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Update pmc stylechecker to 5.39 and jats 1.2 and 1.3 #179

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Update pmc stylechecker to 5.39 and jats 1.2 and 1.3 #179

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58b1ee4
update pmc style guidelines
c-cooperjones Jan 27, 2024
1af883c
update jats
c-cooperjones Jan 28, 2024
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39 changes: 34 additions & 5 deletions schema/Makefile
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Expand Up @@ -15,7 +15,7 @@ $(DOWNLOADS):

# JATS DTD

jats: | jats/publishing/1.0 jats/publishing/1.1
jats: | jats/publishing/1.0 jats/publishing/1.1 jats/publishing/1.2 jats/publishing/1.3

# JATS 1.0

Expand Down Expand Up @@ -47,6 +47,35 @@ $(DOWNLOADS)/JATS-Publishing-1-1-MathML2-DTD.zip: | $(DOWNLOADS)
$(DOWNLOADS)/JATS-Publishing-1-1-MathML2-XSD.zip: | $(DOWNLOADS)
wget -c -P $(DOWNLOADS) ftp://ftp.ncbi.nih.gov/pub/jats/publishing/1.1/xsd/JATS-Publishing-1-1-MathML2-XSD.zip

jats/publishing/1.2: | $(DOWNLOADS)/JATS-Publishing-1-2-MathML3-DTD.zip $(DOWNLOADS)/JATS-Publishing-1-2-MathML3-XSD.zip
mkdir -p jats/publishing/1.2
unzip $(DOWNLOADS)/JATS-Publishing-1-2-MathML3-DTD.zip -d $(DOWNLOADS)
mv $(DOWNLOADS)/JATS-Publishing-1-2-MathML3-DTD/ jats/publishing/1.2

unzip $(DOWNLOADS)/JATS-Publishing-1-2-MathML3-XSD.zip -d $(DOWNLOADS)
mv $(DOWNLOADS)/JATS-Publishing-1-2-MathML3-XSD jats/publishing/1.2/xsd


$(DOWNLOADS)/JATS-Publishing-1-2-MathML3-DTD.zip: | $(DOWNLOADS)
wget -c -P $(DOWNLOADS) ftp://ftp.ncbi.nih.gov/pub/jats/publishing/1.2/JATS-Publishing-1-2-MathML3-DTD.zip

$(DOWNLOADS)/JATS-Publishing-1-2-MathML3-XSD.zip: | $(DOWNLOADS)
wget -c -P $(DOWNLOADS) ftp://ftp.ncbi.nih.gov/pub/jats/publishing/1.2/xsd/JATS-Publishing-1-2-MathML3-XSD.zip

jats/publishing/1.3: | $(DOWNLOADS)/JATS-Publishing-1-3-MathML3-DTD.zip $(DOWNLOADS)/JATS-Publishing-1-3-MathML3-XSD.zip
mkdir -p jats/publishing/1.3
unzip $(DOWNLOADS)/JATS-Publishing-1-3-MathML3-DTD.zip -d $(DOWNLOADS)
mv $(DOWNLOADS)/JATS-Publishing-1-3-MathML3-DTD/ jats/publishing/1.3

unzip $(DOWNLOADS)/JATS-Publishing-1-3-MathML3-XSD.zip -d $(DOWNLOADS)
mv $(DOWNLOADS)/JATS-Publishing-1-3-MathML3-XSD jats/publishing/1.3/xsd

$(DOWNLOADS)/JATS-Publishing-1-3-MathML3-DTD.zip: | $(DOWNLOADS)
wget -c -P $(DOWNLOADS) ftp://ftp.ncbi.nih.gov/pub/jats/publishing/1.3/JATS-Publishing-1-3-MathML3-DTD.zip

$(DOWNLOADS)/JATS-Publishing-1-3-MathML3-XSD.zip: | $(DOWNLOADS)
wget -c -P $(DOWNLOADS) ftp://ftp.ncbi.nih.gov/pub/jats/publishing/1.3/xsd/JATS-Publishing-1-3-MathML3-XSD.zip

