<!– ============================================================= –> <!– MODULE: Journal Archiving and Interchange DTD –> <!– VERSION: NISO 0.4 –> <!– DATE: January 2011 –> <!– –> <!– ============================================================= –>

<!– ============================================================= –> <!– PUBLIC DOCUMENT TYPE DEFINITION –> <!– TYPICAL INVOCATION –> <!– “-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD (OASIS Tables) v0.4 20110131//EN”

Delivered as file "JATS-archive-oasis-article0.dtd"
Available at:
http://jats.nlm.nih.gov/archiving/0.4/JATS-archive-oasis-article0.dtd
                                                              -->

<!– ============================================================= –>

<!– ============================================================= –> <!– SYSTEM: Journal Archiving and Interchange DTD of the –> <!– Archiving and Interchange DTD Suite –> <!– –> <!– PURPOSE: DTD to describe a full-text journal article –> <!– –> <!– The Journal Archiving and Interchange DTD –> <!– describes journal articles and some non-article –> <!– material such as product and book reviews for –> <!– repository or interchange purposes. It describes –> <!– both the metadata for a journal article and the –> <!– full content of the article. –> <!– This DTD was constructed using the modules in the –> <!– Archiving and Interchange DTD Suite, using almost –> <!– no customization. –> <!– –> <!– CONTAINS: 1) Declare and invoke the Archival (Green) DTD- –> <!– specific module of modules, that names any –> <!– modules created expressly for this DTD. –> <!– (%archivecustom-modules.ent;) –> <!– 2) Declare and invoke the DTD Suite module of –> <!– modules (%modules.ent;), the Archiving and –> <!– Interchange Suite module that names all the –> <!– Suite modules this DTD might invoke –> <!– 3) Invoke DTD-specific classes over-ride module –> <!– (%archivecustom-classes.ent;) –> <!– 4) Invoke Suite default classes –> <!– (%default-classes.ent;) –> <!– 5) Invoke DTD-specific mixes over-ride module –> <!– (%archivecustom-mixes.ent;) –> <!– 6) Invoke Suite default mixes –> <!– (%default-mixes.ent;) –> <!– 7) Invoke DTD-specific content model over-ride –> <!– module (%archivecustom-models.ent;) –> <!– 8) Invoke the Common Element Module (from Suite) –> <!– 9) Invoke all the Class Modules (from Suite) as –> <!– well as any DTD-specific element modules –> <!– 10) Parameter Entities for attribute values used –> <!– in this module (DTD-specific definitions) –> <!– 11) Define document element (Article <article>) –> <!– 12) Define Front Matter <front> –> <!– 13) Define Body Matter <body> –> <!– 14) Define Back Matter <back> –> <!– –> <!– CREATED FOR: –> <!– Digital Archive of Journal Articles –> <!– National Center for Biotechnology Information –> <!– (NCBI) –> <!– National Library of Medicine (NLM) –> <!– –> <!– ORIGINAL CREATION DATE: –> <!– December 2002 –> <!– –> <!– CREATED BY: Jeff Beck (NCBI) –> <!– Deborah Lapeyre (Mulberry Technologies, Inc.) –> <!– Bruce Rosenblum (Inera Inc.) –> <!– B. Tommie Usdin (Mulberry Technologies, Inc.) –> <!– –> <!– The Journal Archiving and Interchange DTD is –> <!– built from the Archiving and Interchange DTD –> <!– Suite. –> <!– –> <!– NLM thanks the Harvard University Libraries, both –> <!– for proposing that a draft archiving NLM DTD for –> <!– life sciences journals be extended to accommodate –> <!– journals in all disciplines and for sponsoring –> <!– Bruce Rosenblum's collaboration with other DTD –> <!– authors in completing NLM Version 1.0. The –> <!– Andrew W. Mellon Foundation provided support for –> <!– these important contributions. –> <!– –> <!– Suggestions for refinements and enhancements to –> <!– this DTD should be sent in email to: –> <!– jats@ncbi.nlm.nih.gov –> <!– ============================================================= –>

<!– ============================================================= –> <!– DTD VERSION/CHANGE HISTORY –> <!– ============================================================= –> <!–

Version Reason/Occasion (who) vx.x (yyyy-mm-dd)

