◇◆
Tagged Examples
This section contains samples of various types of citations tagged according to this
Archiving Tag Set. How to tag 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> [<article-title xml:lang="en">Evolution of the infant mortality rate in la Rioja in Spain (1980-1998)</article-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> <article-title xml:lang="en">Evolution of the infant mortality rate in la Rioja in Spain (1980-1998)</article-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>–<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>–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; 07:340–348.</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>; ©<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.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.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> </ref> <ref> <mixed-citation publication-type="journal" publication-format="web"> <string-name><surname>Happell</surname>, <given-names>B</given-names></string-name>. <article-title>The influence of education on the career preferences of undergraduate nursing students</article-title>. <source>Aust Electron J Nurs Educ</source> [Internet]. <year iso-8601-date="2002-04">2002</year> <month>Apr</month> [cited <date-in-citation content-type="access-date" iso-8601-date="2007-01-08">2007 Jan 8</date-in-citation>]; <volume>8</volume>(<issue>1</issue>):<size units="pages">[about 12 p.]</size>. Available from: <uri>http://www.scu.edu.au/schools/nhcp/aejne/vol8-1/refereed/happell_max.html</uri>. </mixed-citation> </ref>
Patent
... <ref> <element-citation publication-type="patent"> <person-group person-group-type="inventor"> <name><surname>Cho</surname> <given-names>ST</given-names></name> </person-group> <collab-name collab-type="assignee">Hospira, Inc.</collab-name> <source>Microneedles for minimally invasive drug delivery</source> <patent country="US">United States patent US 6,980,855</patent> <year iso-8601-date="2005-12-27">2005</year> <month>Dec</month> <day>27</day> </element-citation> </ref> ... ... <ref> <mixed-citation publication-type="patent"> <string-name><surname>Cho</surname> <given-names>ST</given-names></string-name>, inventor; <collab>Hospira, Inc.</collab>, assignee. <article-title>Microneedles for minimally invasive drug delivery</article-title>. <source>United States patent</source> <patent country="US">US 6,980,855</patent>. <year iso-8601-date="2005-12-27">2005</year> <month>Dec</month> <day>27</day>.</mixed-citation> </ref> ...
Thesis or Dissertation
... <ref> <element-citation publication-type="thesis"> <name><surname>Mackowski</surname> <given-names>MP</given-names></name> <source>Human factors: aerospace medicine and the origins of manned space flight in the United States</source> <comment>[dissertation]</comment> <publisher-loc>[Tempe (AZ)]</publisher-loc> <publisher-name>Arizona State University</publisher-name> <year iso-8601-date="2002-05">2002</year> <month>May</month> <part-title>Part 2, Space medicine</part-title> <fpage>188</fpage> <lpage>377</lpage> </element-citation> </ref> ... ... <ref> <mixed-citation publication-type="thesis"> <string-name><surname>Mackowski</surname> <given-names>MP</given-names></string-name>. <source>Human factors: aerospace medicine and the origins of manned space flight in the United States</source> [dissertation]. <publisher-loc>[Tempe (AZ)]</publisher-loc>: <publisher-name>Arizona State University</publisher-name>; <year iso-8601-date="2002-05">2002</year> <month>May</month>. <part-title>Part 2, Space medicine</part-title>; p. <fpage>188</fpage>- <lpage>377</lpage>.</mixed-citation> </ref> ...
Website
<ref> <element-citation publication-type="webpage" publication-format="web"> <source>AMA: helping doctors help patients</source> <comment>[Internet]</comment> <publisher-loc>Chicago</publisher-loc> <publisher-name>American Medical Association</publisher-name> <date-in-citation content-type="copyright-year" iso-8601-date="1995">1995-2007</date-in-citation> <date-in-citation content-type="access-date" iso-8601-date="2007-02-22">cited 2007 Feb 22</date-in-citation> <comment>Available from: <uri>http://www.ama-assn.org/</uri></comment> </element-citation> </ref> <ref> <mixed-citation publication-type="webpage" publication-format="web"> <source>AMA: helping doctors help patients</source> [Internet]. <publisher-loc>Chicago</publisher-loc>: <publisher-name>American Medical Association</publisher-name>; ©<date-in-citation content-type="copyright-year" iso-8601-date="1995">1995-2007</date-in-citation> cited [<date-in-citation content-type="access-date" iso-8601-date="2007-02-22">2007 Feb 22</date-in-citation>]. Available from: <uri>http://www.ama-assn.org/</uri>. </mixed-citation> </ref>