CDR Tickets

I have posted below, email exchanges we had regarding NLM's annual DTD changes.

______________________________
Volker Englisch
NCI OCPL – Office of Communications & Public Liaison
Contractor: Sapient Government Services
NCI: 240-276-6583

---Original Message---
From: Osei-Poku, William William.Osei-Poku@icfi.com
Sent: Tuesday, November 04, 2014 2:07 PM
To: Juthe, Robin (NIH/NCI) [E]; Englisch, Volker (NIH/NCI) [C]; Kline, Robert (NCI); Beckwith, Margaret (NIH/NCI) [E]; Alan Meyer; Henry, Erika (NIH/NCI) [C]
Subject: RE: [Utilities-announce] PubMed E-Utilities 2015 DTD updates

I agree that it should go in the hotfix. In the past we were able to import citations but they remained invalid and unable to use them until our schema was updated.

Thanks,
William

---Original Message---
From: Juthe, Robin (NIH/NCI) [E] robin.juthe@nih.gov
Sent: Tuesday, November 04, 2014 1:30 PM
To: Englisch, Volker (NIH/NCI) [C]; Kline, Robert (NCI); Beckwith, Margaret (NIH/NCI) [E]; Osei-Poku, William; Alan Meyer; Henry, Erika (NIH/NCI) [C]
Subject: RE: [Utilities-announce] PubMed E-Utilities 2015 DTD updates

I think this should go into the hotfix if possible. In the meantime, we run the risk of importing duplicate citations or not being able to import citations at all, right?

Thanks,
Robin

---Original Message---
From: Englisch, Volker (NIH/NCI) [C]
Sent: Tuesday, November 04, 2014 1:27 PM
To: Kline, Robert (NCI); Beckwith, Margaret (NIH/NCI) [E]; Juthe, Robin (NIH/NCI) [E]; Osei-Poku, William; Alan Meyer; Henry, Erika (NIH/NCI) [C]
Subject: RE: [Utilities-announce] PubMed E-Utilities 2015 DTD updates

Do we need to hold up the Mailer hot-fix to include the citation schema hot-fix? I don't think we would be able to launch another hot-fix before December.

Thanks,

Volker
___________________________________
Volker Englisch
NCI OCPL – Office of Communications & Public Liaison
Contractor: Sapient Government Services
NCI: 240-276-6583

---Original Message---
From: Kline, Robert (NCI)
Sent: Friday, October 31, 2014 12:17 PM
To: Beckwith, Margaret (NIH/NCI) [E]; Juthe, Robin (NIH/NCI) [E]; Osei-Poku, William; Alan Meyer; Englisch, Volker (NIH/NCI) [C]; Henry, Erika (NIH/NCI) [C]
Subject: Fwd: [Utilities-announce] PubMed E-Utilities 2015 DTD updates

Just a heads-up that we may need to update our Citation schema in the CDR some time before December. Assuming no CDR release or patch is scheduled between now and then, this will require a ticket to CBIIT to get some of the mods installed on production.

Bob

• • • • • • • • • • Forwarded message ----------
                    From: <utilities-announce@ncbi.nlm.nih.gov>
                    Date: Fri, Oct 31, 2014 at 11:50 AM
                    Subject: [Utilities-announce] PubMed E-Utilities 2015 DTD updates
                    To: NLM/NCBI List utilities-announce <utilities-announce@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

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>