   =============================================================
   Version 0.4                       (DAL/BTU) v0.4 (2011-01-31)
   This Tag Set is in the process of becoming a NISO standard.
   The version numbers are starting over from 0.4", as a Trial
   Use Draft, to be made into "Version 1.0" when the Tag Suite 
   becomes a NISO standard. Thus, NLM "Version 3.1 Draft" has 
   been changed to NISO "Version 0.4". No model, attribute, or
   parameter entity changes were made as part of this renaming.
   Details on NISO Tial Use Draft Version 0.4 are available at
         http://jats.nlm.nih.gov/JATS-0.4.
9. Updated the DTD-version attribute to "0.4" 
8. Updated the public identifier to "v0.4 20110131//EN", 
   modified the formal public identifier to include "JATS (Z39.96)",
   and the filename as delivered to include "JATS" and the
   new version number "0". Also included the phrase 
   "(OASIS Tables)" in the formal name.
   =============================================================
   Version 3.1                       (DAL/BTU) v3.1 (2010-04-30)
   Version 3.1 is fully compatible with Version 3.0, but the
   following change could break some customizations.
   Details on version 3.1 are available at
         http://jats.nlm.nih.gov/3.1.
7. BODY ATTRIBUTES - Added attribute list and new PE %body-atts;
   to the model of <body>. The only current attribute is
   @specific-use, which indicates, for example, not a real
   tagged XML body, but a 'bag of words" for indexing purposes.
6. I18N - Changed the default for @xml:lang from "en" to
   #IMPLIED, so that the @xml:lang would inherit properly and
   not need to be over-ridden in
    - <sub-article> through %sub-article-atts;
    - <response> through %response-atts;
5. XML:LANG - Added @xml:lang to the following elements:
   Added to facilitate multiple languages.
     - article
4. AFFILIATION ALTERNATIVES - Added the element <aff-alternatives>
   to <front-stub> through %front-stub-model;. This element
   will hold multiple <aff>s that are a representation of a
   single affiliation, for example, the name of an institution
   in two languages or two scripts.
3. Updated public identifier to "v3.1 20100830//EN"
   =============================================================
   Version 3.0                       (DAL/BTU) v3.0 (2007-10-31)
   Version 3.0 is the first non-backward-compatible release.
   In addition to the usual incremental changes, some
   elements and attributes have been renamed and/or remodeled
   to better meet user needs and to increase tag set consistency.
   All module change histories are available through the Tag Suite
   web site at http://dtd.nlm.nih.gov.
   Details on version 3.0 are available at
         http://jats.nlm.nih.gov/3.0.
4. AFFILIATION ALTERNATIVES - Added the element <aff-alternatives>
   to <front-stub> through %front-stub-model;. This element
   will hold multiple <aff>s that are a representation of a
   single affiliation, for example, the name of an institution
   in two languages or two scripts.
3. LANGUAGE CODES - Codes for languages as well as variants,
   transliterations, regions, scripts, and combinations
   such as "Jpan"(Han + Hiragana + Katakana). These values should be
   taken from RFC 5646/W3C/IANA Subtag Registry recommendations
   and can be found online at:
     http://www.iana.org/assignments/language-subtag-registry
2. Changed default @xml:lang from "EN" from "en" to match latest
   RFC 4646/W3C/IANA Subtag Registry recommendations
1. Updated public identifier to "v3.0 20080202//EN"              -->

<!– ============================================================= –> <!– DESIGN CONSIDERATIONS –> <!– ============================================================= –>

<!– MODULAR DTD LIBRARY

A set of journal archiving and interchange
DTD modules was written as the basis for
publishing, interchange, and repository
DTDs, with the intention that DTDs for
specific purposes, such as this Journal
Archiving and Interchange DTD, would be
developed based on them.
This archiving DTD has been designed to
be descriptive, open, and inclusive to
allow journal articles to be translated into
this format as conveniently as possible
from a wide variety of proprietary journal
article DTDs (such as Blackwell, Keton, and
Ovid).
This Archiving DTD has been developed from
the Archiving and Interchange DTD Suite
modules, in the approved manner, making
changes to the declarations in those modules
by over-riding Parameter Entity contents
by redefining the entities in the
    %archivecustomize.ent;
module, which is called from this DTD file.
No changes to any of the original Archiving
and Interchange Suite modules are required
in order to use this DTD.                  -->

<!– ============================================================= –> <!– MODULES OF MODULES INVOKED –> <!– ============================================================= –>

