Article Authoring DTD

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<!--  MODULE:    Article Authoring DTD                             -->
<!--  VERSION:   2.1                                               -->
<!--  DATE:      June 2005                                         -->
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<!--                    PUBLIC DOCUMENT TYPE DEFINITION            -->
<!--                        TYPICAL INVOCATION                     -->
"-//NLM//DTD Article Authoring DTD v2.1 20050630//EN"
     Delivered as file "articleauthoring.dtd"                      -->
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<!-- SYSTEM:     Journal Authoring DTD of the                      -->
<!--             Archiving and Interchange DTD Suite               -->
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<!-- PURPOSE:    DTD for creation of new journal articles          -->
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<!--             This subset of the Journal Archiving and          -->
<!--             Interchange DTD is optimized for the authoring    -->
<!--             (or initial XML tagging) of journal articles and  -->
<!--             some non-article material such as product and     -->
<!--             book reviews. 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.              -->
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<!-- CONTAINS:   1) Declare and invoke the Authoring (Pink) DTD-   -->
<!--                specific module of modules, that names  any    -->
<!--                modules created expressly for this DTD.        -->
<!--                             (%journalpubcustom-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   -->
<!--                             (%journalpub-classes.ent;)        -->
<!--             4) Invoke Suite default classes                   -->
<!--                             (%default-classes.ent;)           -->
<!--             5) Invoke DTD-specific mixes over-ride module     -->
<!--                             (%journalpubcustom-mixes.ent;)    -->
<!--             6) Invoke Suite default mixes                     -->
<!--                             (%default-mixes.ent;)             -->
<!--             7) Invoke DTD-specific content model over-ride    -->
<!--                      module (%journalpubcustom-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>                      -->
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<!-- CREATED FOR:                                                  -->
<!--             Digital Archive of Journal Articles               -->
<!--             National Center for Biotechnology Information     -->
<!--                (NCBI)                                         -->
<!--             National Library of Medicine (NLM)                -->
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<!-- ORIGINAL CREATION DATE:                                       -->
<!--             June 2005                                         -->
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<!-- CREATED BY: Deborah Lapeyre (Mulberry Technologies, Inc.)     -->
<!--             B. Tommie Usdin (Mulberry Technologies, Inc.)     -->
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<!--             The Journal Authoring DTD is built from the       -->
<!--             Archiving and Interchange DTD Suite.              -->
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<!--             Suggestions for refinements and enhancements to   -->
<!--             this DTD should be sent in email to:              -->
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<!--                    DTD VERSION\CHANGE HISTORY                 -->
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Version  Reason/Occasion                   (who) vx.x (yyyy-mm-dd)

     Version 2.1                       (DAL/BTU) v2.1 (2005-06-30)
     Initial DTD creation coincides with Suite 2.1 release
  1. Initial creation of this DTD and all its modules with version
     numbers "v2.1 20050630" since this is the version of the DTD
     Suite on which these modules are based. The "dtd-version" fixed 
     attribute was also set to DTD (version "2.1").                -->

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<!--                    DESIGN CONSIDERATIONS                      -->
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                        A set of journal archiving and interchange 
                        DTD modules was written as the basis for 
                        article creation, publishing, interchange, 
                        and repository DTDs, with the intention that 
                        DTDs for specific purposes, such as this 
                        Authoring  DTD, would be developed based on 
                        This Authoring DTD has been optimized for 
                        the creation of new journal articles by
                        individual authors. This means that it lacks
                        all the journal-related material (such as
                        the journal metadata) that are not the
                        responsibility of the author but of the
                        publisher. This DTD is also smaller (fewer 
                        elements and fewer choices in many contexts) 
                        than either the Publishing or Archiving DTDs.
                        It was not the intention to limit the 
                        expressive power licensed by the DTD, but 
                        rather to limit the many paths where there
                        are several ways to tag the same material,
                        where an archiving or publishing DTD needs to
                        be able to accept all styles.              -->
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<!--                    MODULE OF MODULES INVOKED                  -->
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<!--                    MODULE TO NAME DTD-SPECIFIC MODULES        -->
<!--                    Names all DTD-specific external modules    -->
<!ENTITY % articleauthcustom-modules.ent PUBLIC  
"-//NLM//DTD Article Authoring DTD-Specific Modules v2.1 20050630//EN"
"articleauthcustom-modules.ent"                                      >

<!--                    MODULE TO NAME THE MODULES                 -->
<!--                    Names all the external modules (except
                        itself and the Customization Module) that 
                        are part of the modular Journal Archiving
                        and Interchange DTD Suite library. 
                           This DTD then selects from those
                        modules 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 
                        DTD references the external Parameter Entity 
                        of the module that contains the declarations.
<!ENTITY % modules.ent PUBLIC  
"-//NLM//DTD Archiving and Interchange DTD Suite Module of Modules v2.1 20050630//EN"
"modules.ent"                                                        >

