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<TITLE> [Utilities-announce] PubMed E-Utility 2011 DTD updates - please read! Second annoucement.
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<H1>[Utilities-announce] PubMed E-Utility 2011 DTD updates - please read! Second annoucement.</H1>
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<B>utilities-announce at ncbi.nlm.nih.gov</B>
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<A HREF="mailto:utilities-announce%40ncbi.nlm.nih.gov?Subject=Re%3A%20%5BUtilities-announce%5D%20PubMed%20E-Utility%202011%20DTD%20updates%20-%20please%0A%09read%21%20Second%20annoucement.&In-Reply-To=%3CA9D8BF3D8A74DF4A925FB541C0F39D2A14C4831F2B%40NIHMLBX15.nih.gov%3E"
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TITLE="[Utilities-announce] PubMed E-Utility 2011 DTD updates - please read! Second annoucement.">utilities-announce at ncbi.nlm.nih.gov
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<I>Wed Oct 20 11:02:24 EDT 2010</I>
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<PRE>Dear NCBI PubMed E-Utility Users,
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We anticipate updating the PubMed E-Utility DTDs for 2011 in mid-December, approximately on December 13, 2010.
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The forthcoming DTDs are available from:
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<A HREF="http://eutils.ncbi.nlm.nih.gov/corehtml/query/DTD/pubmed_110101.dtd">http://eutils.ncbi.nlm.nih.gov/corehtml/query/DTD/pubmed_110101.dtd</A>
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<A HREF="http://eutils.ncbi.nlm.nih.gov/corehtml/query/DTD/nlmmedlinecitationset_110101.dtd">http://eutils.ncbi.nlm.nih.gov/corehtml/query/DTD/nlmmedlinecitationset_110101.dtd</A>
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1. DTD AND XML CHANGES FOR 2011
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* Changes to NLMMedlineCitationSet DTD AND PubMed XML
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The DTD changes for the 2011 production year are itemized in the Revision Notes section near the top of the DTD. The following describes the substantive changes to NLMMedlineCitationSet dtd and PubMed XML:
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* Accommodating Structured Abstracts<<A HREF="http://www.nlm.nih.gov/bsd/policy/structured_abstracts.html">http://www.nlm.nih.gov/bsd/policy/structured_abstracts.html</A>>
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Two new attributes, Label and NlmCategory, are added to the AbstractText element which is used with both the Abstract and OtherAbstract elements. A valid label name found in published structured abstracts (e.g., Introduction, Goals, Study Design, Findings, Discussion) will be identified in the XML as an Abstract Text Label and each 'parent' concept to which the published Label name is mapped at NLM will be identified as an Abstract Text NlmCategory. Five NLM-assigned mapped-to categories are possible: Background, Objective, Methods, Results, and Conclusions. In general, the lack of Label and NlmCategory attributes in AbstractText means the published abstract is unstructured.
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Note that the content of structured abstracts will be exported in separate segments that need to be joined for display of the complete abstract text.
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DTD:
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<!ELEMENT AbstractText (#PCDATA)>
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<!ATTLIST AbstractText
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Label CDATA #IMPLIED
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NlmCategory (UNLABELLED | BACKGROUND | OBJECTIVE | METHODS | RESULTS | CONCLUSIONS) #IMPLIED>
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In the following example, the published label names are INTRODUCTION; AIMS; DESIGN, SETTING AND PARTICIPANTS; RESULTS; and DISCUSSION which correspondingly map to the five NLM-assigned categories.
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Sample XML:
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<Abstract>
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<AbstractText Label = "INTRODUCTION" NlmCategory = "BACKGROUND">Physicians are often reluctant to prescribe strong opioids for chronic non cancer pain (CNCP). No study has qualitatively examined physicians' beliefs about ...</AbstractText>
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<AbstractText Label = "AIMS" NlmCategory = "OBJECTIVE">To describe physicians' attitudes and experience of prescribing opioids for CNCP to PWHSA.</AbstractText>
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<AbstractText Label = "DESIGN, SETTING AND PARTICIPANTS" NlmCategory = "METHODS">Nineteen individual interviews and two focus groups were conducted with GPs, Addiction Specialists, Pain Specialists and Rheumatologists.</AbstractText>
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<AbstractText Label = "RESULTS" NlmCategory = "RESULTS">Physicians were "reluctant" to prescribe opioids to PWHSA experiencing CNCP for fear of addiction, misuse or diversion of medications. Many exhibited "distrust"...</AbstractText>
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<AbstractText Label = "DISCUSSION" NlmCategory = "CONCLUSIONS">Applying the chronic disease model to comorbid addiction and CNCP would ensure a health and social care system that makes it difficult to stigmatise patients...</AbstractText>
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</Abstract>
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* Implementing Protocol Class 2 Supplementary Concept Record (SCR) and Rare Disease Class 3 SCR terms
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A new element, SupplMeshList, is added to the MedlineCitation element and another new element, SupplMeshName with its attribute Type, is added to SupplMeshList.
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DTD:
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<!ELEMENT MedlineCitation (PMID, DateCreated, DateCompleted?, DateRevised?, Article, MedlineJournalInfo, ChemicalList?, SupplMeshList?, CitationSubset*, CommentsCorrectionsList?, GeneSymbolList?, MeshHeadingList?, NumberOfReferences?, PersonalNameSubjectList?, OtherID*, OtherAbstract*, KeywordList*, SpaceFlightMission*, InvestigatorList?, GeneralNote*)>
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<!ELEMENT SupplMeshList (SupplMeshName+)>
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<!ELEMENT SupplMeshName (#PCDATA)>
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<!ATTLIST SupplMeshName Type (Disease | Protocol) #REQUIRED>
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Sample XML:
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<SupplMeshList>
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<SupplMeshName Type="Disease">disease term</SupplMeshName>
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<SupplMeshName Type="Protocol">protocol term</SupplMeshName>
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</SupplMeshList>
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* Separating MeSH Geographic Descriptor Names from other MeSH Descriptors
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The Type attribute is added to the DescriptorName element.
