(File names JATS-archivearticle1.dtd and JATS-archivearticle1-mathml3.dtd) The top-level Journal Archiving Tag Set DTD Module that declares the document element (<article>) and the other top-level elements that define a journal article (front matter, back matter, and sub-articles or responses). All elements but these few are declared in the modules of the Suite. The DTD invokes all the other modules it uses, by reference, as external parameter entities: first the Archiving Tag-Set-specific Module of Modules is called to name all Archive-specific customized modules, then the Suite Module of Modules is called to name all the potential modules from the Suite, then customized and default modules are called (for parameter entities naming element classes, mixes, and models), then the Common Module for shared elements and attribute lists is called, and finally all the other modules are called as needed.

(parameter entity %archivecustom-modules.ent;) Defines all the external modules that are specific to the Archiving Tag Set (except itself, which must be both named and called inside the DTD). A Tag Set selects from these modules by referencing the module names through external parameter entities. The entities are declared in the Archiving Tag-Set-specific Module of Modules (%archivecustom-modules.ent;), but referenced (or not) in the DTD proper. To include a set of elements (such as all the lists or all the MathML elements), a DTD references the external parameter entity of the module that contains these declarations.

Implementor’s Note: The Archiving Tag-Set-specific Module of Modules and the Suite Module to Name the Modules (along with the MathML 3 modules, if used) need to be the among the first three external modules called by the Archiving DTD. Customization modules for classes, mixes, and models will typically be called following the Archiving Tag-Set-specific modules and the Module of Modules.

(parameter entity %archivecustom-classes.ent;) Sets up parameter entities that will be used to override default classes prescribed by the %default-classes.ent; module.

Implementor’s Note: This module must be called after the Archiving Tag-Set-specific Module of Modules (%archivecustom-modules.ent;) and the Suite Module to Name the Modules (%modules.ent;) but before any other module, including specifically the %default-classes.ent; module (which this module overrides) and the %archivecustom-mixes.ent; and %archivecustom-models.ent; modules (which build on this module).

(parameter entity %archivecustom-mixes.ent;) Sets up parameter entities that will be used to override default mixes (groupings made of “classes”) prescribed by the %default-mixes.ent; module.

Implementor’s Note: This module must be called after the Archiving Customize Classes Module (%archivecustom-classes.ent;) and the Default Classes Module (%default-classes.ent;) but before any other module, including specifically the %default-mixes.ent; module (which this module overrides) and the %archivecustom-models.ent; module (which builds on this module).

(parameter entity %archivecustom-models.ent;) Sets up parameter entities that will be used to override default content model parameter entities set elsewhere in the Suite. Also defines customizable attribute Declared Values and attribute lists for the Tag Set being defined.

Implementor’s Note: This module must be called after the Archiving Tag Set Customize Mixes Module (%archivecustom-mixes.ent;) and Default Mixes Module (%default-mixes.ent;) but before any “base” module of the interchange Suite.

(parameter entity %modules.ent;) Defines all the external modules that are part of the modular NISO JATS DTD Suite (except the module itself, which must be both named and called inside a DTD). A Tag Set selects from the Suite modules by referencing the module names through external parameter entities. The entities are declared in the Module to Name the Modules (%modules.ent;), but referenced (or not) in the DTD proper. To include a set of elements (such as all the article metadata or all the display elements) a DTD references the external parameter entity of the module that contains these declarations.

Implementor’s Note: The Archiving Tag-Set-specific Module of Modules and the Suite Module to Name the Modules (along with the MathML 3 modules, if used) need to be the among the first three external modules called by the Archiving DTD. Customization modules for classes, mixes, and models will typically be called next, following these two.

(parameter entity %JATS-ali-namespace.ent;) Namespace setup for the NISO Access License and Indicators elements (prefix “ali:”). The elements are defined in the JATS Common module (described below).

(parameter entity %JATS-common-atts.ent;) Defines attributes intended to be used on ALL elements defined in the NISO JATS, including table elements for both the XHTML-inspired and OASIS-inspired table models, with the exception of <mml:math> whose namespaces JATS does not control.

