<!-- ============================================================= -->
<!-- MODULE: NCBI Book Content and Attribute Module -->
<!-- VERSION: 2.3 -->
<!-- DATE: February 2007 -->
<!-- -->
<!-- ============================================================= -->
<!-- ============================================================= -->
<!-- PUBLIC DOCUMENT TYPE DEFINITION -->
<!-- TYPICAL INVOCATION -->
<!--
"-//NLM//DTD NCBI Book DTD Content and Attribute Over-ride Module v2.3 20070202//EN"
Delivered as file "bookcustom-models.ent" -->
<!-- ============================================================= -->
<!-- ============================================================= -->
<!-- SYSTEM: NCBI Book 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: -->
<!-- October 2004 -->
<!-- -->
<!-- CREATED BY: Bart Trawick (NCBI) -->
<!-- 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: -->
<!-- archive-dtd@ncbi.nlm.nih.gov -->
<!-- ============================================================= -->
<!-- ============================================================= -->
<!-- DTD VERSION/CHANGE HISTORY -->
<!-- ============================================================= -->
<!--
Version Reason/Occasion (who) vx.x (yyyy-mm-dd)
=============================================================
Version 2.3 (DAL/BTU) v2.3 (2007-02-02)
Enhancement Release (2.3) following the Working Group meetings
of Oct-Nov/2006-Jan/2007. No backward-incompatible changes.
Archiving loosened even more. New structures for all the DTDs.
16. BOOK META MODEL - Moved to this module from the Book DTD
module because the Collection DTD also needed to use it.
15. TITLE ATTRIBUTES
a) Removed the attribute list for <title>. Now that the Suite
also have an -%title-atts; it can be redefined in this module
without being declared in this module.
b) Added "content-type" attribute.
c) Added "id attribute
14. CONTENT TYPE - The attribute "content-type" added to the
following elements to preserve/add semantic distinctions:
- graphic (through graphic-atts)
- issn (through issn-atts)\
- title (through title-atts)
13. GRAPHIC ATTS - In the parameter entity -%graphic-atts;
made the following changes:
a) Unfixed the "mimetype" attribute from
mimetype CDATA #FIXED 'image'
into this:
mimetype CDATA #IMPLIED
b) Made the "mime-subtype" attribute into a CDATA rather
than a list of values
c) Added "content-type" attribute to preserve or add semantic
distinctions.
12. SECTION METADATA - Deleted the parameter entity
-%sec-meta-model because the default Suite model was
changed to be the same, and Book need no longer redefine
section metadata.
11. REF-MODEL - Changed content (but not intent or value) by
replacing <citation> with -%citation.class; and
<note> with -%note.class;
10. NLM CITATION - Added <nlm-citation> as an alternative to
unstructured <citation>s by adding <nlm-citation>
to %citation.class;. This changed the models for:
- <ref>, which uses -%citation.class; inside %ref-model;
9. Updated public identifier to "v2.3 20070202//EN"
=============================================================
Version 2.2 (DAL/BTU) v2.2 (2006-10-13)
Updated base Suite to latest version (2.2) Other minor
modifications for processing.
8. Added "tax" and "pubchem" as suggested values for
"ext-link-type" attribute
7. Added %sec-meta-model; to over-ride the PE in %common.ent;
for book section metadata to include <kwd-group> and
<permissions>
6. Updated public identifier to "v2.3 20070202".
=============================================================
Version 2.1 (DAL/BTU) v2.1 (2005-06-30)
Changed to MathML 2.0 and MathML 2.0 Character Sets
Added new material requested by the online list
5. DATE-TYPEs - Deleted the parameter entity that named these,
since the "date-type" attribute has been set to CDATA. The
suggested values are retained as part of the documentation.
4. REFERENCE-TYPES - Book needed the same new reference types
which Historical already had, so moved the ref-type
over-ride to this module from the Historical override
module. Book will uses these. The Historical DTD first
calls bookcustom-models then historical-models, so it will
use them as well.
