Bibliography Styles

The eXtyles NLM Bibliographic References process automatically identifies many elements of bibliographic references by using a range of character styles. This page explains what these styles mean, and how they are ultimately represented in the XML file.

By default, eXtyles NLM will fully style references to journal articles. For other reference types, the number (if used), authors, publication year and URL (if used) will be styled. References can be styled carefully by hand, if necessary, but this should be avoided where possible. Instead, we recommend that you correct the reference (e.g., by fixing problems with punctuation in the author list) and then reprocess the reference by removing the start and end tags from the appropriate paragraph(s) and rerunning the Bibliographic Processing function.

Your eXtyles NLM template may include other bib_ styles that are not included here. These are used by the optional book and conference reference processing modules.

As with the other classes of character styles, the bib_base style is not used itself. Instead, it can be used as a basis for the other bib_ character styles. Do not apply bib_base to the contents of your document.

bib_number

In numbered reference styles, the bib_number character style is applied to the reference number. It is critical that the reference number is correctly styled for all references in numbered reference styles, as otherwise the Citation Matching process will be unable to style reference citations in the text.

bib_surname, bib_fname

The bib_surname and bib_fname character styles are applied to the surnames and first names or initials, respectively, of the reference contributors. All identifiable contributors should be styled using these styles and the styles bib_suffix, bib_organization, and bib_etal, as appropriate, not just the authors of journal articles.

bib_suffix

The character style bib_suffix is used for generational suffixes encountered in contributor names, such as "Jr.", "III", etc.

bib_organization

Some contributors are not individual authors. The names of these contributors are styled using the bib_organization character style. Among other heuristic techniques, eXtyles NLM uses data files to identify organization names that might otherwise be mistaken for individual authors. If you encounter organization names that have been mishandled in this way, please send the original version of the misparsed reference to extyles-support@inera.com.

bib_etal

Depending on your particular reference style, eXtyles NLM Bibliographic Processing may be set to truncate a list of contributors after a certain number, followed by some text like "et al." or "and others". This added text is styled using the bib_etal character style. Note that the XML contains only the empty <etal/> element, not the contents of the bib_etal-styled text.

bib_year

The bib_year character style is applied to the year of publication. This style should be applied to all references that have an identifiable publication year, not just journal articles. In name-date citation styles, it is critical that the publication year is correctly styled for each reference, in order for the Citation Matching process to successfully mark all bibliographic citations. Also, in name-date citation styles, note that letters used to distinguish otherwise identically cited articles (such as "Smith, 2001a, b") will also be styled with the bib_year character style.

bib_article

The bib_article character style is used for the title of journal articles.

bib_journal

The character style bib_journal is applied to the journal name in references to journal articles. If eXtyles NLM Bibliographic References processing fails to recognize a particular journal, please send the entire original reference to journals@inera.com and we will add the title to our journal database if appropriate.

bib_volume, bib_issue, bib_suppl

The character styles bib_volume, bib_issue, and bib_suppl are respectively used to style the volume, issue, and supplement number (if present) in journal references. Depening on your reference style, issue information may or may not be retained by Bibliographic References processing.

bib_fpage, bib_lpage

The bib_fpage and bib_lpage character styles are used to identify the first and last (if present) page numbers for journal references. If the article only has a single page number, or has an electronic location ID instead of a page number, the bib_fpage style will be used. If the article has complex pagination, such as "11-23, discussion 24", and such complex pagination is supported by your reference style, the bib_lpage style will be applied to the last page of the article itself, as well as any extra page information, i.e. <bib_fpage>23</bib_fpage>-<bib_lpage>23, discussion 24</bib_lpage> in this example.

bib_doi

If the reference contains a DOI, either provided by the author or added automatically be the eXtyles NLM Crossref Reference Checking process, the DOI will be styled using the bib_doi character style.

bib_url

For references that include web addresses, other than DOIs or PubMed links added by the eXtyles NLM CrossRef and PubMed Reference Checking processes, the web address will be styled using the bib_url character style. URLs should be styled as bib_url in all reference types, not just journal references.