<!– MODULE TO NAME DTD-SPECIFIC MODULES –> <!– Names all DTD-specific external modules –> <!ENTITY % archive-oasis-custom-modules.ent PUBLIC “-//NLM//DTD JATS (Z39.96) Journal Archiving DTD-Specific Modules (OASIS Tables) v0.4 20110131//EN” “JATS-archive-oasis-custom-modules0.ent” > %archive-oasis-custom-modules.ent;

<!– MODULE TO NAME THE MODULES –> <!– Declares all the external modules that are

part of the modular Journal Archiving and
Interchange DTD Suite library. Thus it does
NOT declare itself; the DTD-specific
module-of-modules; any DTD-specific class,
mix, or model over-ride modules; or any new
new content modules specific to this DTD.
Those are declared in the DTD-specific
module of modules.
   Since this module declares but does not
invoke modules, this DTD then invokes any
modules it uses by referencing the external
Parameter Entities defined in the Module of
Modules. To include a set of elements (such
as all the lists or the MathML elements) this
module defines the external Parameter Entity
for the module(s) that contains the MathML
declarations and the DTD references that
entity.                                    -->

<!ENTITY % modules.ent PUBLIC “-//NLM//DTD JATS (Z39.96) Archiving and Interchange DTD Suite Module of Modules v0.4 20110131//EN” “JATS-modules0.ent” > %modules.ent;

<!– ============================================================= –> <!– CUSTOMIZATION MODULES INVOKED –> <!– Note: These modules must be called after –> <!– all Module of Modules but before any other –> <!– modules. Unlike any other grouping, order –> <!– of these modules matters. –> <!– ============================================================= –>

<!– DTD-SPECIFIC CLASS CUSTOMIZATIONS MODULE –> <!– Names the module that holds the DTD-specific

class definitions for the Journal Archiving
and Interchange DTD that over-rides the Suite
defaults.
(Defined in %archivecustom-modules.ent; )  -->

%archive-oasis-custom-classes.ent;

<!– DEFAULT ELEMENT CLASSES MODULE –> <!– Names the module that holds the standard

class definitions for the Journal Archiving
and Interchange DTD Suite.                 -->

%default-classes.ent;

<!– DTD-SPECIFIC MIX CUSTOMIZATIONS MODULE –> <!– Set up the Parameter Entities and element

class definitions that will be used to
over-ride some element mixes in this DTD.
(Defined in %archivecustom-modules.ent; )  -->

%archive-oasis-custom-mixes.ent;

<!– DEFAULT MIX CUSTOMIZATIONS MODULE –> <!– Names the module that holds the standard

mix definitions for the Journal Archiving
and Interchange DTD Suite.                 -->

%default-mixes.ent;

<!– DTD-SPECIFIC MODELS/ATTRIBUTES CUSTOMIZATIONS

MODULE                                     -->

<!– Names the module that holds the over-rides

of content models, attribute lists, elements
lists to be used in content models, and
attribute values. These are DTD-specific.
(Defined in %archivecustom-modules.ent; )  -->

%archivecustom-models.ent;

<!– ============================================================= –> <!– COMMON (SHARED) ELEMENTS MODULE INVOKED –> <!– ============================================================= –>

<!– COMMON (SHARED) DECLARATIONS –> <!– Declarations for elements, attributes,

entities, and Notations that are shared by
more than one class module. Note: Must be
called before any of the class modules.    -->

%common.ent;

<!– ============================================================= –> <!– JOURNAL ARTICLE CLASS ELEMENTS (alpha) –> <!– ============================================================= –>

<!– ARTICLE METADATA ELEMENTS –> %articlemeta.ent;

<!– BACK MATTER ELEMENTS –> %backmatter.ent;

<!– DISPLAY (GRAPHICAL) ELEMENTS –> %display.ent;

<!– FORMATTING ELEMENT CLASSES –> <!– Elements that change rendition/display. –> %format.ent;

<!– FUNDING ELEMENTS –> <!– Elements that describe the sponsorship or

open access                                -->

%funding.ent;

<!– JOURNAL METADATA ELEMENTS –> %journalmeta.ent;

<!– LINK CLASS ELEMENTS –> %link.ent;

<!– LIST CLASS ELEMENTS –> %list.ent;

<!– MATH ELEMENTS –> %math.ent;

<!– NLM CITATION ELEMENT –> %nlmcitation.ent;

<!– PARAGRAPH-LEVEL ELEMENTS –> %para.ent;

