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>).
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>
...

Subsidiary sections:

Conferences in Citations

Length and Size

Tagging Ordinal Numbers

Sample Citations for Authoring