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Deprecated Structures (JATS 1.4d1)

JATS 1.4d1 has identified several structures, elements, and attributes, as “deprecated”. When something is deprecated, it means that, while these structures are still available in the tag set, the best practice suggestion is that they not be used. In most cases, the JATS documentation recommends alternatives.
Such deprecated structures will remain in this version of JATS and all 1.x versions to ensure backward compatibility. When JATS releases a non-backwards-compatible version, probably to be called JATS 2.0, we expect all deprecated structures to be removed from the tag set. At this time (this is written in Spring 2024) we cannot predict when JATS 2.0 will be released.
Why Deprecate?
The most common reason structures may be deprecated is that JATS users have new requirements, and these new requirements cannot be accommodated either with existing structures or with backwards-compatible additions to existing structures. This is an unfortunate, but not uncommon, occurrence in the maintenance of complex specifications that are used in many contexts and in changing environments. As JATS is adopted by more and more users who are encoding an increasing variety of article types, new requirements are identified. Similarly, as the world and our expectations change, new requirements are identified.
Structures may also be deprecated:
  • When a new structure is created that meets new requirements, but also includes the functionality of an existing structure. In an effort to minimize duplication in the tag sets, the old structure is deprecated.
  • When it is realized that two or more old elements are members of a growing class of structures, and one element should be created to represent the entire class.
  • If a JATS structure is difficult to understand/use correctly and has been abused in the past, sometimes it can be replaced by simpler or more easily understood structures. To reduce duplication in the tag sets, the old structure is deprecated.

Multi-language Documents

Changing JATS to enable tagging an article in more than one language added a new element, changed some element models, added many new attributes, and deprecated several elements. Why? Changing, or perhaps, more completely understood requirements.
When the predecessor to JATS, the NLM DTD, was created, user experience was with mono-lingual articles that had metadata in the same language as the article. An occasional article might contain phrases, quotations, examples, or boxed text in other languages, but the article as a whole was in one language. Similarly, the metadata for the article was in the language of the article. Translations of some key portions of the metadata, such as the article title or abstract, might be provided for the convenience of users in other language communities, but these were considered translations of the primary single-language metadata.
Over time, it became clear that JATS modeling of a single language, with a few translated metadata elements, was based on some faulty assumptions. The JATS Standing Committee learned that:
  • There are articles that have much, or all, of their content in two or more languages.
  • There can be more than one “original” language, both for article content and in article metadata. The assumption that any language(s) in addition to a primary language are “translations” is false.
  • Whether a version of some portion of text or metadata is a “translation” is only one of many things we might know about that content, not a primary defining aspect of the content.
In modifying JATS to enable better modeling of multi-language materials, we have added the multi-lang attributes (see Multiple Languages/scripts), an extension mechanism to identify where the same content occurs in multiple languages. Also as part of the multi-language changes, we have deprecated the following elements:
<trans-source> and <trans-title>
Instead of using the elements above named “trans-xxx” (<trans-source>, etc.), the appropriate structure (<source>, etc.) should be repeated as many times as needed, with each repetition identified by language. Any translations can be explicitly identified.
Table of Deprecated Elements and Attributes
The JATS Tag Libraries clearly identify each deprecated element or attribute:
  • The name of the element or attribute concludes with the text “(deprecated)”.
  • The Remarks section of each of the deprecated structures provides information on how JATS recommends information formerly encoded with that structure be encoded in the future.
All of the structures now deprecated in JATS 1.4d1:
Deprecated Structure Replacements
<access-date> Replace with <date-in-citation>
<chapter-title> Replace with <part-title>
<collab> Replace with <collab-name> or <collab-wrap>, depending on context
<collab-alternatives> Replace with <collab-name-alternatives>
<nlm-citation> Replace with <mixed-citation> or <element-citation>
<std> Replace with <pub-id>
<std-organization> Do not use
<time-stamp> Replace with <date-in-citation>
<trans-source> Repeat <source>
<trans-title>
In <title-group>, Repeat <article-title>
In citations and related articles, Repeat <article-title> or <part-title>
Deprecated Attributes
@mimetype and @mime-subtype While these attributes will not be deprecated, best practice is to avoid using @mimetype and @mime-subtype as separate attributes. Instead, combine mimetype and mime-subtype values separated by a slash inside @mimetype (e.g., mimetype="application/excel").
@pub-type Replace with @date-type and @publication-format