From 9ea066c5de4e8d64d16f2774bed78e0b69777b8a Mon Sep 17 00:00:00 2001
From: mdehoon <mdehoon@anx136.genome.gsc.riken.jp>
Date: Fri, 17 Sep 2010 21:25:08 +0900
Subject: [PATCH] Adding two DTD files for the NCBI E-Utilities

---
 .../DTDs/nlmmedlinecitationset_110101.dtd     | 197 ++++++++++++++++++
 Bio/Entrez/DTDs/pubmed_110101.dtd             |  79 +++++++
 2 files changed, 276 insertions(+)
 create mode 100644 Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd
 create mode 100644 Bio/Entrez/DTDs/pubmed_110101.dtd

diff --git a/Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd b/Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd
new file mode 100644
index 00000000000..c520c6d600c
--- /dev/null
+++ b/Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd
@@ -0,0 +1,197 @@
+<!-- NLM MedlineCitationSet DTD
+
+     This is the DTD which NLM has written for Internal and External Use.
+     January 1, 2011
+  
+  **THIS IS THE FORTHCOMING DTD FOR 2011 NOT CURRENTLY IN USE.  
+    SEE http://www.nlm.nih.gov/databases/dtd/nlmmedlinecitationset_100101.dtd
+    FOR THE NLMMedlineCitationSet DTD DATED JANUARY 1, 2010 CURRENTLY IN USE.**  
+     
+     
+     NOTE:  The use of "Medline" in a DTD or element name does not mean the record 
+     represents a citation from a Medline-selected journal.  When the NLM DTDs and 
+     XML elements were first created, MEDLINE records were the only data exported. 
+     Now NLM exports citations other than MEDLINE records using these tools. To 
+     minimize unnecessary disruption to users of the data and tools, NLM has
+     retained the original DTD and element names (e.g., NLMMedlineCitationSet, 
+     MedlineTA, MedlineJournalInfo)).  
+
+     NOTE:  StartPage and EndPage in Pagination element and NameID in Author
+     and Investigator elements are not currently used; are reserved for future use.  
+                
+
+        * = 0 or more occurrences (optional element, repeatable)
+        ? = 0 or 1 occurrences (optional element, at most 1)
+        + = 1 or more occurrences (required element, repeatable)
+        | = choice, one or the other but not both
+        no symbol = required element
+-->
+<!-- ================================================================= -->
+<!--             Revision Notes Section
+
+  The following changes were made:
+  
+        a. Changed nlmmedlinecitationset_100101.dtd to
+           nlmmedlinecitationset_110101.dtd. 
+        b. Added Label and NlmCategory attributes to AbstractText. 
+        c. Added element SupplMeshList to MedlineCitation.
+        d. Added element SupplMeshName with Type attribute to SupplMeshList.
+        e. Added Type attribute to DescriptorName.
+        f. Added VersionID and VersionDate attributes to MedlineCitation.
+        g. Added Version attribute to PMID.
+        h. Repositioned NameID element in Author.
+        i. Changed NameID Source attribute to unspecified values.
+        j. Added new Owner attribute valid value NLM-AUTO.
+
+See http://www.nlm.nih.gov/databases/dtd/history_dtd_nlmmedline.html for historic Revision Notes for previous versions of NLMMedlineCitationSet DTD.