<!– PHRASE-LEVEL ELEMENTS –> %phrase.ent;

<!– BIBLIOGRAPHIC REFERENCE (CITATION)

CLASS ELEMENTS                             -->

%references.ent;

<!– RELATED OBJECT ELEMENT –> <!– Defines the <related-object> element to

describe a related object such as a
related book or a dataset.                 -->

%related-object.ent;

<!– SECTION ELEMENTS –> %section.ent;

<!– ============================================================= –> <!– THE REST OF THE EXTERNAL MODULES INVOKED –> <!– ============================================================= –>

<!– MATHML SETUP MODULE –> <!– Invoke the MathML modules –> %mathmlsetup.ent;

<!– XHTML TABLE SETUP MODULE –> <!– Set up the necessary Parameter Entity values

and then invoke XHTML (HTML 4.0) table
module                                     -->

%XHTMLtablesetup.ent;

<!– OASIS EXCHANGE (CALS) TABLE SETUP MODULE –> <!– Set up the necessary Parameter Entity values

and then invokes OASIS Exchange table
module                                     -->

%oasis-tablesetup.ent;

<!– SPECIAL CHARACTERS DECLARATIONS –> <!– Standard XML special character entities

used in this DTD                           -->

%xmlspecchars.ent;

<!– CUSTOM SPECIAL CHARACTERS DECLARATIONS –> <!– Custom special character entities created

specifically for use in this DTD Suite     -->

%chars.ent;

<!– NOTATION DECLARATIONS MODULE –> %notat.ent;

<!– ============================================================= –> <!– PARAMETER ENTITIES FOR ATTRIBUTE LISTS –> <!– ============================================================= –>

<!– DTD VERSION –> <!– What version of this DTD was used to make

the document instance under consideration.
Note that this is a fixed value that should
change every time the DTD changes versions or
revisions.                                 -->

<!ENTITY % dtd-version

"dtd-version
            CDATA                         #FIXED '0.4'"  >

<!– ARTICLE ATTRIBUTES –> <!– Attributes for the top-level element

<article>                                  -->

<!ENTITY % article-atts

"article-type
            CDATA                             #IMPLIED
 specific-use
            CDATA                             #IMPLIED
 xml:lang   NMTOKEN                           'en'
 %dtd-version;
 %XLINK.xmlns.attrib;
 %MATHML.xmlns.attrib;
 %Schema.xmlns.attrib;
 %oasis.xmlns.attrib;"                                   >

<!– BODY ATTRIBUTES –> <!– Attributes for the <body> element –> <!ENTITY % body-atts

"specific-use
            CDATA                             #IMPLIED"  >

<!– SUB-ARTICLE ATTRIBUTES –> <!– Attributes for the <sub-article> element –> <!ENTITY % sub-article-atts

"article-type
            CDATA                             #IMPLIED
 id         ID                                #IMPLIED
 specific-use
            CDATA                             #IMPLIED
 xml:lang   NMTOKEN                           #IMPLIED"  >

<!– RESPONSE ATTRIBUTES –> <!– Attributes for the <response> element –> <!ENTITY % response-atts

"response-type
            CDATA                             #IMPLIED
 id         ID                                #IMPLIED
 specific-use
            CDATA                             #IMPLIED
 xml:lang   NMTOKEN                           #IMPLIED"  >

<!– ============================================================= –> <!– JOURNAL ARTICLE ELEMENTS –> <!– ============================================================= –>

<!– ARTICLE MODEL (LIMITED) –> <!– Article-like model used for, for example,

a short sub-article such as a news brief that
is contained in side a journal article.
                                           -->

<!ENTITY % article-short-model

"((front | front-stub), body?, back?,
  floats-group?)"                            >

<!– ARTICLE MODEL WITH SUBARTICLE OR RESPONSE –> <!– Typical journal article model, which may

contain extended components, such as
sub-articles or responses, but which usually
contains neither.                          -->

<!ENTITY % article-full-model

"(front, body?, back?, floats-group?,
  (sub-article* | response*) )"              >

<!– ARTICLE –> <!– The complete content of a journal article.

