <given-names>M</given-names></name>
  <name><surname>Garijo Ayestaran</surname>
   <given-names>M</given-names></name>
  <name><surname>Poch Olive</surname>
   <given-names>ML</given-names></name>
  <article-title xml:lang="es">Evolucion de la mortalidad
   infantil de La Rioja (1980-1998)</article-title>
  <trans-title xml:lang="en">Evolution of the infant
   mortality rate in la Rioja in Spain
   (1980-1998)</trans-title>
  <source>An Esp Pediatr</source>
  <year iso-8601-date="2001-11">2001</year>
  <month>Nov</month>
  <volume>55</volume>
  <issue>5</issue>
  <fpage>413</fpage>
  <lpage>420</lpage>
  <comment>Figura 3, Tendencia de mortalidad infantil
   [Figure 3, Trends in infant mortality]; p. 418.
   Spanish</comment>
 </element-citation>
</ref>
...
A Woodford-Williams citation, first in mixed-citation style and then in element-citation style. 
<ref id="B7">
 <mixed-citation publication-type="journal">
  <string-name><surname>Woodford-Williams</surname>
  <given-names>E</given-names></string-name>,
  <string-name><surname>McKeon</surname>
  <given-names>JA</given-names></string-name>,
  <string-name><surname>Trotter</surname>
  <given-names>IS</given-names></string-name>,
  <string-name><surname>Watson</surname>
  <given-names>D</given-names></string-name>, and
  <string-name><surname>Bushby</surname>
  <given-names>C</given-names></string-name>.
  <article-title>The day hospital in the community care 
  of the elderly</article-title>. <source>Gerontology 
  Clinic</source> <year iso-8601-date="1962">1962</year>;
  <volume>4</volume>:<fpage>241</fpage>&ndash;<lpage>256</lpage>.
 </mixed-citation>
</ref>

<ref id="B7">
 <element-citation publication-type="journal">
  <string-name><surname>Woodford-Williams</surname>
   <given-names>E</given-names></string-name>
  <string-name><surname>McKeon</surname>
   <given-names>JA</given-names></string-name>
  <string-name><surname>Trotter</surname>
   <given-names>IS</given-names></string-name>
  <string-name><surname>Watson</surname>
   <given-names>D</given-names></string-name>
  <string-name><surname>Bushby</surname>
   <given-names>C</given-names></string-name> 
  <article-title>The day hospital in the community
   care of the elderly</article-title> 
  <source>Gerontology Clinic</source>
  <year iso-8601-date="1962">1962</year> 
  <volume>4</volume> 
  <fpage>241</fpage>
  <lpage>256</lpage>
 </element-citation>
</ref>
Although JATS recommends rich citation tagging and encourages rich citation tagging, it does not require rich citation tagging. The first example is sparsely but usefully tagged. The second example contains the absolute minimal tagging, is valid JATS tagging, but is of far less use. 
<ref id="C10">
 <mixed-citation publication-type="journal">Carter, A.P., 
  Clemons, W.M., Brodersen, D.E., Morgan-Warren, R.J., 
  Wimberly, B.T., and Ramakrishnan, V. Functional insights 
  from the structure of the 30S ribosomal subunit and its 
  interactions with antibiotics. <source>Nature</source> 
  <year iso-8601-date="2002">2002</year>;
  <volume>07</volume>:<fpage>340</fpage>&#x02013;348.
 </mixed-citation>
</ref>

<ref id="C10">
 <mixed-citation publication-type="journal">Carter, A.P., 
  Clemons, W.M., Brodersen, D.E., Morgan-Warren, R.J., 
  Wimberly, B.T., and Ramakrishnan, V. Functional insights 
  from the structure of the 30S ribosomal subunit and its 
  interactions with antibiotics. Nature 
  2002; 07:340&#x02013;348.</mixed-citation>
</ref>
Book Citations
Citing a chapter in a book:
...
<ref>
 <element-citation publication-type="book" publication-format="print">
  <name><surname>Al-Ibrahim</surname>
   <given-names>MS</given-names></name>
  <name><surname>Gross</surname>
   <given-names>JY</given-names></name>
  <part-title>Tobacco use</part-title>
  <person-group person-group-type="editor">
   <name><surname>Walker</surname>
    <given-names>HK</given-names></name>
   <name><surname>Hall</surname>
    <given-names>WD</given-names></name>
   <name><surname>Hurst</surname>
    <given-names>JW</given-names></name>
  </person-group>
  <source>Clinical methods: the history, physical,
   and laboratory examinations</source>
  <publisher-loc>Stoneham (MA)</publisher-loc>
  <publisher-name>Butterworth Publishers</publisher-name>
  <date-in-citation content-type="copyright-year"
    iso-8601-date="1990">1990</date-in-citation>
  <fpage>214</fpage>
  <lpage>216</lpage>
 </element-citation>
</ref>
...