+-->
+<!-- ====================================================================== -->
+<!ENTITY % format	" b | i | sup | sub | u " >
+<!ENTITY % text             "(#PCDATA | %format;)*" >
+<!ELEMENT b		%text; > <!-- bold -->
+<!ELEMENT i		%text; > <!-- italic -->
+<!ELEMENT sup	%text; > <!-- superscript -->
+<!ELEMENT sub	%text; > <!-- subscript -->
+<!ELEMENT u		%text; > <!-- underline -->
+<!-- ================================================================= -->
+<!ELEMENT	MedlineCitationSet (MedlineCitation*, DeleteCitation?)>
+<!ELEMENT	MedlineCitation (PMID, DateCreated, DateCompleted?, DateRevised?,
+                Article, MedlineJournalInfo, ChemicalList?,SupplMeshList?,
+                CitationSubset*, CommentsCorrectionsList?, GeneSymbolList?,
+                MeshHeadingList?,NumberOfReferences?, PersonalNameSubjectList?,
+                OtherID*, OtherAbstract*, KeywordList*, SpaceFlightMission*, 
+                InvestigatorList?, GeneralNote*)>
+<!ATTLIST	MedlineCitation 
+                Owner  (NLM | NASA | PIP | KIE | HSR | HMD | NOTNLM) "NLM"
+		Status (Completed | In-Process | PubMed-not-MEDLINE | 
+                        In-Data-Review | Publisher | MEDLINE | 
+                        OLDMEDLINE) #REQUIRED
+                VersionID CDATA #IMPLIED
+                VersionDate CDATA #IMPLIED>
+<!ELEMENT	Abstract (AbstractText+,CopyrightInformation?)>
+<!ELEMENT	AbstractText %text;>
+<!ATTLIST       AbstractText
+                Label CDATA #IMPLIED
+                NlmCategory (UNLABELLED | BACKGROUND | OBJECTIVE | METHODS |
+                             RESULTS | CONCLUSIONS) #IMPLIED>
+<!ELEMENT	AccessionNumber (#PCDATA)>
+<!ELEMENT	AccessionNumberList (AccessionNumber+)>
+<!ELEMENT	Acronym (#PCDATA)>
+<!ELEMENT	Affiliation %text;>
+<!ELEMENT	Agency (#PCDATA)>
+<!ELEMENT	Article (Journal,ArticleTitle,((Pagination, ELocationID*) | 
+                        ELocationID+),Abstract?, Affiliation?, AuthorList?, 
+                        Language+, DataBankList?, GrantList?,PublicationTypeList, 
+                        VernacularTitle?, ArticleDate*)>
+<!ATTLIST	Article 
+                PubModel (Print | Print-Electronic | Electronic | 
+                          Electronic-Print) #REQUIRED>
+<!ELEMENT	ArticleDate (Year,Month,Day)>
+<!ATTLIST	ArticleDate DateType CDATA  #FIXED "Electronic">
+<!ELEMENT	ArticleTitle %text;>
+<!ELEMENT	Author (((LastName, ForeName?, Initials?, Suffix?) | 
+                         CollectiveName),NameID*)>
+<!ATTLIST	Author ValidYN (Y | N) "Y">
+<!ELEMENT	AuthorList (Author+)>
+<!ATTLIST	AuthorList CompleteYN (Y | N) "Y">
+<!ELEMENT	Chemical (RegistryNumber,NameOfSubstance)>
+<!ELEMENT	ChemicalList (Chemical+)>
+<!ELEMENT	CitationSubset (#PCDATA)>
+<!ELEMENT	CollectiveName %text;>
+<!ELEMENT	CommentsCorrections (RefSource,PMID?,Note?)>
+<!ATTLIST   CommentsCorrections 
+                RefType (CommentOn | CommentIn | ErratumIn | ErratumFor | 
+                PartialRetractionIn | PartialRetractionOf | RepublishedFrom |
+                RepublishedIn | RetractionOf | RetractionIn | UpdateIn |
+                UpdateOf | SummaryForPatientsIn | OriginalReportIn |
+                ReprintOf | ReprintIn | Cites) #REQUIRED >
+<!ELEMENT	CommentsCorrectionsList (CommentsCorrections+)>
+<!ELEMENT	CopyrightInformation (#PCDATA)>
+<!ELEMENT	Country (#PCDATA)>
+<!ELEMENT	DataBank (DataBankName, AccessionNumberList?)>
+<!ELEMENT	DataBankList (DataBank+)>
+<!ATTLIST	DataBankList CompleteYN (Y | N) "Y">
+<!ELEMENT	DataBankName (#PCDATA)>
+<!ELEMENT	DateCompleted (Year,Month,Day)>
+<!ELEMENT	DateCreated (Year,Month,Day)>
+<!ELEMENT	DateRevised (Year,Month,Day)>
+<!ELEMENT	Day (#PCDATA)>
+<!ELEMENT	DescriptorName (#PCDATA)>
+<!ATTLIST	DescriptorName 