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DTD:
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<!ELEMENT DescriptorName (#PCDATA)>
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<!ATTLIST DescriptorName
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MajorTopicYN (Y | N) "N"
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Type (Geographic) #IMPLIED>
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Sample XML:
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<MeshHeadingList>
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<MeshHeading>
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<DescriptorName MajorTopicYN="N" Type="Geographic">New York</DescriptorName>
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</MeshHeading>
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</MeshHeadingList>
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* Accommodating Versioned Articles; Corresponding Change to PMID
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There is a new model of publishing referred to as 'versioning' whereby multiple versions of the same online article are released, sometimes in quick succession and sometimes almost as soon as the original article has been published. Beginning in the 2011 production year, NLM will create an individual citation for each article's version and link the versions via new attributes for the MedlineCitation and PMID elements.
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The new attributes for the MedlineCitation element are VersionID and VersionDate.
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DTD:
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<!ELEMENT MedlineCitation (PMID, DateCreated, DateCompleted?, DateRevised?, Article, MedlineJournalInfo, ChemicalList?,
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SupplMeshList?, CitationSubset*, CommentsCorrectionsList?, GeneSymbolList?, MeshHeadingList?, NumberOfReferences?,
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PersonalNameSubjectListOtherID*, OtherAbstract*, KeywordList*, SpaceFlightMission*, InvestigatorList?, GeneralNote*)>
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<!ATTLIST MedlineCitation
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Owner (NLM | NASA | PIP | KIE | HSR | HMD | NOTNLM) "NLM"
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Status (Completed | In-Process | PubMed-not-MEDLINE | In-Data-Review |Publisher | MEDLINE | OLDMEDLINE) #REQUIRED
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VersionID CDATA #IMPLIED
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VersionDate CDATA #IMPLIED>
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The new attribute for the PMID element is Version.
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DTD:
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<!ELEMENT PMID (#PCDATA)>
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<!ATTLIST PMID
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Version CDATA #REQUIRED>
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Sample XML:
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<MedlineCitation Status = "MEDLINE" Owner ="NLM" VersionID = "PMC2781303.2" VersionDate = 20091207">
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<PMID Version = "2">20029669</PMID>
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Search and display implementation in PubMed is under consideration at this time; all implementation decisions will be documented in a forthcoming NLM Technical Bulletin<<A HREF="http://www.nlm.nih.gov/pubs/techbull/tb.html">http://www.nlm.nih.gov/pubs/techbull/tb.html</A>> article. Details are:
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* The PMID combined with its version attribute value (e.g., 1, 2, 3) becomes the citation's new unique identifier, represented as <PMID Version="2">12345678</PMID>.
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* The PMID Version attribute value '1' will be assigned to all existing records at the time the 2011 baseline files are produced and exported.
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* The PubDate value on citations of versions of the same article will be identical. The MedlineCitation Version Date and VersionID attribute values supplied by the publisher will identify the specific version.
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* If a citation is not for PMID Version 1, it must contain MedlineCitation Version Date and VersionID attribute values, and the original publication date for Version 1 as the PubDate.
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* A PMID Version attribute value higher than 1 indicates that there is a citation for at least one prior version (although it might happen, rarely, that a prior version subsequently gets deleted). Although the MedlineCitation VersionDate value may be different from the PubDate, it might be the same as PubDate if the new version was released later the same day.
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* In the future, when non-PubMed Central journals are included, the publisher-supplied VersionID value will be whatever the publisher decides it to be; e.g. the 2nd publisher-supplied VersionID may be 'b' or '2b' and the PMID Version attribute value assigned by NLM will still be 2.
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* Eliminating Pre-defined Source Attribute Values for NameID Element
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The 2010 DTD specifies the values that may be used for the Source attribute for the NameID element. Please note that the NameID element has not yet been used; it is expected to be implemented at some point during the 2011.
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DTD:
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<!ELEMENT NameID (#PCDATA)>
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<!ATTLIST NameID Source CDATA #REQUIRED>
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Sample XML:
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<NameID Source = "NCBI">
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* Simplifying Author Element Structure
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The NameID element has been repositioned in the Author element to simplify the DTD structure. The XML is not affected.
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DTD:
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<!ELEMENT Author (((LastName, ForeName?, Initials?, Suffix? ) | CollectiveName),NameID*)>
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* Accommodating Identification of Machine-generated Keywords. A new valid value, NLM-AUTO, is added to the Owner attribute of the element KeywordList.
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DTD:
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<!ELEMENT KeywordList (Keyword+)>
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<!ATTLIST KeywordList Owner (NLM | NLM-AUTO | NASA | PIP | KIE | NOTNLM) "NLM">
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Sample XML:
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<KeywordList Owner ="NLM-AUTO">
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1. ENHANCED CHARACTER SET<<A HREF="http://www.nlm.nih.gov/databases/dtd/medline_characters.html">http://www.nlm.nih.gov/databases/dtd/medline_characters.html</A>>
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A subset of UTF-8 characters is currently supported for PubMed data. PubMed data now supports the full UTF-8 Character Set.
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Exceptions:
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All instances that represent a Double Quote will be translated to the straight double quote (Unicode 0022).
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All instances that represent a Single Quote (including the prime and apostrophe) will be translated to the straight single quote (Unicode 0027).
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Em Dash, En Dash, Hyphen, or Minus will be translated to the single dash (Unicode 002D).
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Those three Unicode values are part of the current Character Set.
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