...
<ref>
 <mixed-citation publication-type="book" publication-format="print">
  <string-name><surname>Al-Ibrahim</surname>, 
  <given-names>MS</given-names></string-name>,
  <string-name><surname>Gross</surname>, 
  <given-names>JY</given-names></string-name>. In:
  <part-title>Tobacco use</part-title>.
  <person-group person-group-type="editor">
  <string-name><surname>Walker</surname>, 
  <given-names>HK</given-names></string-name>,
  <string-name><surname>Hall</surname>, 
  <given-names>WD</given-names></string-name>,
  <string-name><surname>Hurst</surname>, 
  <given-names>JW</given-names></string-name></person-group>, 
  editors. <source>Clinical methods: the history, 
  physical, and laboratory examinations</source>.
  <publisher-loc>Stoneham (MA)</publisher-loc>:
  <publisher-name>Butterworth Publishers</publisher-name>;
  &copy;<date-in-citation content-type="copyright-year"
  iso-8601-date="1990">1990</date-in-citation>.
  p. <fpage>214</fpage>-<lpage>216</lpage>.</mixed-citation>
</ref>
...
Citing a book that is in videocassette format:
<ref>
 <element-citation publication-type="book"
   publication-format="videocassette" publisher-type="gov">
  <name><surname>Stryker</surname>
   <given-names>MP</given-names></name>
  <source>Making maps in the brain</source>
  <comment>[videocassette]</comment>
  <publisher-loc>Bethesda (MD)</publisher-loc>
  <publisher-name>National Institutes of Health (US),
   Medical Arts and Photography Branch, Office of
   Research Services</publisher-name>
  <year iso-8601-date="2006">2006</year>
  <comment>1 videocassette: 63 min., sound,
   color, 1/2 in</comment>
 </element-citation>
</ref>

<ref>
 <mixed-citation publication-type="book"
  publication-format="videocassette" publisher-type="gov">
  <string-name><surname>Stryker</surname>
  <given-names>MP</given-names></string-name>.
  <source>Making maps in the brain</source> [videocassette].
  <publisher-loc>Bethesda (MD)</publisher-loc>:
  <publisher-name>National Institutes of Health (US),
  Medical Arts and Photography Branch, Office of
  Research Services</publisher-name>;
  <year iso-8601-date="2006">2006</year>.
  1 videocassette: 63 min., sound, color, 1/2 in.</mixed-citation>
</ref>
Conference Proceedings
There is disagreement concerning Best practice for tagging citations to conference papers, conference proceedings, and unpublished conference material. See a fuller discussion under Conferences in Citations. 
...
<ref>
 <element-citation publication-type="conf-proc">
  <person-group person-group-type="editor">
   <name><surname>van Pelt</surname>
    <given-names>J</given-names></name>
   ...
   <role>editors</role>
  </person-group>
  <source>Development, dynamics, and pathology of
   neuronal networks: from molecules to functional
   circuits</source> 
  <comment>Proceedings of the </comment>
  <conf-name>23rd International
   Summer School of Brain Research</conf-name>
  <conf-date iso-8601-date="2003-08-25">2003 Aug 25-29</conf-date>
  <conf-sponsor>Royal Netherlands Academy of Arts and
   Sciences, Amsterdam, the Netherlands</conf-sponsor>
  <publisher-loc>Amsterdam</publisher-loc>
  <publisher-name>Elsevier</publisher-name>
  <year iso-8601-date="2005">2005</year>
  <size units="pages">385 p</size>
  <comment>(Progress in brain research; vol. 147)</comment>
 </element-citation>
</ref>
...

...
<ref>
 <mixed-citation publication-type="conf-proc">
  <person-group person-group-type="editor">
  <string-name><surname>van Pelt</surname>
  <given-names>J</given-names></string-name>, ...
  <role>editors</role>.</person-group>
  <source>Development, dynamics, and pathology of neuronal
  networks: from molecules to functional circuits</source>.
  Proceedings of the <conf-name>23rd International
  Summer School of Brain Research</conf-name>;
  <conf-date iso-8601-date="2003-08-25">2003 Aug 25-29</conf-date>;
  <conf-sponsor>Royal Netherlands Academy of Arts and
  Sciences, Amsterdam, the Netherlands</conf-sponsor>.
  <publisher-loc>Amsterdam</publisher-loc>:
  <publisher-name>Elsevier</publisher-name>;
  <year iso-8601-date="2005">2005</year>.
  <size units="pages">385 p</size>. (Progress in
  brain research; vol. 147).</mixed-citation>
</ref>
...
Conference (Unpublished)
There is disagreement concerning Best practice for tagging citations to conference papers, conference proceedings, and unpublished conference material. See a fuller discussion under Conferences in Citations. 
...
<ref>
 <element-citation publication-type="paper">
  <name><surname>Thabet</surname>
   <given-names>A</given-names></name>
  <article-title>Clinical value of two serial pulmonary
   embolism-protocol CT studies performed within ten
   days</article-title>
  <conf-name>Annual Scientific Meeting and Postgraduate
   Course of the American Society of Emergency Radiology</conf-name>
  <conf-date iso-8601-date="2006-09-27">2006 Sep 27-30</conf-date>
  <conf-loc>Washington, DC</conf-loc>
 </element-citation>
</ref>
...