+                MajorTopicYN (Y | N) "N"
+                Type (Geographic) #IMPLIED>
+<!ELEMENT	ELocationID (#PCDATA)>
+<!ATTLIST	ELocationID EIdType (doi | pii) #REQUIRED 
+            ValidYN  (Y | N) "Y">
+<!ELEMENT   EndPage (#PCDATA)>
+<!ELEMENT	ForeName (#PCDATA)>
+<!ELEMENT	GeneSymbol (#PCDATA)>
+<!ELEMENT	GeneSymbolList (GeneSymbol+)>
+<!ELEMENT	GeneralNote (#PCDATA)>
+<!ATTLIST	GeneralNote Owner (NLM | NASA | PIP | KIE | HSR | HMD) "NLM">
+<!ELEMENT	Grant (GrantID?, Acronym?, Agency, Country)>
+<!ELEMENT	GrantID (#PCDATA)>
+<!ELEMENT	GrantList (Grant+)>
+<!ATTLIST	GrantList CompleteYN (Y | N) "Y">
+<!ELEMENT	ISOAbbreviation (#PCDATA)>
+<!ELEMENT	ISSN (#PCDATA)>
+<!ATTLIST	ISSN IssnType  (Electronic | Print) #REQUIRED>
+<!ELEMENT   ISSNLinking (#PCDATA)>
+<!ELEMENT	Initials (#PCDATA)>
+<!ELEMENT	Investigator (LastName,ForeName?, Initials?,Suffix?,NameID*,Affiliation?)>
+<!ATTLIST	Investigator ValidYN (Y | N) "Y">
+<!ELEMENT	InvestigatorList (Investigator+)>
+<!ELEMENT	Issue (#PCDATA)>
+<!ELEMENT	Journal (ISSN?, JournalIssue, Title?, ISOAbbreviation?)>
+<!ELEMENT	JournalIssue (Volume?, Issue?, PubDate)>
+<!ATTLIST	JournalIssue CitedMedium (Internet | Print) #REQUIRED>
+<!ELEMENT	Keyword %text;>
+<!ATTLIST	Keyword MajorTopicYN (Y | N) "N">
+<!ELEMENT	KeywordList (Keyword+)>
+<!ATTLIST	KeywordList Owner (NLM | NLM-AUTO | NASA | PIP | KIE | NOTNLM) "NLM">
+<!ELEMENT	Language (#PCDATA)>
+<!ELEMENT	LastName (#PCDATA)>
+<!ELEMENT	MedlineDate (#PCDATA)>
+<!ELEMENT	MedlineJournalInfo (Country?, MedlineTA, NlmUniqueID?,ISSNLinking?)>
+<!ELEMENT   MedlinePgn (#PCDATA)>
+<!ELEMENT	MedlineTA (#PCDATA)>
+<!ELEMENT	MeshHeading (DescriptorName, QualifierName*)>
+<!ELEMENT	MeshHeadingList (MeshHeading+)>
+<!ELEMENT	Month (#PCDATA)>
+<!ELEMENT   NameID (#PCDATA)>
+<!ATTLIST   NameID 
+            Source CDATA #REQUIRED >
+<!ELEMENT	NameOfSubstance (#PCDATA)>
+<!ELEMENT	NlmUniqueID (#PCDATA)>
+<!ELEMENT	Note (#PCDATA)>
+<!ELEMENT	NumberOfReferences (#PCDATA)>
+<!ELEMENT	OtherAbstract (AbstractText+,CopyrightInformation?)>
+<!ATTLIST	OtherAbstract Type (AAMC | AIDS | KIE | PIP | 
+                                    NASA | Publisher) #REQUIRED>
+<!ELEMENT	OtherID (#PCDATA)>
+<!ATTLIST	OtherID Source (NASA | KIE | PIP | POP | ARPL | CPC | 
+                                IND | CPFH | CLML | NRCBL | NLM) #REQUIRED>
+<!ELEMENT	PMID (#PCDATA)>
+<!ATTLIST       PMID Version CDATA #REQUIRED>
+<!ELEMENT	Pagination ((StartPage, EndPage?, MedlinePgn?) | MedlinePgn)>
+<!ELEMENT	PersonalNameSubject (LastName,ForeName?, Initials?,Suffix?)>
+<!ELEMENT	PersonalNameSubjectList (PersonalNameSubject+)>
+<!ELEMENT	PubDate ((Year, ((Month, Day?) | Season)?) | MedlineDate)>
+<!ELEMENT	PublicationType (#PCDATA)>
+<!ELEMENT	PublicationTypeList (PublicationType+)>
+<!ELEMENT	QualifierName (#PCDATA)>
+<!ATTLIST	QualifierName MajorTopicYN (Y | N) "N">
+<!ELEMENT	RefSource (#PCDATA)>
+<!ELEMENT	RegistryNumber (#PCDATA)>
+<!ELEMENT	Season (#PCDATA)>
+<!ELEMENT	SpaceFlightMission (#PCDATA)>
+<!ELEMENT       StartPage (#PCDATA)>
+<!ELEMENT	Suffix %text;>
+<!ELEMENT       SupplMeshList (SupplMeshName+)>
+<!ELEMENT       SupplMeshName (#PCDATA)>
+<!ATTLIST       SupplMeshName Type (Disease | Protocol) #REQUIRED>
+<!ELEMENT	Title (#PCDATA)>
+<!ELEMENT	VernacularTitle %text;>
+<!ELEMENT	Volume (#PCDATA)>
+<!ELEMENT	Year (#PCDATA)>
+<!ELEMENT	DeleteCitation (PMID+)>
diff --git a/Bio/Entrez/DTDs/pubmed_110101.dtd b/Bio/Entrez/DTDs/pubmed_110101.dtd
new file mode 100644
index 00000000000..6298eb64bd6
--- /dev/null
+++ b/Bio/Entrez/DTDs/pubmed_110101.dtd
@@ -0,0 +1,79 @@
+<!--    
+	   This is the Current DTD which NLM has written for 
+        External  Use.  If you are a NCBI User, use the information
+        from the PubmedArticleSet.