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<!--                    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.                  -->
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<!--                    Names the module that holds the DTD-specific
                        class definitions for the Article Authoring
                        DTD that will over-ride the Suite defaults. 
                        (Defined in %archivecustom-modules.ent;)   -->

<!--                    DEFAULT ELEMENT CLASSES MODULE             -->
<!--                    Names the module that holds the standard
                        class definitions for the Journal Archiving
                        and Interchange DTD Suite.                 -->

<!--                    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;)   -->

<!--                    DEFAULT MIX CUSTOMIZATIONS MODULE          -->
<!--                    Names the module that holds the standard
                        mix definitions for the Journal Archiving
                        and Interchange DTD Suite.                 -->

                        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;)   -->

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<!--                    COMMON (SHARED) ELEMENTS MODULE INVOKED    -->
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<!--                    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.    -->


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<!--                    JOURNAL ARTICLE CLASS ELEMENTS (alpha)     -->
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<!--                    ARTICLE METADATA ELEMENTS                  -->

<!--                    BACK MATTER ELEMENTS                       -->

<!--                    DISPLAY (GRAPHICAL) ELEMENTS               -->

<!--                    FORMATTING ELEMENT CLASSES                 -->
<!--                    Elements that change rendition/display.    -->

<!--                    LINK CLASS ELEMENTS                        -->

<!--                    LIST CLASS ELEMENTS                        -->

<!--                    MATH ELEMENTS                              -->

<!--                    NLM CITATION ELEMENT                       -->

<!--                    PARAGRAPH-LEVEL ELEMENTS                   -->

<!--                    PHRASE-LEVEL ELEMENTS                      -->

                        CLASS ELEMENTS                             -->

<!--                    SECTION ELEMENTS                           -->

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<!--                    THE REST OF THE EXTERNAL MODULES INVOKED   -->
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<!--                    MATHML SETUP MODULE                        -->
<!--                    Invoke the MathML modules                  -->

<!--                    XHTML TABLE SETUP MODULE                   -->
<!--                    Set up the necessary Parameter Entity values
                        and then invoke XHTML (HTML 4.0) table 
                        module                                     -->

<!--                    SPECIAL CHARACTERS DECLARATIONS            -->
<!--                    Standard XML special character entities 
                        used in this DTD                           -->

<!--                    CUSTOM SPECIAL CHARACTERS DECLARATIONS     -->
<!--                    Custom special character entities created 
                        specifically for use in this DTD Suite     -->

<!--                    NOTATION DECLARATIONS MODULE               -->

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<!--                    PARAMETER ENTITIES FOR ATTRIBUTE VALUES    -->
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<!--                    ARTICLE TYPES                              -->
<!--                    What kind of article is this?  All articles
                        should have types assigned if possible.
<!ENTITY % article-types    
                        "abstract | addendum | announcement | 
                         article-commentary | book-review | 
                         books-received | brief-report | calendar | 
                         case-report | correction | discussion | 
                         editorial | in-brief | introduction | 
                         letter | meeting-report | news | obituary |
                         oration | other | product-review | reply |
                         research-article | retraction |  
                         review-article"                             >

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<!--                    PARAMETER ENTITIES FOR ATTRIBUTE LISTS     -->
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<!--                    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   
                        CDATA                          #FIXED '2.1'" >

<!--                    ARTICLE ATTRIBUTES                         -->
<!--                    Attributes for the top-level element
                        <article>                                  -->
<!ENTITY % article-atts
                        (%article-types;)                  #IMPLIED
             xml:lang   NMTOKEN                            'EN'     
             %MATHML.xmlns.attrib;"                                  >


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<!--                    JOURNAL ARTICLE ELEMENTS                   -->
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<!--                    ARTICLE MODEL (LIMITED)                    -->
<!ENTITY % article-short-model    
                        "(front, body, back?)"                       >

<!--                    ARTICLE                                    -->
<!--                    The complete content of a journal article.
                        An article is potentially divided into 
                        four (more typically three) parts: 1) the
                        Front Matter (article metadata or header),
                        the body of the article (main content), any
                        ancillary information such as a glossary or
                        appendix, and (the least common) a
                        response, that is a commentary on the
                        article itself.                            -->
<!ELEMENT  article      %article-short-model;                        >