Example


The following example demonstrates the use of the bibliographic character styles. This illustration is an excerpt from the sample document: Sample_4_Character-styles.docx

JATS XML Example
<ref id="r1">
	<label>
		1
	</label>
	<mixed-citation publication-type="journal">
		<person-group person-group-type="author">
			<name>
				<surname>
					Hanson
				</surname>
				<given-names>
					M.R.
				</given-names>
			</name>
			<name>
				<surname>
					Bentolila
				</surname>
				<given-names>
					S.
				</given-names>
			</name>
		</person-group>
		(
		<year>
			2004
		</year>
		). 
		<article-title>
			Interactions of mitochondrial and nuclear genes that affect male gametophyte development.
		</article-title>
		<source>
			Plant Cell
		</source>
		<volume>
			16
		</volume>
		(
		<supplement>
			Suppl
		</supplement>
		), 
		<fpage>
			S154
		</fpage>
		&#x2013;
		<lpage>
			S169
		</lpage>
		<pub-id pub-id-type="doi">
			10.1105/tpc.015966
		</pub-id>
		<pub-id pub-id-type="pmid">
			15131248
		</pub-id>
	</mixed-citation>
</ref>
<ref id="r2">
	<label>
		2
	</label>
	<mixed-citation publication-type="book">
		Conan Doyle, A. (1888). A Study in Scarlet, 1st edn. London: Ward, Lock &amp; Co.
	</mixed-citation>
</ref>
<ref id="r3">
	<label>
		3
	</label>
	<mixed-citation publication-type="web">
		<person-group person-group-type="author">
			<collab>
				FAO
			</collab>
		</person-group>
		. (
		<year>
			2013
		</year>
		). 
		<ext-link ext-link-type="uri" xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://faostat.fao.org">
			http://faostat.fao.org
		</ext-link>
		.
	</mixed-citation>
</ref>
<ref id="r4">
	<label>
		4
	</label>
	<mixed-citation publication-type="journal">
		<person-group person-group-type="author">
			<name>
				<surname>
					Miyazaki
				</surname>
				<given-names>
					T.
				</given-names>
			</name>
			<name>
				<surname>
					Plotto
				</surname>
				<given-names>
					A.
				</given-names>
			</name>
			<name>
				<surname>
					Goodner
				</surname>
				<given-names>
					K.
				</given-names>
			</name>
			<name>
				<surname>
					Gmitter
				</surname>
				<given-names>
					F.G.
				</given-names>
				<suffix>
					Jr
				</suffix>
			</name>
		</person-group>
		. (
		<year>
			2011
		</year>
		). 
		<article-title>
			Distribution of aroma volatile compounds in tangerine hybrids and proposed inheritance.
		</article-title>
		<source>
			J. Sci. Food Agric.
		</source>
		<volume>
			91
		</volume>
		(
		<issue>
			3
		</issue>
		), 
		<fpage>
			449
		</fpage>
		&#x2013;
		<lpage>
			460
		</lpage>
		<pub-id pub-id-type="doi">
			10.1002/jsfa.4205
		</pub-id>
		<pub-id pub-id-type="pmid">
			21218478
		</pub-id>
	</mixed-citation>
</ref>
<ref id="r5">
	<label>
		5
	</label>
	<mixed-citation publication-type="journal">
		<person-group person-group-type="author">
			<name>
				<surname>
					Janssen
				</surname>
				<given-names>
					B.J.
				</given-names>
			</name>
			<name>
				<surname>
					Thodey
				</surname>
				<given-names>
					K.
				</given-names>
			</name>
			<name>
				<surname>
					Schaffer
				</surname>
				<given-names>
					R.J.
				</given-names>
			</name>
			<name>
				<surname>
					Alba
				</surname>
				<given-names>
					R.
				</given-names>
			</name>
			<name>
				<surname>
					Balakrishnan
				</surname>
				<given-names>
					L.
				</given-names>
			</name>
			<name>
				<surname>
					Bishop
				</surname>
				<given-names>
					R.
				</given-names>
			</name>
			<name>
				<surname>
					Bowen
				</surname>
				<given-names>
					J.H.
				</given-names>
			</name>
			<name>
				<surname>
					Crowhurst
				</surname>
				<given-names>
					R.N.
				</given-names>
			</name>
			<name>
				<surname>
					Gleave
				</surname>
				<given-names>
					A.P.
				</given-names>
			</name>
			<name>
				<surname>
					Ledger
				</surname>
				<given-names>
					S.
				</given-names>
			</name>
			<etal/>
		</person-group>
		(
		<year>
			2008
		</year>
		). 
		<article-title>
			Global gene expression analysis of apple fruit development from the floral bud to ripe fruit.
		</article-title>
		<source>
			BMC Plant Biol.
		</source>
		<volume>
			8
		</volume>
		(
		<issue>
			1
		</issue>
		), 
		<fpage>
			16
		</fpage>
		<pub-id pub-id-type="doi">
			10.1186/1471-2229-8-16
		</pub-id>
		<pub-id pub-id-type="pmid">
			18279528
		</pub-id>
	</mixed-citation>
</ref>