Must be called after all module-of-modules modules and any namespacing modules, but before all customization (over-ride) modules.

(parameter entity %default-classes.ent;) Sets up the parameter entities that name the element members of each class that will be used to establish the content models.

Implementor’s Note: This module must be called before the Archiving Customize Mixes Module (%archivecustom-mixes.ent;) and the Default Element Mixes Module (%default-mixes.ent;), as well as the Archiving Customize Models Module, %archivecustom-models.ent; (which builds on those modules).

(parameter entity %default-mixes.ent;) Sets up the parameter entities that name mixes (groupings made of “classes”) that will be used to establish the content models.

Implementor’s Note: This module must be called before the Archiving Customize Models Module (%archivecustom-models.ent;) or any “base” module of the interchange Suite.

(parameter entity %common.ent;) Declarations for elements, attributes, entities, and notations that are shared by more than one class module.

Implementor’s Note: This module must be called before any of the modules comprising the interchange Suite.

(parameter entity %articlemeta.ent;) Declares the metadata elements (issue elements and article header elements) used to describe a journal article.

Design Note: Metadata elements that describe the journal are in the Journal Metadata Module, %journalmeta.ent;.

(parameter entity %backmatter.ent;) Declares elements that are not part of the main textual flow of a work, but are considered to be ancillary material such as appendices, glossaries, and bibliographic reference lists.

(parameter entity %display.ent;) Declares the display-related elements, such as figures, graphics, math, chemical expressions and structures, tables, etc.

(parameter entity %format.ent;) Declares elements concerned with rendition of output, for example, printing on a page or display on a screen. This module includes the elements in the Appearance Class, the Break Class, and the Emphasis Class.

(parameter entity %funding.ent;) Declares elements that model open access, grant, sponsorship, or other funding information, for example, the grant number (<award-id>) and the grant holder (<principal-award-recipient>).

(parameter entity %journalmeta.ent;) Declares the elements used to describe the journal in which a journal article is published.

Design Note: The issue and article metadata is defined in the Article Metadata module, %articlemeta.ent;.

(parameter entity %link.ent;) Declares elements that are links (internal or external) by definition, such as URLs (<uri>) and internal cross references (<xref>).

(parameter entity %list.ent;) Declares the elements in the List Class; these are all lists except the lists of bibliographic references (citations). Lists are considered to be composed of items.

(parameter entity %math.ent;) Declares the elements in the math classes such as display equations.

(parameter entity %nlmcitation.ent;) Adds the model for the NLM structured bibliographic citation element (<nlm-citation>). This element is now obsolete and should be replaced by either an <element-citation> element or a <mixed-citation> element.

(parameter entity %para.ent;) Declares structural, non-display elements that may appear in the same places as a paragraph. These elements are named in the various paragraph class parameter entities.

(parameter entity %phrase.ent;) Declares the Phrase Class elements, that is, names the inline, subject-specific elements.

(parameter entity %references.ent;) Declares the bibliographic reference elements.

(parameter entity %related-object.ent;) Defines the container element <related-object>, which is used as a container for text links and description of an external object such as a spreadsheet or a book that is related to the current work.

(parameter entity %section.ent;) Declares the elements of the Section Class, that is, declares all section-level elements in the Journal Archiving Tag Set.

(parameter entity %xmlspecchars.ent;) Standard ISO XML special character entities used in this Tag Set.

(parameter entity %chars.ent;) Custom special character entities created specifically for use in this Tag Set.

(parameter entity %notat.ent;) Container module for the Notation Declarations to be used with this Suite. These notations have been placed in their own module for easy expansion or replacement.

(parameter entity %mathmlsetup.ent;) Invokes the MathML 2.0 modules.

Implementor’s Note:: To include the MathML 2.0 elements, a DTD must reference this module. This module sets up all parameter entities needed to use the MathML 2.0 Tag Set and references (invokes) the MathML 2.0 Tag Set Module, which, in turn, invokes all the other MathML 2.0 modules. Warning: MathML 2.0 and MathML 3.0 may not be used together; a Tag Set must choose one or the other.