3. TRANS-SUBTITLE - Added optional <trans-subtitle> element to
to <book-meta> model through -%book-title-group-model;
also added to %title-group; for book parts.
2. Updated public identifier to "v2.3 20070202"
=============================================================
Version 2.0 (DAL/BTU/TRG) v2.0 (2005-01-25)
1. Comments for this module were cleaned up as part of the delivery
of the NCBI Historical DTD. Since only comments were changed,
this was not even considered to be a dot release and the
formal public identifier remained unchanged. -->
<!-- ============================================================= -->
<!-- INLINE MIXES TO OVER-RIDE CONTENT MODELS -->
<!-- (ELEMENTS TO BE ADDED TO #PCDATA IN MODELS)-->
<!-- ============================================================= -->
<!-- STRUCTURAL TITLE ELEMENTS -->
<!-- The elements that can be included along with
data characters inside the content model of
the <title> element
Design Note: All inline mixes begin with an
OR bar, but since %simple-phrase; is an
inline mix, the OR bar is already there. -->
<!ENTITY % struct-title-elements
"%simple-phrase; | %break.class; |
%citation.class;" >
<!-- TITLE ELEMENTS -->
<!-- Elements for use in all the title elements
such as <title>, <subtitle>, <trans-title>,
etc.
Design Note: All inline mixes begin with an
OR bar, but since %simple-phrase; is an
inline mix, the OR bar is already there. -->
<!ENTITY % title-elements
"%simple-phrase; | %break.class; |
%citation.class;" >
<!-- ============================================================= -->
<!-- COMPLETE CONTENT MODEL OVER-RIDES -->
<!-- ============================================================= -->
<!-- BOOK METADATA OVER-RIDE -->
<!-- Content model for the Book Metadata
<book-meta> element -->
<!ENTITY % book-meta-model
"(book-id+, book-title-group,
volume?, volume-id*, edition?, series*,
(contrib-group | aff | author-notes)*,
publisher*, isbn*,
pub-date*, history?, copyright-statement?,
copyright-year?, permissions?,
self-uri*, alternate-form*,
abstract*, trans-abstract*, kwd-group*,
counts?,
(%address-link.class; | %custom-meta.class; |
%front-back.class;)* )" >
<!-- BODY MODEL OVER-RIDE -->
<!-- Defines the body of both a <book> and a
<book-part> such as a chapter -->
<!ENTITY % body-model "( (%para-level;)*, (%sec-level;)*,
(%book-part-level;)*, back? )" >
<!-- REFERENCE ITEM MODEL OVER-RIDE -->
<!-- Content model for the <ref> element -->
<!ENTITY % ref-model "(label?,
(%citation.class; | %note.class;)+ )" >
<!-- TITLE GROUP MODEL OVER-RIDE -->
<!-- Content model for the <title-group> element.
In the DTD suite, this contains the element
<article-title> and is used to hold all
the titles. In this DTD, it is used for
document parts, which contain titles, just
not <article-title>. -->
<!ENTITY % title-group-model
"(title, subtitle*,
(trans-title, trans-subtitle?)*,
alt-title*, fn-group?)" >
<!-- ============================================================= -->
<!-- DUPLICATE ATT-LISTS USED IN THE OVER-RIDES -->
<!-- BELOW, THUS REPEATED HERE -->
<!-- ============================================================= -->
<!-- DATE ATTRIBUTES FOR HISTORY -->
<!-- The <history> element contains one or more
<date> elements that record events in the
life of a publication. These are the
attributes for the <date> elements.
date-type Attribute should only be used if the date
is one of the known types; otherwise omit
the attribute.