+
+        Comments and suggestions are welcome.
+        (May 9, 2000)
+	
+        Corrections:
+        ~~~~~~~~~~~
+        Oct. 09 2002 
+        - "PubMedArticle" has been renamed to "PubmedArticle"
+        - All referencies to "PubMedArticle" has been removed
+        - "ProviderId" has been removed from PubmedData
+        - "URL" has been removed from PubmdeData
+		
+		$Id: pubmed_110101.dtd 204806 2010-09-10 17:50:53Z korobtch $
+        
+       -->
+<!-- ================================================================= -->
+<!-- ================================================================= -->
+<!-- Reference to Where the MEDLINECITATION DTD is located  -->
+<!ENTITY % Medline PUBLIC "-//NLM//DTD Medline, 01 Jan 2011//EN"
+      "nlmmedlinecitationset_110101.dtd">
+%Medline;
+<!-- ================================================================= -->
+<!ENTITY % ArticleTitle.Ref "ArticleTitle">
+<!ENTITY % ISSN.Ref "ISSN?">
+<!ENTITY % Pub.Date.Ref "PubDate?">
+<!ENTITY % iso.language.codes "(AF|AR|AZ|BG|CS|DA|DE|EN|EL|ES|FA|FI|FR|HE|
+                                   HU|HY|IN|IS|IT|IW|JA|KA|KO|LT|MK|ML|NL|NO|
+                                   PL|PT|PS|RO|RU|SL|SK|SQ|SR|SV|SW|TH|TR|UK|
+                                   VI|ZH)">
+<!ENTITY % pub.status.int "pmc | pmcr | pubmed | pubmedr | 
+                             premedline | medline | medliner | entrez | pmc-release">
+<!ENTITY % pub.status "(received | accepted | epublish | 
+                              ppublish | revised | aheadofprint | 
+                              retracted | %pub.status.int;)">
+<!ENTITY % art.id.type.int "pubmed | medline | pmcid | pmcbook | bookaccession">
+							
+<!ENTITY % art.id.type "(doi | pii | pmcpid | pmpid | pmc | mid |
+                              sici | %art.id.type.int;)">
+<!-- ================================================================= -->
+<!ELEMENT PubmedArticleSet (PubmedArticle | PubmedBookArticle)+>
+<!-- ================================================================= -->
+<!-- This is the top level element for PubMedArticle -->
+<!ELEMENT PubmedArticle (MedlineCitation, PubmedData?)>
+<!-- ================================================================= -->
+<!ENTITY % normal.date "Year, Month, Day, (Hour, (Minute, Second?)?)?">
+<!ELEMENT PubmedData (History?, PublicationStatus, ArticleIdList, ObjectList?)>
+<!ELEMENT PubMedPubDate (%normal.date;)>
+<!ATTLIST PubMedPubDate
+	PubStatus %pub.status; #REQUIRED
+>
+<!ELEMENT PublicationStatus (#PCDATA)>
+<!ELEMENT ArticleIdList (ArticleId+)>
+<!ELEMENT ArticleId (#PCDATA)>
+<!ATTLIST ArticleId
+	IdType %art.id.type; "pubmed"
+>
+<!ELEMENT History (PubMedPubDate+)>
+<!ELEMENT URL (#PCDATA)>
+<!ATTLIST URL
+	lang %iso.language.codes; #IMPLIED
+	Type ( FullText | Summary | fulltext | summary) #IMPLIED
+>
+<!ELEMENT ObjectList (Object)+>
+<!ELEMENT Object (Param)*>
+<!ATTLIST Object Type CDATA #REQUIRED>
+<!ELEMENT Param (#PCDATA)>
+<!ATTLIST Param Name CDATA #REQUIRED>
+<!ELEMENT Hour (#PCDATA)>
+<!ELEMENT Minute (#PCDATA)>
+<!ELEMENT Second (#PCDATA)>
+
+<!-- ================================================================= -->
+<!ENTITY % Bookdoc PUBLIC "-//NLM//DTD Bookdoc, 01 Jan 2011//EN" "bookdoc_110101.dtd">
+%Bookdoc;
+<!-- ================================================================= -->