# CrossRef Schema, this is now being hosted on gitlab, the zip includes examples, which we don't copy
crossref: | crossref/schematron.xsl (DOWNLOADS)/schema-0.1.1.zip
mkdir -p crossref
Expand Down Expand Up @@ -142,12 +171,12 @@ doaj:

# NLM PMC Style Checker

nlm-stylechecker: | $(DOWNLOADS)/nlm-style-5.12.tar.gz
nlm-stylechecker: | $(DOWNLOADS)/nlm-style-5.39.tar.gz
mkdir -p nlm-stylechecker
tar xvz -C nlm-stylechecker -f $(DOWNLOADS)/nlm-style-5.12.tar.gz
tar xvz -C nlm-stylechecker -f $(DOWNLOADS)/nlm-style-5.39.tar.gz

$(DOWNLOADS)/nlm-style-5.12.tar.gz: | $(DOWNLOADS)
wget -c -P $(DOWNLOADS) http://www.ncbi.nlm.nih.gov/pmc/assets/nlm-style-5.12.tar.gz
$(DOWNLOADS)/nlm-style-5.39.tar.gz: | $(DOWNLOADS)
wget -c -P $(DOWNLOADS) https://www.ncbi.nlm.nih.gov/core/assets/pmc/files/nlm-style-5.39.tar.gz

# NLM DTDs
# http://www.ncbi.nlm.nih.gov/data_specs/dtd/
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2 changes: 2 additions & 0 deletions schema/catalog.xml
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<rewriteURI uriStartString="http://jats.nlm.nih.gov/" rewritePrefix="jats/"/>
<nextCatalog catalog="jats/publishing/1.0/catalog-test-jats-v1.xml"/>
<nextCatalog catalog="jats/publishing/1.1/catalog-jats-v1-1-no-base.xml"/>
<nextCatalog catalog="jats/publishing/1.2/catalog-jats-v1-2-no-base.xml"/>
<nextCatalog catalog="jats/publishing/1.3/catalog-jats-v1-3-no-base.xml"/>
</catalog>
323 changes: 323 additions & 0 deletions schema/jats/publishing/1.2/BITS-embedded-index2.ent
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587 changes: 587 additions & 0 deletions schema/jats/publishing/1.2/JATS-XHTMLtablesetup1.ent
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240 changes: 240 additions & 0 deletions schema/jats/publishing/1.2/JATS-ali-namespace1.ent
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@@ -0,0 +1,240 @@
<!-- ============================================================= -->
<!-- MODULE: ALI Namespace Module (NISO RP-22-2015) -->
<!-- NISO Access License and Indicators (ALI) -->
<!-- VERSION: ANSI/NISO JATS Version 1.2 (Z39.96-2019) -->
<!-- DATE: February 2019 -->
<!-- -->
<!-- ============================================================= -->

<!-- ============================================================= -->
<!-- PUBLIC DOCUMENT TYPE DEFINITION -->
<!-- TYPICAL INVOCATION -->
<!--
"-//NLM//DTD JATS ALI Namespace Module v1.2 20190208//EN"
Delivered as file "JATS-ali-namespace1.ent" -->
<!-- ============================================================= -->


