[Utilities-announce] PubMed E-Utilities 2015 DTD updates

[utilities-announce at ncbi.nlm.nih.gov]

Dear NCBI PubMed E-Utilities Users,

We anticipate updating the PubMed E-Utilities DTDs for 2015 in mid-December, approximately on December 15, 2014.

The forthcoming DTDs are now available:
http://eutils.ncbi.nlm.nih.gov/entrez/query/DTD/bookdoc_150101.dtd
http://eutils.ncbi.nlm.nih.gov/entrez/query/DTD/nlmmedlinecitationset_150101.dtd
http://eutils.ncbi.nlm.nih.gov/entrez/query/DTD/pubmed_150101.dtd

The DTD changes for the 2015 production year are itemized in the Revision Notes section near the top of the DTDs. The following describes the substantive changes:

Add new UI attribute to DescriptorName, QualifierName, NameOfSubstance, SupplMeshName and PublicationType elements. The new required UI attribute will carry the MeSH unique identifier for DescriptorName, QualifierName, NameOfSubstance, SupplMeshName and PublicationType elements.

DTD:
<!ELEMENT   DescriptorName (#PCDATA)>
<!ATTLIST   DescriptorName
MajorTopicYN (Y | N) "N"
Type (Geographic) #IMPLIED
UI CDATA #REQUIRED>

<!ELEMENT   QualifierName (#PCDATA)>
<!ATTLIST   QualifierName
MajorTopicYN (Y | N) "N"
UI CDATA #REQUIRED>

<!ELEMENT   NameOfSubstance (#PCDATA)>
<!ATTLIST   NameOfSubstance
UI CDATA #REQUIRED>

<!ELEMENT   SupplMeshName (#PCDATA)>
<!ATTLIST   SupplMeshName
Type (Disease | Protocol) #REQUIRED
UI CDATA #REQUIRED>

<!ELEMENT   PublicationTypeList (PublicationType+)>
<!ELEMENT   PublicationType (#PCDATA)>
<!ATTLIST   PublicationType
UI CDATA #REQUIRED>

Sample XML:
<DescriptorName MajorTopicYN="N" UI="D054971">Orthostatic Intolerance</DescriptorName>
<QualifierName MajorTopicYN="N" UI="Q000628">therapy</QualifierName>

<NameOfSubstance UI="C058787">royal jelly</NameOfSubstance>
<SupplMeshName Type="Disease" UI="C537735">Oculofaciocardiodental syndrome</SupplMeshName>

<PublicationType UI="D016428">Journal Article</PublicationType>

Add new optional and repeatable envelope element AffiliationInfo to Author and Investigator elements. AffiliationInfo envelope element includes Affliliation and Identifier elements.

DTD:
<!ELEMENT   Author (((LastName, ForeName?, Initials?, Suffix?) | CollectiveName), Identifier*,

AffiliationInfo*)>
<!ATTLIST   Author ValidYN (Y | N) "Y">
<!ELEMENT   Investigator (LastName, ForeName?, Initials?, Suffix?, Identifier*, AffiliationInfo*)>
<!ATTLIST   Investigator ValidYN (Y | N) "Y">

<!ELEMENT   AffiliationInfo(Affiliation, Identifier*)>
<!ELEMENT   Affiliation (#PCDATA)>
<!ELEMENT   Identifier (#PCDATA)>
<!ATTLIST   Identifier
Source CDATA #REQUIRED)>

Sample XML:
<AuthorList CompleteYN="Y">
<Author ValidYN="Y">
<LastName>Rome</LastName>
<ForeName>Benjamin N</ForeName>
<Initials>BN</Initials>
<Identifier Source="ORCID">0000000111111111</Identifier>
<AffiliationInfo>
<Affiliation>Harvard Medical School, Boston, Massachusetts</Affiliation>
<Identifier Source="Ringgold">123456</Identifier>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>Program on Regulation, Therapeutics, and Law, Division of Pharmacoepidemiology and Pharmacoeconomics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>Beth Israel Deaconess Medical</Affiliation>
<Identifier Source="Ringgold">678922</Identifier>
</AffiliationInfo>
</Author>
</AuthorList>

<InvestigatorList>
<Investigator ValidYN="Y">
<LastName>Salloway</LastName>
<ForeName>S</ForeName>
<Initials>S</Initials>
<AffiliationInfo>
<Affiliation>University of Missouri at Kansas City</Affiliation>
<Identifier Source="Ringgold">11223344</Identifier>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>Kansas City AIDS Research Consortium</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>AIDS Administration Missouri</Affiliation>
<Identifier Source="Ringgold">66778899</Identifier>
</AffiliationInfo>
</Investigator>
</InvestigatorList>

The valid value UNLABELLED is removed from the AbstractText NlmCategory attribute because it is not used.

DTD:
<!ELEMENT   AbstractText (#PCDATA)>
<!ATTLIST   AbstractText
Label CDATA #IMPLIED
NlmCategory (BACKGROUND | OBJECTIVE | METHODS | RESULTS | CONCLUSIONS | UNASSIGNED) #IMPLIED>

The valid values AssociatedDataset and AssociatedPublication are added to the CommentsCorrections RefType attribute.


DTD:
<!ELEMENT    CommentsCorrectionsList (CommentsCorrections+)>
<!ELEMENT    CommentsCorrections (RefSource, PMID?, Note?)>
<!ATTLIST    CommentsCorrections
RefType (AssociatedDataset | AssociatedPublication | CommentOn | CommentIn | ErratumIn | ErratumFor |
PartialRetractionIn | PartialRetractionOf | RepublishedFrom | RepublishedIn | RetractionOf |
RetractionIn | UpdateIn | UpdateOf | SummaryForPatientsIn | OriginalReportIn |ReprintOf | ReprintIn | Cites) #REQUIRED>

Sample XML:

PMID 24872877
<CommentsCorrectionsList>
<CommentsCorrections RefType="AssociatedPublication">
<RefSource>Gigascience. 2014 May 28;3:8. doi: 10.1186/2047-217X-3-8. eCollection 2014.</RefSource>
<PMID Version="1">24872878</PMID>
</CommentsCorrections>
</CommentsCorrectionsList>

PMID 24872878
<CommentsCorrectionsList>
<CommentsCorrections RefType="AssociatedDataset">
<RefSource>Gigascience. 2014 May 28;3:7. doi: 10.1186/2047-217X-3-7. eCollection 2014.</RefSource>
<PMID Version="1">24872877</PMID>
</CommentsCorrections>
</CommentsCorrectionsList>
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