<!– ============================================================= –> <!– MODULE: Journal Publishing DTD Customize Content and –> <!– Attributes Module –> <!– VERSION: NISO 0.4 –> <!– DATE: January 2011 –> <!– –> <!– ============================================================= –>

<!– ============================================================= –> <!– PUBLIC DOCUMENT TYPE DEFINITION –> <!– TYPICAL INVOCATION –> <!– “-//NLM//DTD JATS (Z39.96) Journal Publishing DTD Customize Content and Attributes Module v0.4 20110131//EN” Delivered as file “JATS-journalpubcustom-models0.ent” –> <!– ============================================================= –>

<!– ============================================================= –> <!– SYSTEM: Journal Publishing DTD of the –> <!– Archiving and Interchange DTD Suite –> <!– –> <!– PURPOSE: To declare the Parameter Entities (PEs) used to –> <!– over-ride content models or parts of content –> <!– models when making a new DTD from the modules of –> <!– the Archiving and Interchange DTD Suite. –> <!– –> <!– Or-groups within models should use mixes or –> <!– classes rather than name elements directly. –> <!– –> <!– Note: Since PEs must be declared before they –> <!– are used, this module must be called before the –> <!– content modules that declare elements. –> <!– –> <!– CONTAINS: 1) PEs that define OR lists of elements to be –> <!– mixed with #PCDATA in element content models –> <!– (all PEs are named “yyy-elements”, where “yyy” –> <!– is the name of the primary element whose –> <!– content model will use the declared PE.) –> <!– 2) PEs that define complete content models. –> <!– (names ending in the suffix “-model”) –> <!– 3) PEs that define attribute list or attribute –> <!– value over-rides –> <!– –> <!– CREATED FOR: –> <!– Digital Archive of Journal Articles –> <!– National Center for Biotechnology Information –> <!– (NCBI) –> <!– National Library of Medicine (NLM) –> <!– –> <!– ORIGINAL CREATION DATE: –> <!– September 2004 –> <!– –> <!– CREATED BY: Jeff Beck (NCBI) –> <!– Deborah Lapeyre (Mulberry Technologies, Inc.) –> <!– B. Tommie Usdin (Mulberry Technologies, Inc.) –> <!– –> <!– 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.

10. 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".

    =============================================================
    Version 3.1                       (DAL/BTU) v3.1 (2010-04-30)

    Version 3.1 is fully compatible with Version 3.0.

    Details on version 3.1 are available at
          http://jats.nlm.nih.gov/3.1.

 9. POSITION ATTRIBUTE - Added the value "background"

 8. PREFORMAT - Added <alt-text> and <long-desc> to <preformat> by
    adding %access.class; to %preformat-elements;

 7. INITIALS - Removed the attribute over-ride for <surname> and
    <given-names> to allow the use of @initials.

 6. JOURNAL METADATA- Added <notes> to repeat within <journal-meta>
    (through %journal-meta-model; and added @xml:lang and
    @specific-use to the attributes of <notes> through %notes-atts;

 7. AFFILIATION ALTERNATIVES - Added the element <aff-alternatives>
    to <article-meta> through %article meta-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.

 6. PERSON-GROUP - Became a mixed-content model, so the parameter
    entity %person-group-model: was changed to
    %person-group-elements;, which will be mixed with #PCDATA
    as defined in references.ent. The PE person-group-model has
    been retained in references.ent for compatibility, but has been
    set to the mixed model using person-group-elements.

 5. @SPECIFIC-USE and @XML:LANG - Added the @specific-use and
    @xml:lang to %display-atts;. Also added these attributes
    to the following over-rides:
     - inline-graphic through inline-graphic-atts (both)
     - fn through fn-atts (added @specific-use, @xml:lang already
         there)
     - person-group through person-group-atts (both)

 4. LABEL - Added optional <label> to <fig-group> using
    %fig-group-model; as the first element in model, before caption

 3. SELF URI - Added <self-uri> to <journal-meta> (directly
    following <notes>) so that an XML document can point to the
    journal home page.

 2. 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.

 1. Updated public identifier to "v3.0 20080202//EN"              -->

<!– ============================================================= –> <!– INLINE MIXES TO OVER-RIDE CONTENT MODELS –> <!– (ELEMENTS TO BE ADDED TO #PCDATA IN MODELS)–> <!– ============================================================= –>

<!– ABBREVIATED JOURNAL TITLE ELEMENTS –> <!– The elements that can be included along with

data characters inside the content model of
a <abbrev-journal-title>
Removed the face markup, %just-rendition;  -->

<!ENTITY % abbrev-journal-title-elements

""                                           >

<!– CONFERENCE ACRONYM ELEMENTS –> <!– The elements that can be included along with

data characters inside the content model of
the conference acronym.
Removed %simple-text;                      -->

<!ENTITY % conf-acronym-elements

""                                           >

<!– CONFERENCE LOCATION ELEMENTS –> <!– Elements for use in the <conf-loc> element

Removed %simple-text;                      -->

<!ENTITY % conf-loc-elements

""                                           >

<!– CONFERENCE NAME ELEMENTS –> <!– Elements for use in the <conf-name> element.