Details at:
http://jats.nlm.nih.gov/archiving/tag-library/0.4/index.html?elem=article
                                           -->

<!ELEMENT article %article-full-model; > <!ATTLIST article

%article-atts;                                          >

<!– ============================================================= –> <!– FRONT MATTER ELEMENTS –> <!– ============================================================= –>

<!– FRONT MATTER MODEL –> <!– Model for the <front> matter (the header

metadata) of a journal article)            -->

<!ENTITY % front-model “(journal-meta?, article-meta,

(%list.class; | %front-back.class;)* )"    >

<!– FRONT MATTER –> <!– The metadata concerning an article, such as

the name and issue of the journal in which it
appears and the name and author(s) of the
article.
Details at:
http://jats.nlm.nih.gov/archiving/tag-library/0.4/index.html?elem=front
                                           -->

<!ELEMENT front %front-model; >

<!– ============================================================= –> <!– BODY ELEMENTS –> <!– ============================================================= –>

<!– BODY MODEL –> <!– Content model for the Body (main textual

content) of a journal article.             -->

<!ENTITY % body-model “((%para-level;)*, (%sec-level;)*,

sig-block?)"                               >

<!– BODY OF THE ARTICLE –> <!– The main textual portion of the article that

conveys the content.
Details at:
http://jats.nlm.nih.gov/archiving/tag-library/0.4/index.html?elem=body
                                           -->

<!ELEMENT body %body-model; > <!ATTLIST body

%body-atts;                                             >

<!– ============================================================= –> <!– BACK MATTER ELEMENTS –> <!– ============================================================= –>

<!– BACK MATTER MODEL –> <!– Content model for the Back Matter (ancillary

material such as appendices) of a journal
article.                                   -->

<!ENTITY % back-model “(label?, title*,

(%doc-back-matter-mix;)* )"                >

<!– BACK MATTER –> <!– Ancillary or supporting material not included

as part of the main textual content of a
journal article, for example appendices and
acknowledgments.
Details at:
http://jats.nlm.nih.gov/archiving/tag-library/0.4/index.html?elem=back
                                           -->

<!ELEMENT back %back-model; >

<!– ============================================================= –> <!– SUBARTICLE –> <!– ============================================================= –>

<!– SUBARTICLE MODEL –> <!– Content model for the <sub-article> element

-->

<!ENTITY % sub-article-model

"( (front | front-stub), body?, back?,
   floats-group?,
   (sub-article* | response*) )"             >

<!– SUBARTICLE –> <!– An article that is completely contained

inside another article. Both the article and
the subarticle have their own metadata. The
article has at very least journal and issue
information and start and end pages; it may
have a title, author, or other metadata.
Details at:
http://jats.nlm.nih.gov/archiving/tag-library/0.4/index.html?elem=sub-article
                                           -->

<!ELEMENT sub-article %sub-article-model; > <!ATTLIST sub-article

%sub-article-atts;                                      >

<!– FRONT MODEL STUB –> <!– Content model for the <front-stub> element

-->

<!ENTITY % front-stub-model

"(article-id*, article-categories?,
 title-group?,
 (%contrib-group.class; |
  %aff-alternatives.class; | %x.class;)*,
 author-notes?, pub-date*,
 volume?, volume-id*, volume-series?,
 issue?, issue-id*, issue-title*,
 issue-sponsor*, issue-part?, isbn*,
 supplement?,
 ( ( (fpage, lpage?)?, page-range?) |
   elocation-id )?,
 (%address-link.class; | product |
  supplementary-material)*,
 history?, permissions?, self-uri*,
 related-article*, abstract*,
 trans-abstract*, kwd-group*,
 funding-group*, conference*, counts?,
 custom-meta-group?)"                        >

<!– STUB FRONT METADATA –> <!– A reduced metadata set for use in

sub-articles and responses, which will
inherit metadata not defined in the stub
from the enclosing article
Details at:
http://jats.nlm.nih.gov/archiving/tag-library/0.4/index.html?elem=front-stub
                                           -->

<!ELEMENT front-stub %front-stub-model; >

<!– ============================================================= –> <!– RESPONSE ELEMENTS –> <!– ============================================================= –>

<!– RESPONSE –> <!– Reply, response, or commentary concerning the

journal article. In the typical case, the
response is included in the same XML package
as the original article, and thus attached
at the end of the article proper.
Details at:
http://jats.nlm.nih.gov/archiving/tag-library/0.4/index.html?elem=response
                                           -->

<!ELEMENT response %article-short-model; > <!ATTLIST response

%response-atts;                                         >

<!– ================== End Journal Archiving and Interchange DTD –>