tax-treatment-NS0.dtd

<!-- $Id: tax-treatment-NS0.dtd 176 2011-06-06 19:44:41Z tcatapano $ -->
<!-- ============================================================= -->
<!-- ============================================================= 
This DTD is a modification of the orignal TaxPub DTD extension to the 
NLM Journal Publishing DTD version 3.0 created in September 2008.

This is version 0.5 and should be considered a beta version. 

This version was created on June 6, 2011. 

Donat Agosti, Terry Catapano, Lyubomir Penev, Bob Morris, Scott Federhen,
Laura Kelly, Jeff Beck.

-->

<!-- ============================================================= -->
<!--                    PUBLIC DOCUMENT TYPE DEFINITION            -->
<!--                        TYPICAL INVOCATION                     -->
<!--
"-//TaxPub//DTD Taxonomic Treatment Publishing DTD v0.5 20110606//EN"
     Delivered as file "tax-treatment0.dtd"                     -->
<!-- ============================================================= -->

 
 
<!-- ============================================================= -->
<!--                    MODULES OF MODULES INVOKED                 -->
<!-- ============================================================= -->


<!--                    MODULE TO NAME DTD-SPECIFIC MODULES        -->
<!--                    Names all DTD-specific external modules    -->
<!ENTITY % taxpubcustom-modules.ent 
                        PUBLIC  
"//TaxPub//DTD Taxonomic Treatment DTD-Specific Modules v0.5 20110606//EN"
"taxpubcustom-modules-NS0.ent"                                      >
%taxpubcustom-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; or the DTD-specific class,
                        mix, or model over-ride modules. Those are
                        declared in the DTD-specific module of modules.
                           Since this module declares but does not
                        invoke modules, this DTD 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 Archiving and Interchange DTD Suite Module of Modules v3.0 20080202//EN"
"modules3.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 Publishing
                        DTD that will over-ride classes in the Suite.
                        (Defined in %journalpubcustom-modules.ent;)-->
%taxpubcustom-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 %journalpubcustom-modules.ent;)-->
%taxpubcustom-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 %journalpubcustom-modules.ent;)-->
%taxpubcustom-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)     -->
<!-- ============================================================= -->


<!--                    TAXONOMIC TREATMENT ELEMENTS                  -->
%taxpubcustom-elements.ent;



<!--                    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; 


<!--                    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 '3.0'" >



<!--                    ARTICLE ATTRIBUTES                         -->
<!--                    Attributes for the top-level element
                        <article>                                  -->
<!ENTITY % article-atts
            "article-type   
                        CDATA                              #IMPLIED
             %dtd-version;                              
             xml:lang   NMTOKEN                            'en'     
             %XLINK.xmlns.attrib;
             %MATHML.xmlns.attrib;
             %Schema.xmlns.attrib;
                         xmlns:tp 		CDATA                            #FIXED
                                     'http://www.plazi.org/taxpub'	         "                                  >


<!--                    SUB-ARTICLE ATTRIBUTES                     -->
<!--                    Attributes for the <sub-article> element   -->
<!ENTITY % sub-article-atts
            "article-type   
                        CDATA                              #IMPLIED
             id         ID                                 #IMPLIED  
             xml:lang   NMTOKEN                            'en'"     >


<!--                    RESPONSE ATTRIBUTES                        -->
<!--                    Attributes for the <response> element      -->
<!ENTITY % response-atts
            "response-type   
                        CDATA                              #IMPLIED
             id         ID                                 #IMPLIED  
             xml:lang   NMTOKEN                            'en'"     >
                                                               

<!-- ============================================================= -->
<!--                    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://dtd.nlm.nih.gov/publishing/tag-library/3.0/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, 
                          (%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://dtd.nlm.nih.gov/publishing/tag-library/3.0/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://dtd.nlm.nih.gov/publishing/tag-library/3.0/index.html?elem=body
                                                                   -->
<!ELEMENT  body         %body-model;                                 >


<!-- ============================================================= -->
<!--                    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://dtd.nlm.nih.gov/publishing/tag-library/3.0/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 sub-article have their own metadata.
                        Details at: 
                        http://dtd.nlm.nih.gov/publishing/tag-library/3.0/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,
                        a reduced metadata set for use in 
                        sub-articles and responses                 -->
<!ENTITY % front-stub-model  
                        "(article-id*, article-categories?, 
                         title-group?, (contrib-group | aff)*, 
                         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://dtd.nlm.nih.gov/publishing/tag-library/3.0/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://dtd.nlm.nih.gov/publishing/tag-library/3.0/index.html?elem=response
                                                                   -->
<!ELEMENT  response     %article-short-model;                        >
<!ATTLIST  response
             %response-atts;                                         >


<!-- ================== End Journal Publishing DTD =============== -->