Removed %simple-text;                      -->

<!ENTITY % conf-name-elements

""                                           >

<!– CONFERENCE NUMBER ELEMENTS –> <!– The elements that can be included along with

data characters inside the content model of
the conference number.
Removed %simple-text;                      -->

<!ENTITY % conf-num-elements

""                                           >

<!– CONFERENCE SPONSOR ELEMENTS –> <!– The elements that can be included along with

data characters inside the content model of
the conference sponsor.
Removed %simple-text;                      -->

<!ENTITY % conf-sponsor-elements

""                                           >

<!– DEGREE(S) ELEMENTS –> <!– The elements that can be included along with

data characters inside the content model of
<degrees>
Removed %just-rendition;                   -->

<!ENTITY % degrees-elements

""                                           >

<!– EDITION ELEMENTS –> <!– The elements that can be included along with

data characters inside the content model of
Removed %just-rendition;                   -->

<!ENTITY % edition-elements

""                                           >

<!– FAX NUMBER ELEMENTS –> <!– The elements that can be included along with

data characters inside the content model of
a <fax>
Removed %just-rendition;                   -->

<!ENTITY % fax-elements

""                                           >

<!– GIVEN (FIRST) NAMES ELEMENTS –> <!– The elements that can be included along with

data characters inside the content model of
a <given-names>
Removed %just-rendition;                   -->

<!ENTITY % given-names-elements

""                                           >

<!– INSTITUTION NAME ELEMENTS –> <!– Elements for use in the <institution>

element
Removed %break.class; and %emphasis.class; -->

<!ENTITY % institution-elements

"| %subsup.class;"                           >

<!– ISSUE TITLE ELEMENTS –> <!– Elements for use with data characters inside

the model for the <issue> element
Removed %just-rendition;                   -->

<!ENTITY % issue-elements

""                                           >

<!– JOURNAL TITLE ELEMENTS –> <!– The elements that can be included along with

data characters inside the content model of
a <journal-title>
Removed %just-rendition;                   -->

<!ENTITY % journal-title-elements

""                                           >

<!– KEYWORD CONTENT ELEMENTS –> <!– The elements that can be included along with

data characters inside the content model of
a keyword <kwd>.                           -->

<!ENTITY % kwd-elements

"| %emphasis.class; | %phrase-content.class; |
 %subsup.class;"                             >

<!– PATENT NUMBER ELEMENTS –> <!– The elements that can be included along with

data characters inside the content model of
<patent>
Removed %just-rendition;                   -->

<!ENTITY % patent-elements

""                                           >

<!– PERSON GROUP MODEL –> <!– Content model for the <person-group> element

-->

<!ENTITY % person-group-elements

" | %name.class; | %person-group-info.class; |
  %string-name.class;"                       >

<!– PHONE NUMBER ELEMENTS –> <!– The elements that can be included along with

data characters inside the content model of
a <phone number>
Removed %just-rendition;                   -->

<!ENTITY % phone-elements

""                                           >

<!– PREFIX ELEMENTS –> <!– The elements that can be included along with

data characters inside the content model of
a <prefix>
Removed %just-rendition;                   -->

<!ENTITY % prefix-elements

""                                           >

<!– PREFORMATTED TEXT ELEMENTS –> <!– Elements that may be used, along with data

characters, inside the content model for the
<preformat> element, in which white space,
such as tabs, line feeds, and spaces will
be preserved                               -->

<!ENTITY % preformat-elements

"| %access.class; | %address-link.class; |
 %display-back-matter.class; |
 %emphasis.class; | %phrase.class; |
 %subsup.class;"                             >

<!– PUBLISHER'S LOCATION ELEMENTS –> <!– Elements for use in the Publisher Location

<publisher-loc> element
Removed %address.class;, %address-link.class;,
%emphasis.class;, and %subsup.class;       -->

<!ENTITY % publisher-loc-elements

"| %address-link.class;"                     >

<!– PUBLISHER'S NAME ELEMENTS –> <!– The elements that can be included along with

data characters inside the content model of
a <publisher-name>
Removed %just-rendition;                   -->

<!ENTITY % publisher-name-elements

""                                           >

<!– SUFFIX ELEMENTS –> <!– The elements that can be included along with

data characters inside the content model of
a <suffix>
Removed %just-rendition;                   -->

<!ENTITY % suffix-elements

""                                           >

<!– SURNAME ELEMENTS –> <!– The elements that can be included along with

data characters inside the content model of
a <surname>
Removed %just-rendition;                   -->