(parameter entity %mathml3-mathmlsetup.ent;) Invokes the MathML 3.0 modules.

Implementor’s Note:: To include the MathML 3.0 elements, a DTD must reference this module. This module sets up all parameter entities needed to use the MathML 3.0 Tag Set and references (invokes) the MathML 3.0 Tag Set Module, which, in turn, invokes all the other MathML 3.0 modules. Warning: MathML 2.0 and MathML 3.0 may not be used together; a Tag Set must choose one or the other.

(parameter entity %mathml3-modules.ent;) Names the modules needed for MathML 3.0.

(parameter entity %mathml.dtd;) Used for either the Mathematical Markup Language (MathML) 2.0 or the MathML 3.0, an XML application for describing mathematical notation and capturing both its structure and content.

(parameter entity %mathml-qname.mod;) Declares parameter entities to support namespace-qualified names, namespace declarations, and name prefixing for MathML, as well as declares the parameter entities used to provide namespace-qualified names for all MathML element types. Used for either MathML 2.0 or MathML 3.0.

(parameter entity %ent-mmlextra;) Used for MathML processing. Used for either MathML 2.0 or MathML 3.0.

(parameter entity %ent-mmlalias;) Used for MathML processing. Used for either MathML 2.0 or MathML 3.0.

(parameter entity %XHTMLtablesetup.ent;) Sets all parameter entities needed by the NISO JATS XHTML-inspired Table Module, and then invokes the module containing that model.

To include the NISO JATS XHTML-inspired table model in a tag set, a DTD must reference this module. This module sets up all parameter entities needed to use the XHTML-inspired Table Module and references (invokes) the NISO JATS XHTML-inspired Table Module. (See next item.)

(parameter entity %xhtml-table-1.mod;) The public XML DTD version of the XHTML-inspired Table Module. This module is invoked from the module %XHTMLtablesetup.ent;. (See previous item.) This is the default table model for this Tag Set.

(parameter entity %xhtml-inlstyle-1.mod;) Declares the @style attribute, which supports inline style markup for elements such as <td> and <tr> within XHTML-inspired Table.

Complete Archiving (Green) DTD for the creation of new journal articles. This extension of the Journal Archiving and Interchange DTD replaces the Archiving DTD module and invokes both the XHTML table and the CALS OASIS XML Exchange Table models.

The DTD-specific modules for the new Journal Archiving and Interchange DTD that includes OASIS Tables.

The class overrides for this new DTD. These repeat all the class overrides of the regular Archiving DTD, with the table and alternative classes modified to use the OASIS XML Exchange (CALS) table elements. There is no equivalent mix override module because this DTD uses the ordinary Archiving mix overrides.

This modules establishes the prefix for the OASIS Exchange (CALS) table model, by default “oasis” (“<oasis:table>”).

(parameter entity %oasis-tablesetup.ent;) Implementor’s Note: Not used in the current Archiving Tag Set. Sets all parameter entities needed by the OASIS XML Exchange (CALS) table model, and then invokes the module containing that model.

To include the OASIS XML Exchange (CALS) table model, a DTD must reference this module. This module sets up all parameter entities needed to use the OASIS table model and references (invokes) the OASIS XML Exchange (CALS) Table Model Module. This module has been modified to use a namespace prefix of “oasis” for all table elements, to permit both the OASIS Exchange (CALS) table models and XHTML-inspired table models to be used in one tag set. There is a separate Tag Library (https://jats.nlm.nih.gov/options/OASIS/tag-library/19990315/index.html) describing the OASIS elements, attributes, and parameter entities.

This is the OASIS XML Exchange (CALS) table model DTD fragment, modified to use the OASIS namespace and the “oasis” prefix. This module is invoked from the JATS OASIS XML Exchange (CALS) setup module.

(parameter entity %xmlspecchars.ent;) Standard ISO XML special character entities used in this Tag Set.

(parameter entity %chars.ent;) Custom special character entities created specifically for use in this Tag Set.

(parameter entity %notat.ent;) Container module for the Notation Declarations to be used with this Suite. These notations have been placed in their own module for easy expansion or replacement.