<!--         article-type   
                        What kind of article is this?  
                        Note: When the article is a commentary on 
                        another article, for example a correction or
                        addendum, this attribute is metadata for the 
                        commentary itself, it does NOT define the 
                        kind of article that is being corrected or
                        Authoring Note: All articles
                        should have types assigned if possible.
                          abstract   The article itself is an 
                                     abstract (of a paper or
                                     presentation), usually that 
                                     has been presented or published 
                          addendum   A published item that adds
                                     additional information or
                                     clarification to another item
                                     Similar value "correction"
                                     corrects an error in previously
                                     published material
                                     Material announced in the 
                                     publication (may or may not be
                                     directly related to the pub)
                                     An item whose subject or focus
                                     is another article or articles; 
                                     this article comments on the 
                                     other article(s) (For example,
                                     for a controversial article, the
                                     editors of the publication 
                                     might invite an author of the
                                     opposing opinion to comment on
                                     the first article, and publish
                                     the two together.)
                                     Review or analysis of one or more
                                     printed or online books (Note
                                     that product reviews are a
                                     separate type.)
                                     Notification of items such as
                                     books that have been received
                                     by the publication for review
                                     or other consideration
                                     A short and/or rapid announcement 
                                     of research results
                          calendar   A list of events
                                     Case study, case report, or other
                                     description of a case
                          correction A modification, or
                                     correction of previously
                                     published material (sometimes
                                     called "errata") Similar value
                                     "addendum" merely adds to 
                                     previously published material
                          discussion Invited discussion related to a 
                                     specific article or issue
                          editorial  Opinion piece, policy statement,
                                     or general commentary, typically
                                     written by staff of the
                                     publication. Note: similar value
                                     "article-commentary" is reserved 
                                     for a commentary on a specific
                                     article or articles.
                          in-brief   Summary of items in the current 
                                     An introduction to the
                                     publication, a series of articles
                                     within the publication, etc.,
                                     typically for a special section
                                     or issue
                          letter     Letter to the publication,
                                     typically commenting upon a
                                     published item
                                      Report of a conference, 
                                      symposium, or meeting
                          news        News item
                          obituary    Announcement of a death or
                                      appreciation of a colleague
                                      who has recently died
                          oration     Reprint of a speech or oral 
                          other       Not any of the article types
                                      explicitly named in this list
                                      Description, analysis, or review
                                      of a product or service, for
                                      example a software package (note
                                      that book review is a separate
                          reply       Reply to a letter or commentary,
                                      typically by the original
                                      author commenting upon the
                                      Research article
                          retraction  Retraction of previously
                                      published material
                                      Review or state-of-the-art
                                      summary article                   
                        Which version of the DTD does this article
                        use? The value is a #FIXED attribute, so
                        the entire attribute definition is defined
                        in a Parameter Entity, so the next version
                        of the DTD can use a different #FIXED value.
             xml:lang   The language in which the value of the
                        element is expressed.  Recommended best 
                        practice is to use values as defined in
                        RFC 1766, typically 2-letter language
                        codes such as "FR" (French), "EN" (English),
                        and "DE" (German).  These values are NOT
                        case sensitive, so "EN" = "en". The values
                        may include hyphenated differentiations such 
                        as "EN-AU" (Australian English) and "EN-US"
                        (United States English).
                        Processing and Conversion Note: All other
                        xml:lang attributes within the article
                        inherit the value set on <article> unless
                        explicitly set themselves with their own
                        "xml:lang" attribute.                      
             xmlns      Set up the pseudo-attributes for the
                        namespaces for any namespaces used in this
                        DTD.  XLink and MathML are set up in the
                        MathML modules. These xmlns are called
                        here because certain older tools will not
                        work properly with namespaces unless they
                        are declared on the top level element.
                        The PEs are defined in the MathML modules. -->
<!ATTLIST  article
             %article-atts;                                          >

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<!--                    FRONT MATTER ELEMENTS                      -->
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<!--                    FRONT MATTER MODEL                         -->
<!ENTITY % front-model  "(article-meta)"                             > 

<!--                    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 
                        In some journal DTDs this is called the
                        header information, and it includes metadata
                        concerning the journal <journal-meta> and 
                        metadata concerning the issue of the journal 
                        and the individual article <article-meta>. -->
<!ELEMENT  front        %front-model;                                > 

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<!--                    BODY ELEMENTS                              -->
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<!--                    BODY MODEL                                 -->
<!--                    Content model for the Body (main textual
                        content) of a journal article.             -->
<!ENTITY % body-model   "((%para-level;)*, (%sec-level;)*)"          > 

<!--                    BODY OF THE ARTICLE                        -->
<!--                    The main textual portion of the article that
                        conveys the content.                       -->
<!ELEMENT  body         %body-model;                                 >

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<!--                    BACK MATTER ELEMENTS                       -->
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<!--                    BACK MATTER MODEL                          -->
<!--                    Content model for the Back Matter (ancillary
                        material such as appendices) of a journal
                        article.                                   -->
<!ENTITY % back-model   "(ack?, glossary?,ref-list*, app-group?)"    >

<!--                    BACK MATTER                                -->
<!--                    Ancillary or supporting material not included
                        as part of the main textual content of a 
                        journal article, for example appendices and
                        acknowledgments.                           -->
<!ELEMENT  back         %back-model;                                 >

<!-- ================== End Article Authoring DTD ================ -->