<!ENTITY % surname-elements

""                                           >

<!– URI ELEMENTS –> <!– The elements that can be included along with

data characters inside the content model of
a <uri>
Removed %just-rendition;                   -->

<!ENTITY % uri-elements

""                                           >

<!– VOLUME NUMBER ELEMENTS –> <!– The elements that can be included along with

data characters inside the content model of
a <volume>
Removed %just-rendition;                   -->

<!ENTITY % volume-elements

""                                           >

<!– ============================================================= –> <!– OVER-RIDES OF CONTENT MODELS (FULL MODELS) –> <!– ============================================================= –>

<!– ABSTRACT MODEL –> <!– Abstracts may contain one or more paragraphs

(as a typical abstract does) or titled
sections, as is done in many physics
articles.
Unlike the default model in the base DTD
Suite, this <abstract> requires that all
sections in the abstract start with titles.-->

<!ENTITY % abstract-model

"(label?, title?, p*, sec*)"                 >

<!– ACKNOWLEDGMENTS MODEL –> <!– Content model for the <ack> element –> <!ENTITY % ack-model “(label?, title?, p*, sec*, ref-list*)” >

<!– ANONYMOUS MODEL –> <!– Unlike in Green, <anonymous> is empty. When

present, it is used to generate the text
"anonymous" or "anon.", etc.               -->

<!ENTITY % anonymous-model

"EMPTY"                                      >

<!– ARRAY CONTENT MODEL –> <!– The element used to contain material in

rows and columns that is just a block insert
into the text flow, not numbered or called a
table, and not titled or captioned         -->

<!ENTITY % array-model “((%access.class; | %address-link.class;)*,

( (%just-base-display.class;)* |
  %tbody.class; ),
(%display-back-matter.class;)* )"          >

<!– ARTICLE METADATA MODEL –> <!– Full content model for the metadata that is

specific to the article.
Unlike in Archive DTD, some of the metadata
is required here.                          -->

<!ENTITY % article-meta-model

"(article-id*, article-categories?,
 title-group,
 (%contrib-group.class; |
  %aff-alternatives.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?)"                        >

<!– CONFERENCE MODEL –> <!– The content model of the <conference>

element                                    -->

<!ENTITY % conference-model

"(conf-date, (conf-name | conf-acronym )+,
 conf-num?, conf-loc?, conf-sponsor*,
 conf-theme?)"                               >

<!– CONTRIBUTOR MODEL –> <!– Content model for the <contrib> element –> <!ENTITY % contrib-model

"((%name.class;)*, (%degree.class;)*,
  (%contrib-info.class;)* )"                 >

<!– DATE ELEMENTS MODEL –> <!– The content models for elements that describe

dates, such as Publication Date <pub-date> and
History Dates <date>.  The <string-date>
element holds dates for which months and
years are not given, for example "first
quarter", "spring", etc.
Unlike the base DTD Suite, this <date>
requires a <year> and may not take a string
date as an alternative.                    -->

<!ENTITY % date-model “(((day?, month?) | season)?, year)” >

<!– DEFINITION LIST: DEFINITION ITEM ELEMENTS –> <!– The content model of a <def-item>. –> <!ENTITY % def-item-model

"(term, def*)"                               >

<!– FIGURE-LIKE CONTENT MODEL –> <!– Content model for the Figure element and any

similarly structured elements
Made <label> and <caption> non-repeatable. -->

<!ENTITY % fig-model “((%id.class;)*, label?, (%caption.class;)?,

(%access.class; | %address-link.class;)*,
(%block-math.class; |
 %chem-struct-wrap.class; |
 %intable-para.class; |
 %just-table.class; | %just-para.class; |
 %list.class; | %simple-display.class;)*,
(%display-back-matter.class;)* )"          >

<!– FIGURE GROUP MODEL –> <!– Content model for a <fig-group> –> <!ENTITY % fig-group-model

"(label?, (%caption.class;)?,
  (%access.class; | %address-link.class;)*,
  (%fig-display.class; |
   %just-base-display.class;)* )"            >

<!– JOURNAL METADATA MODEL –> <!– Content model for the journal metadata

element <journal-meta>                     -->

<!ENTITY % journal-meta-model

"(journal-id+, journal-title-group*,
  issn+, isbn*, publisher?, notes*,
  self-uri*)"                                >

<!– LIST MODEL –> <!– Content model for the <list> element –> <!ENTITY % list-model “(label?, title?, list-item+)” >

<!– REFERENCE ITEM MODEL –> <!– Content model for the <ref> element –> <!ENTITY % ref-model “(label?,