This is a data content attribute, suggested
values include:
accepted - Date manuscript was
accepted
created - original creation date of
the work
received - Date manuscript received
rev-request - Date revisions were
requested or manuscript
was returned
rev-recd - Date revised manuscript
was received
updated - most recent modification
date for the work -->
<!ENTITY % date-atts
"date-type CDATA #IMPLIED" >
<!-- DISPLAY ATTRIBUTES OPTIONAL ID -->
<!-- position Must this display object (figure, boxed text,
etc.) be anchored in its exact location
within the text or may it float, for example
to the top of the next page, next column, or
within a separate window? Values are:
anchor Object must remain in place
float Object is not anchored and
may be moved to a new column,
a new window, etc.
margin In print, item should be placed
in the margin or gutter.
Online the item should
remain closely associated
with the text. -->
<!ENTITY % display-atts
"position (anchor | float | margin) 'float'" >
<!-- ISSN ATTRIBUTES -->
<!-- Attribute list for <issn> -->
<!-- pub-type Used to record the type of publication, for
example a print-only publication versus
an electronic-only publication, in any of
several life stages.
Suggested values include:
epub - Electronic publication
ppub - Print publication
epub-ppub - Published in both print and
electronic form
epreprint - Electronic preprint
dissemination
ppreprint - Print preprint dissemination
ecorrected - Corrected in electronic
pcorrected - Corrected in print
eretracted - Retracted in electronic
pretracted - Retracted in print
primary Is this the current or primary ISSN? (yes or
no)
Typically used only in the negation
content-type
"content-type" attribute provides a way to
preserve or add semantic distinctions, for
multiple conference dates -->
<!ENTITY % issn-atts
"pub-type CDATA #IMPLIED
primary (yes | no) #IMPLIED
content-type
CDATA #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" >
<!-- ============================================================= -->
<!-- ATTRIBUTE LIST OVER-RIDES -->
<!-- ============================================================= -->
<!-- EXTERNAL LINK ATTRIBUTE LIST -->
<!-- Replacing the attribute list for the element
<ext-link>. The link type is required and has
a longer list of values than in the base DTD.
two new attributes, "taxonomic-id" and
"qualifier" have been added. Previous Book DTD
attribute "access" as been replaced by
"xlink:href" -->
<!-- id Unique identifier so the element may be
referenced
ext-link-type
Type of external link. Use this attribute
if the type of external link is one of the
ones below or another named type.
Suggested values include:
aoi Astronomical Object Identifier
cdd Conserved Domain Database
doi Digital Object Identifier
ec Enzyme nomenclature - see
http://www.chem.qmw.ac.uk/iubmb/enzyme/
email An email message
entrez-gene Entrez Gene
ftp File transfer protocol
gen GenBank identifier
genpept Translated Protein-encoding
sequence Database
highwire HighWire press intrajournal
hmh Human-Mouse Homology Maps
mgi Mouse Genome Informatics
omim Online Mendelian Inheritance
in Man
pdb Protein data bank. See
http://www.rcsb.org/pdb/
pgr Plant gene register. See
http://www.tarweed.com/pgr/
pir Protein Information Resource
see http://pir.georgetown.edu
pirdb Protein Information Resource
see http://pir.georgetown.edu
pmc PubMed Central identifier.
Used to link between articles
in PubMed Central. Access is
PMID
pmid PubMed identifier
pubchem PubChem. Repository of information on
the biological activities of small
molecules and their chemical structures.
See http://pubchem.ncbi.nlm.nih.gov/
sgd Saacharomyces Genome Database
snp Single Nucleotide Polymorphism
sprot Swiss-Prot. See
http://www.ebi.ac.uk/swissprot/
tax Taxonomy database. See
http://http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Taxonomy
uri Website or web service
wbase Wormbase
taxonomic-id
Taxonomic identifier, such as a genus name
qualifier Additional qualifier for the taxonomic
identification, for example, a locus, cell,
or cell-group
xlink:href Provides an address or identifier of the
object to which the link points, for
example a URI, a filename, or a database
-->
<!ENTITY % ext-link-atts
"id ID #IMPLIED
ext-link-type
CDATA #REQUIRED
taxonomic-id
CDATA #IMPLIED
qualifier CDATA #IMPLIED
%might-link-atts;" >
<!-- GRAPHIC ATTRIBUTES -->
<!-- Attributes for the element <graphic>. This
list adds only one attribute to the base list
"graphic-type", but the entire list is
repeated here because some XML processors
do not handle multiple ATTLISTs as the XML
specification says they should. This is
safer, but puts a burden on the maintainer.
graphic-type
Display or formatting type (style) for the
graphic. This is an artifact, a hold-over
from previous NLM DTDs, used so as not to
disturb existing processing.