...
<ref>
 <mixed-citation publication-type="paper">
  <string-name><surname>Thabet</surname>
  <given-names>A</given-names></string-name>.
  <article-title>Clinical value of two serial pulmonary
  embolism-protocol CT studies performed within ten
  days</article-title>. <conf-name>Annual Scientific
  Meeting and Postgraduate Course of the American
  Society of Emergency Radiology</conf-name>;
  <conf-date iso-8601-date="2006-09-27">2006 Sep
  27-30</conf-date>; <conf-loc>Washington, DC</conf-loc>.
 </mixed-citation>
</ref>
...
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:
...
<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:
...
<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:
...
<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. 
...
<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>
...
Forthcoming Publication 
<ref>
 <element-citation publication-type="journal" publication-format="print">
  <name><surname>Laking</surname>
   <given-names>G</given-names></name>
  <name><surname>Lord</surname>
   <given-names>J</given-names></name>
  <name><surname>Fischer</surname>
   <given-names>A</given-names></name>
  <article-title>The economics of diagnosis</article-title>
  <source>Health Econ</source>
  <comment>Forthcoming 2006</comment>
 </element-citation>
</ref>

<ref>
 <mixed-citation publication-type="journal" publication-format="print">
  <string-name><surname>Laking</surname>
  <given-names>G</given-names></string-name>,
  <string-name><surname>Lord</surname>
  <given-names>J</given-names></string-name>,
  <string-name><surname>Fischer</surname>
  <given-names>A</given-names></string-name>.
  <article-title>The economics of
  diagnosis</article-title>. <source>Health
  Econ</source>. Forthcoming 2006.</mixed-citation>
</ref>
Government Report
Government report treated as a book:
...
<ref>
 <element-citation publication-type="report">
  <name><surname>Doebler</surname>
   <given-names>JA</given-names></name>
  <source>Autoradiographic localization of
   [<sup>125</sup>I]-ricin in lungs and trachea of
   mice following an aerosol inhalation exposure</source>
  <publisher-loc>Aberdeen Proving Ground (MD)</publisher-loc>
  <publisher-name>Army Medical Research Institute of
   Chemical Defense (US)</publisher-name>
  <year iso-8601-date="1996">1996</year>
  <size units="pages">8 p</size>
  <gov>Report No.: USAMRICD-TR-96-03</gov>
 </element-citation>
</ref>
...

...
<ref>
 <mixed-citation publication-type="report">
  <string-name><surname>Doebler</surname>, 
  <given-names>JA</given-names></string-name>.
  <source>Autoradiographic localization of
  [<sup>125</sup>I]-ricin in lungs and trachea of
  mice following an aerosol inhalation exposure</source>.
  <publisher-loc>Aberdeen Proving Ground
  (MD)</publisher-loc>: <publisher-name>Army 
  Medical Research Institute of Chemical Defense
  (US)</publisher-name>; <year iso-8601-date="1996">1996</year>.
  <size units="pages">8</size> p. <gov>Report No.:
  USAMRICD-TR-96-03</gov>.</mixed-citation>
</ref>
...
Internet Journal 
<ref>
 <element-citation publication-type="journal" publication-format="web">
  <name><surname>Happell</surname>
   <given-names>B</given-names></name>
  <article-title>The influence of education on
   the career preferences of undergraduate nursing
   students</article-title>
  <source>Aust Electron J Nurs Educ</source>
  <comment>[Internet]</comment>
  <year iso-8601-date="2002-04">2002</year>
  <month>Apr</month>
  <date-in-citation content-type="access-date"
    iso-8601-date="2007-01-08">cited 2007 Jan 8</date-in-citation>
  <volume>8</volume>
  <issue>1</issue>
  <size units="pages">[about 12 p.]</size>
  <comment>Available from:
   <uri>http://www.scu.edu.au/schools/nhcp/aejne/vol8-1/refereed/happell_max.html</uri></comment>
 </element-citation>
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Patent 
...
<ref>
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  <person-group person-group-type="inventor">
   <name><surname>Cho</surname>
    <given-names>ST</given-names></name>
  </person-group>
  <collab collab-type="assignee">Hospira, Inc.</collab>
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...

...
<ref>
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Thesis or Dissertation 
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<ref>
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...

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Website 
<ref>
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  <source>AMA: helping doctors help patients</source>
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  <date-in-citation content-type="copyright-year"
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  <source>AMA: helping doctors help patients</source> [Internet].
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