(%citation.class; | %note.class;)+ )"       >

<!– CONTENT MODEL FOR A STRUCTURAL SECTION –> <!– The model for a section that requires that a

either <title> or a <label> (which in some
journals takes the place of a title) must be
present. One or the other must be present
for autogeneration of a Table of Contents or
other navigation.                          -->

<!ENTITY % sec-model “(sec-meta?, ( (label, title?) | title ),

(%para-level;)*,
(%sec-level;)*,
(%sec-back-matter-mix;)* )"                >

<!– TRANSLATED ABSTRACT MODEL –> <!– Content model for an <trans-abstract>

element                                    -->

<!ENTITY % trans-abstract-model

"(label?, title?, p*, sec*)"                 >

<!– ============================================================= –> <!– DUPLICATE ATTRIBUTE DECLARATIONS –> <!– (These are unchanged from the base Suite, –> <!– but are used in attribute over-rides below)–> <!– ============================================================= –>

<!– DISPLAY ATTRIBUTES –> <!– Attributes used for several of the block

display elements                           -->

<!ENTITY % display-atts

"position   (anchor | background | float | margin)
                                              'float'
 orientation
            (portrait | landscape)            'portrait'
 specific-use
            CDATA                             #IMPLIED
 xml:lang   NMTOKEN                           #IMPLIED"  >

<!– XLINK LINK ATTRIBUTES –> <!– Attributes for any element that must be a

link                                       -->

<!ENTITY % link-atts

"xmlns:xlink CDATA                            #FIXED
                         'http://www.w3.org/1999/xlink'
 xlink:type  (simple)                   #FIXED 'simple'
 xlink:href  CDATA                            #REQUIRED
 xlink:role  CDATA                            #IMPLIED
 xlink:title CDATA                            #IMPLIED
 xlink:show  (embed | new | none | other | replace)
                                              #IMPLIED
 xlink:actuate
             (none | onLoad | onRequest | other)
                                              #IMPLIED"  >

<!– MIGHT LINK XLINK ATTRIBUTES –> <!– Attributes for any element that may be a link

but need not be one                        -->

<!ENTITY % might-link-atts

"xmlns:xlink CDATA                            #FIXED
                         'http://www.w3.org/1999/xlink'
 xlink:type  (simple)                   #FIXED 'simple'
 xlink:href  CDATA                            #IMPLIED
 xlink:role  CDATA                            #IMPLIED
 xlink:title CDATA                            #IMPLIED
 xlink:show  (embed | new | none | other | replace)
                                              #IMPLIED
 xlink:actuate
             (none | onLoad | onRequest | other)
                                              #IMPLIED"  >

<!– ============================================================= –> <!– OVER-RIDES OF ATTRIBUTE LISTS –> <!– ============================================================= –>

<!– FOOTNOTE TYPE VALUES –> <!– Used to mark the semantics of the footnote,

what information does this footnote convey.
                                           -->

<!ENTITY % fn-types “abbr | com | con | conflict |

corresp | current-aff | deceased |
edited-by | equal |
financial-disclosure | on-leave |
participating-researchers |
presented-at | presented-by |
present-address | previously-at |
study-group-members |
supplementary-material |
supported-by | other"                       >

<!– FOOTNOTE ATTRIBUTES –> <!– Attribute list for Footnote element

Unlike base, "fn-type" values have been made
explicit and removed the symbol attribute  -->

<!ENTITY % fn-atts

"id         ID                                #IMPLIED
 fn-type    (%fn-types;)                      #IMPLIED
 specific-use
            CDATA                             #IMPLIED
 symbol     CDATA                             #IMPLIED
 xml:lang   NMTOKEN                           #IMPLIED"  >

<!– INLINE GRAPHIC ATTRIBUTES –> <!– Attributes for Inline Graphic

<inline-graphic>                           -->

<!ENTITY % inline-graphic-atts

"id        ID                                 #IMPLIED
 content-type
           CDATA                              #IMPLIED
 baseline-shift
           CDATA                              #IMPLIED
 mimetype  CDATA                              #IMPLIED
 mime-subtype
           CDATA                              #IMPLIED
 specific-use
            CDATA                             #IMPLIED
 xml:lang   NMTOKEN                           #IMPLIED
 %link-atts;"                                            >

<!– PERSON GROUP ATTRIBUTES –> <!– Attributes for the <person-group> element –> <!ENTITY % person-group-atts

"id        ID                                 #IMPLIED
 person-group-type
            (allauthors | assignee | author | compiler |
             director | editor | guest-editor | inventor |
             translator | transed)            #IMPLIED
 specific-use
            CDATA                             #IMPLIED
 xml:lang   NMTOKEN                           #IMPLIED" >

<!– SECTION ATTRIBUTES –> <!– Attribute list for Section element –> <!ENTITY % sec-atts

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

<!– ================== End Publishing Content/ATT Override ====== –>