Values may be any text, but may include
any of the following:
offset Used for display formulae, to
to be set off from text. Since
all display formula are so
offset in the new DTDs, this
is effectively the default
intext Used to display graphics in the
text. Such elements should be
tagged as <inline-graphic>
inlinefig
Used to display graphics as inline
(not called out) figure. Such
elements should be tagged as
<inline-graphic> -->
<!ENTITY % graphic-atts
"graphic-type
CDATA #IMPLIED
alternate-form-of
IDREF #IMPLIED
alt-version
(yes|no) 'no'
id ID #IMPLIED
content-type
CDATA #IMPLIED
mime-subtype
CDATA #IMPLIED
mimetype CDATA #IMPLIED
%display-atts;
%link-atts;" >
<!-- ISBN ATTRIBUTE LIST -->
<!-- Adding attributes to the <isbn> element,
which has no ATTLIST in the DTD Suite
pub-type Used to record the type of publication, for
example a print-only publication versus
an electronic-only publication, in any of
several life stages.
Suggested values include:
epub - Electronic publication
ppub - Print publication
epub-ppub - Published in both print and
electronic form
epreprint - Electronic preprint
dissemination
ppreprint - Print preprint dissemination
ecorrected - Corrected in electronic
pcorrected - Corrected in print
eretracted - Retracted in electronic
pretracted - Retracted in print
primary Is this the current or primary ISBN?
Typically used only in the negation
no The number is not the primary number.
yes The number is the primary number
content-type
"content-type" attribute provides a way to
preserve or add semantic distinctions -->
<!ENTITY % isbn-atts
"%issn-atts;" >
<!-- DEFAULT TYPE OF CROSS(X)-REFERENCE -->
<!-- Used to say to what the reference is pointing.
May be used for type-specific processing or
validation. Values are, for example:
Affiliation "aff", Figure "fig", and
Bibliographic ref (to a Citation <citation> or
to a Reference Item <ref>) "bibr"
Added "glossary" and "bookpart" -->
<!ENTITY % ref-types "aff | app | author-notes | bibr |
book-part | boxed-text | chem | contrib |
corresp | disp-formula | fig | fn |
glossary | kwd | list | plate | scheme |
sec | statement | supplementary-material |
table | table-fn |
other" >
<!-- SECTION ATTRIBUTES -->
<!-- Attribute list for Section element. This
list adds only one attribute to the base list
"indexed", but the entire list is
repeated here because some XML processors
do not handle multiple ATTLISTs as the XML
specification says they should. This is
safer, but puts a burden on the maintainer.
The "sec-type" attribute can be used, for\
example, to mark a section as the
equivalent of the old link group element.
"sec-type='multi-link'" indicates a section
used to contain groups of links, as the
old link group used to do in the previous
DTD. -->
<!ENTITY % sec-atts
"id ID #IMPLIED
xml:lang NMTOKEN #IMPLIED
sec-type CDATA #IMPLIED
disp-level CDATA #IMPLIED
indexed (true | false) 'true'" >
<!-- TITLE ATTRIBUTE LIST -->
<!-- Adding attributes to the <title> element. -->
<!-- id Unique identifier so the element may be
referenced
content-type
"content-type" attribute provides a way to
preserve or add semantic distinctions.
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 differentiators such
as "EN-AU" (Australian English) and "EN-US"
(United States English). -->
<!ENTITY % title-atts
"id ID #IMPLIED
content-type
CDATA #IMPLIED
xml:lang NMTOKEN #IMPLIED" >
<!-- ================== End NCBI BOOK Content/Attribute Over-ride= -->