Tagging References
The publishing industry uses the words “citation” and
“reference” both interchangeably and in two rather different senses. One
meaning is a description of a work in a bibliography (bibliographic reference list). The
other is as a pointer to a description of a work in a bibliography. There is no consensus
on which word has which meaning, so this Tag Suite uses these (and other) bibliographic
reference terms in the following way:
Reference List (<ref-list>) | A list of bibliographic descriptions of material, for example, descriptions of
journal articles or books. The list typically has a title such as
“References”, “Bibliography”, or
“Additional Reading”. This Tag Set makes no distinction between
lists of cited references and lists of suggested references; both would be tagged
as <ref-list>. This Tag Library will
refer to these lists as references lists or as bibliographic references
lists. |
|---|---|
Reference (<ref>) | One item in a bibliographic references list. Each item may (in
the final publishing) be numbered, take a
prefix symbol, or a prefixed designator such as [Lapeyre 2009]. The publisher
is typically responsible for such numbering. A <ref> is not a textual description of cited
material, but it may contain one or more such descriptions, or it may contain a
note. A very typical <ref> contains
the description of one work inside a citation element (<element-citation> or <mixed-citation>). A <ref> does not contain text
directly because some publishers place multiple works into a single numbered item
in a bibliographic reference list. The <ref> is the element for that item. Each cited work will be contained
in a citation element (<element-citation> or <mixed-citation>). |
Citation (<element-citation> or
<mixed-citation>) | The bibliographic description of a single work, such as a journal article.
This element will contain text, bibliographic elements, or a mixture of the two,
for example, listing the title of a work, the
author, the date of publication, the page in the
journal on which the article starts, and similar information. Single citations are almost never numbered or given a prefix designator
because the publisher places the prefix and identifying attribute on the containing
<ref> element. But citations are
allowed to take numbers or designators to handle those cases where a single item in a reference list
describes multiple works. |
Pointer | Inside the text of a work, it is common to refer to (cite) external sources
such as journal articles that were influential in forming the ideas expressed in
that part of the text. These too are commonly called “citations”.
This Tag Set will use the term cross-reference (the element <xref>) to name the text that points to the
description of a cited work in a bibliographic references list. The @ref-type on the <xref> can be set to “bibr” to
indicate that the cross-reference is pointing to an item in a reference list.
Typically, the @rid attribute will
point the unique identifier (@id) of
a <ref>. But when a <ref> contains multiple citations, the
@rid may point to the identifier
of a particular citation (<element-citation> or <mixed-citation>). |
Subsidiary sections:
Two Citation Styles
Titles in Citations
Dates in Citations
Personal Names in Citations
Citation Attributes
Citing Data
Examples of Data Citations
We would like to thank the Force11 group for the data citation examples given below.
Protein Data Bank in Europe sample:
... <ref> <mixed-citation publication-type="data">Kollman JM, Charles EJ, Hansen JM, <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">Dubuis JO, Samanta R, Gregor T (<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> ...