Reference Lists & Bibliographies
- Jo Ripoll
In the context of eXtyles JATS, References are expected to be cited in the text, whereas items in the Bibliography may or may not be cited (e.g., Further Reading). This page describes the styles available for use with bibliographic material.
Check out the Reference List page in the JATS Export section for XML export examples.
In this section
Reference Head
The Reference Head style is used for the title of a list of bibliographic items, irrespective of whether they are references (i.e., cited in the text) or a bibliography (not required to be cited in the text).
Reference List Introduction
The Reference List Introduction style can be used with either a reference list or a bibliography, for an introductory paragraph of text that puts the bibliographic items in context.
The style must only be used before the first of the references; it must not be placed within the list of references.
For paragraphs that refer to individual items in the reference list or bibliography, the Reference Annotation style should be used.
References, Bibliography
The difference between the References and Bibliography styles is that eXtyles Citation Matching will warn if an item styled as References is not cited in the text, but it will not warn if an item styled as Bibliography is not cited. Otherwise, the two styles are treated the same by eXtyles processes, including XML export.
If an item styled as Bibliography is cited in the text, eXtyles JATS will still create an id-rid link between the citation and the cited item.
The character styles used within individual items styled as References and Bibliography may be custom-configured, and the precise editorial style used to display bibliographic items in Word may differ from the examples shown in the JATS XML Export section.
Both styles must be used in the document for the Bibliography references to remain uncited throughout eXtyles processing.
Bibliography Character Styles
The eXtyles JATS Bibliographic References process automatically identifies many elements of bibliographic references by using a range of character styles.
By default, eXtyles JATS 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 JATS template may include other bib_ styles that are not included in the following table.
These are used by the optional book and conference reference processing modules.
The example text in the table is pulled from the image after the table.
Character Style | Use/Description | Example Text |
|---|---|---|
bib_number | applied to the reference number It is critical that the reference number is correctly styled for all references in numbered reference styles, as otherwise Citation Matching will be unable to style reference citations in the text. | 1. |
bib_surname bib_fname | applied to the surnames and first names or initials, respectively, of the reference contributors | Bentolila M.R. |
bib_suffix | used for generational suffixes encountered in contributor names, such as "Jr.", "III", etc. | Jr. |
bib_organization | used for contributors that are not individual authors | FAO |
bib_etal | used on added text like “et al.” or “an others” when a reference style is set to truncate a list of contributors after a certain number the XML contains only the empty | et al. |
bib_year | applied to the year of publication | 2004 |
bib_article | used for the title of journal articles | Interactions of mitochondrial and nuclear genes that affect male gametophyte development. |
bib_journal | applied to the journal name in references to journal articles | Plan Cell |
bib_volume bib_issue bib_suppl | respectively used to style the volume, issue, and supplement number (if present) in journal references Depending on your reference style, issue information may or may not be retained by Bibliographic References processing. | 8 (1) (Suppl) |
bib_fpage bib_lpage | used to identify the first and last (if present) page numbers for journal references | 449 460 |
bib_doi | used to style a DOI if provided in the reference either by an author or by Crossref Reference Checking | https://doi.org/10/1105/tpc.015966 |
bib_url | used to style web addresses other than DOIs or PubMed links included in a reference | http://faostat.fao.org |
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.
Among other heuristic techniques, eXtyles JATS 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.
In name-date citation styles, it is critical that the publication year is correctly styled for each reference, in order for Citation Matching to successfully mark all bibliographic citations.
Also, in name-date citation styles, letters used to distinguish otherwise identically cited articles (such as "Smith, 2001a, b") will also be styled with the bib_year character style.
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
Reference Annotation
The Reference Annotation style is used for paragraphs of explanatory text that accompany items in the reference list or bibliography.
By default, the annotation paragraphs must appear after the item to which they refer.
If the Reference Annotation style is used, not all items in the reference list or bibliography must be annotated.
Citation Character Styles
The various citation styles are used by eXtyles JATS to create links in the XML between cited items, such as boxes, figures, tables, and bibliographic references, and citations of these items elsewhere in the document.
These character styles are added automatically to the Word document by the eXtyles JATS Citation Matching process. However, they can also be applied carefully by hand if eXtyles NLM fails to identify a citation correctly or if a citation needs to be added to the text.
The example text is taken from the image below the table.
Character Style | Use/Description | Example Text |
|---|---|---|
cite_app | used to mark citations of appendixes or annexes | (Appendix A) |
cite_bib | used to mark citations to items in the reference list or bibliography | [1] |
cite_box | used to identify citations of numbered boxes | Box 1 |
cite_en, cite_fn | used to mark citations of endnotes and footnotes, respectively | 1 (superscript 1) |
cite_eq | used to mark citations of numbered equations | (Equation 1) |
cite_fig | the default style applied by Citation Matching for citations of numbered figures | (Figure 1) |
cite_fig_nomove | used when it’s not appropriate to move the figure to where it’s first cited must be applied by hand | not pictured |
cite_tbl | used to mark citations of numbered tables during Citation Matching | (Table 1) |
cite_tbl_nomove | used when it’s not appropriate to move the figure to where it’s first cited must be applied by hand | not pictured |
As with the other classes of character styles, the cite_base character style is not used itself. However, it can be used to specify properties to be inherited by the other citation character styles. Do not apply cite_base to the contents of your document.
The numbered boxes themselves may be placed anywhere in the Word file. By default, in the exported XML, numbered boxes will be placed immediately after the paragraph in which they are first cited.
By default, the text of footnotes will be placed in the XML immediately after the citation. Endnotes will be placed in a fn-group element at the end of the file.
The figure or table itself can be placed either close to where it is cited, or at the end of the Word file (or anywhere else in the document). On export to XML, by default eXtyles JATS will move the elements for the associated figure or table to immediately after the paragraph at which the figure/table is first cited.
Copyright © 2022 Atypon Systems, LLC. All Rights Reserved.