<!-- ============================================================= -->
<!-- SYSTEM: JATS DTD Suite -->
<!-- -->
<!-- PURPOSE: Establish the prefix for the NISO Access and -->
<!-- Indicators elements (prefix "ali:"). -->
<!-- -->
<!-- TAG SET SPONSOR -->
<!-- National Center for Biotechnology -->
<!-- Information (NCBI) -->
<!-- National Library of Medicine (NLM) -->
<!-- -->
<!-- CREATED FOR: -->
<!-- This module was created for the JATS DTD Suite. -->
<!-- Digital archives and publishers may use the -->
<!-- DTD as is for markup of journal literature or -->
<!-- related material for archiving and transferring -->
<!-- such material between archives or create a -->
<!-- custom XML DTD from the Suite for -->
<!-- these purposes. -->
<!-- -->
<!-- This DTD is in the public domain. An organization -->
<!-- that wishes to create its own DTD from the suite -->
<!-- may do so without permission from NLM. -->
<!-- -->
<!-- The suite has been set up to be extended using a -->
<!-- new DTD file and a new DTD-specific customization -->
<!-- module to redefine the many Parameter Entities. -->
<!-- Do not modify the suite directly or redistribute -->
<!-- modified versions of the suite. -->
<!-- -->
<!-- In the interest of maintaining consistency and -->
<!-- clarity for potential users, NLM requests: -->
<!-- -->
<!-- 1. If you create a DTD from the JATS DTD Suite -->
<!-- and intend to stay compatible with the suite, -->
<!-- then please include the following statement -->
<!-- as a comment in all of your DTD modules: -->
<!-- "Created from, and fully compatible with, -->
<!-- the ANSI/NISO Z39.96 Journal Article Tag -->
<!-- Suite (JATS)." -->
<!-- -->
<!-- 2. If you alter one or more modules of the suite, -->
<!-- then please rename your version and all its -->
<!-- modules to avoid any confusion with the -->
<!-- original suite. Also, please include the -->
<!-- following statement as a comment in all your -->
<!-- DTD modules: -->
<!-- "Based in part on, but not fully compatible -->
<!-- with, the ANSI/NISO Z39.96 Journal Article -->
<!-- Tag Suite (JATS)." -->
<!-- -->
<!-- ORIGINAL CREATION DATE: -->
<!-- February 2015 -->
<!-- -->
<!-- CREATED BY: Mulberry Technologies, Inc. for the NISO Z39.96 -->
<!-- Working Group. Mulberry Technologies was -->
<!-- supported by National Center for Biotechnology -->
<!-- Information (NCBI), a center of the US National -->
<!-- Library of Medicine (NLM). -->
<!-- -->
<!-- The Journal Publishing DTD is built from the -->
<!-- Journal Archiving and Interchange DTD Suite. -->
<!-- -->
<!-- Suggestions for refinements and enhancements to -->
<!-- this DTD should be sent in email to: -->
<!-- [email protected] -->
<!-- ============================================================= -->


<!-- ============================================================= -->
<!-- DTD VERSION/CHANGE HISTORY -->
<!-- ============================================================= -->
<!--
Version Reason/Occasion (who) vx.x (yyyy-mm-dd)
==============================================================
JATS Version 1.2 (ANSI/NISO Z39.96-2019)
(DAL/BTU) v1.2 (2019-02-08)

NISO JATS is a continuing maintenance NISO Standard, which
requires voting by the both the NISO and ANSI membership
to be changed. This version of the NISO JATS was approved
by ANSI vote on Feb 08, 2019, so it supersedes all Committee
Drafts as well as the draft version JATS 1.2 2018 (the version
submitted for vote), becoming NISO JATS v1.2 20190208
(ANSI/NISO Z39.96-2019).

6. JATS "1.2" becomes "v1.2 20190208" (final ANSI vote date)
"ANSI/NISO Z39.96-2015" becomes "ANSI/NISO Z39.96-2019"

==============================================================
JATS Version 1.2 (ANSI/NISO Z39.96-2018)
and BITS 2.1 (v2.0 20180401)
(DAL/BTU) v1.2 (2018-11-30)

NISO JATS is a continuing maintenance NISO Standard, which
requires voting by the both the NISO and ANSI membership
to be changed. This version of the NISO JATS was approved
by ANSI and NISO vote, so it supersedes all Committee Drafts
and becoming NISO JATS 1.2 (ANSI/NISO Z39.96-2018).

5. BITS "2.1" and "v2.0 20180401" remains unchanged.
JATS "1.2d2" and "v1.2d2 20180401" became
JATS "1.2" and "v1.2 20181130"

=============================================================
BITS Version 2.1 (DAL/BTU) v2.1 (2018-04-01)
JATS Version 1.2d2 (DAL/BTU) v1.2d2 (2018-04-01)

JATS is a continuing maintenance NISO Standard, which
requires voting by the ANSI and NISO memberships to be changed.
BITS is under continuous maintenance, and is modified at the
discretion of the working group.

This draft DTD represents an interim version of the
non-normative JATS DTD Suite, as an indication to JATS users
the decisions that have been made by the JATS Standing
Committee. This draft has not yet been given public review
or voting. The formal public identifiers were changed in the
modules and the catalogs.

4. BITS "2.0" and "v2.0 20151225" became
BITS "2.1" and "v2.1 20180401".

JATS "1.2d1" and "v1.2d1 20171231" became
JATS "1.2d2" and "v1.2d2 20180401".

No module names were changed.

=============================================================
JATS Version 1.2d2 (ANSI/NISO Z39.96-2015)
(DAL/BTU) v1.2d2 (2017-12-31)

NISO JATS is a continuing maintenance NISO Standard, which
requires voting by the ANSI and NISO memberships to be changed.

This draft DTD represents an interim version of the
non-normative JATS DTD Suite, as an indication to JATS users
the decisions that have been made by the JATS Standing
Committee. This draft has not yet been given public review
or voting. The formal public identifiers were changed in the
modules and the catalogs.

3. JATS "1.2d1" and "v1.2d1 20170631" became
JATS "1.2d2" and "v1.2d2 20171231".

=============================================================
JATS Version 1.2d1 (DAL/BTU) v1.2d1 (2017-06-31)

NISO JATS is a continuing maintenance NISO Standard, which
requires voting by the ANSI and NISO memberships to be changed.

This draft DTD represents an interim version of the
non-normative JATS DTD Suite, as an indication to JATS users
the decisions that have been made by the JATS Standing
Committee. This draft has not yet been given public review
or voting. The formal public identifiers were changed in the
modules and the catalogs.

2. JATS became version "1.2d1" and "v1.2d1 20170631"

=============================================================
JATS Version 1.1 (DAL/BTU) v1.1 (2015-12-15)

JATS is a continuing maintenance NISO Standard, which
requires voting by the ANSI and NISO memberships to be changed.
JATS 1.1 was approved in late 2015, so the formal public
identifiers were changed in the modules and the catalogs.
No model or attribute changes were made at this time.

1. JATS became version "1.1" and "v1.1 20151215"

=============================================================

Details concerning ANSI/NISO Z39.96-2015 JATS-based DTDs, XSDs,
RNGs and supporting documentation are available at
http://jats.nlm.nih.gov/1.1/
-->
<!-- ============================================================= -->
<!-- ALI NAMESPACE SETUP -->
<!-- ============================================================= -->


<!-- NAME ALI NAMESPACE BASE URI -->
<!-- Set the ALI namespace URI,as named in
NISO RP-22-2015 -->
<!ENTITY % ali.xmlns
"http://www.niso.org/schemas/ali/1.0/" >


<!-- NAME ALI NAMESPACE PREFIX -->
<!-- Set the namespace prefix for the ALI
elements to the JATS-named prefix "ali".
Implementor's Note: This parameter entity
should always be set, even if you need to turn
off the namespace prefix. -->
<!ENTITY % ali.prefix "ali" >


<!-- NAME OASIS NAMESPACE PREFIX -->
<!-- Construct the ALI namespace prefix to be
used in the xmlns pseudo-attribute from:
- the word "xmlns",
- a colon, and
- the prefix just defined in %ali.prefix;
-->
<!ENTITY % ali.xmlns.attrname
"xmlns:%ali.prefix;" >


<!-- DEFAULT ALI NAMESPACE -->
<!-- The default namespace to be used when
calling in the ALI elements. This is set on
the article level as well as on the ALI
elements themselves.
Implementor's Note: The parameter entity is
constructed from the parameter entities set
above. -->
<!ENTITY % ali.xmlns.attrib
"%ali.xmlns.attrname;
CDATA #FIXED '%ali.xmlns;'" >


<!-- ================== End ALI Namespace Setup ================= -->
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