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XML Help for PubMed Data Providers

Created: ; Last Update: November 24, 2017.

Publishers of journals in PubMed must submit citation and abstract data electronically. Electronic submissions ensure that citations and abstracts are available to the public within 24 hours of uploading a properly formatted XML file and meet one of the requirements to add an icon on PubMed citations via participation in LinkOut. LinkOut is a service that allows you to link directly from a PubMed citation to the journal website.

PubMed only accepts citation and abstract data uploaded by File Transfer Protocol (FTP) that is in the PubMed XML tagged format. FTP accounts are provided for publishers to send data in a confidential and reliable manner. These citations are then added to PubMed, and PubMed Unique Identifiers (PMIDs) are returned to the publisher.

Interested in uploading citation and abstract data to PubMed for your journal? Check out the Data Provider Quick Start Guide.

Have questions about the process? Please contact the Data Provider Support Team [vog.hin.mln.ibcn@rehsilbup].

FAQs

Data Provider Quick Start Guide

XML

FTP and File Submission

Understanding Loader Reports

FAQs

Correcting Errors in PubMed

With the release of the PubMed Data Management System (PMDM) in October 2016, PubMed data providers are now responsible for accurately presenting their own citations in PubMed. See the PMDM Quick Start Guide for details about accessing and using PMDM.

Using PMDM, data providers can update or correct nearly all elements of their citations at any time after initial receipt of the records by PubMed. There is no longer a period of time when citations are unavailable for update by the data provider.

Going forward, NLM will not as a matter of course update or correct publisher-supplied citations. Instead, requests for corrections received by NLM Customer Service will be directed to the appropriate publisher for resolution however the publisher deems best and on the publisher's timeline.

Please note, NLM's Errata, Retraction, Duplicate Publication, and Comment Policy has not changed. Journals should continue to follow best practices and publish errata to correct errors appearing in the original article.

Note: We accept Replaces files for ahead of print citations and data in the following fields, regardless of the citation’s status in PubMed:

  • AuthorList (includes Author, Affiliation, Identifier)
  • InvestigatorList (includes Investigator, Affiliation, Identifier)
  • Pagination
  • ELocationID
  • OtherAbstract
  • PII
  • DOI

Our loader will compare the content of these fields in the Replaces file with the existing PubMed citation and only modify the content if it is different.

Can Collaborator Names be supplied to PubMed?

Yes. Investigators (also known as collaborators in PubMed) are individuals who contribute to a scientific article but are not authors. The group name author should be placed in the <Author> tags, and the investigators’ names should be included by using the <IndividualName> tag within a <GroupName> tag. Please see an example of the XML tagging below:

<AuthorList>
<Author>
<CollectiveName>Cancer Genome Center</CollectiveName>
</Author>
<Author>
<CollectiveName>North American Barley Genome Project</CollectiveName>
</Author>
</AuthorList>
<GroupList>
<Group>
<GroupName>Cancer Genome Center</GroupName>
<IndividualName>
<FirstName>John</FirstName>
<LastName>Smith</LastName>
</IndividualName>
<IndividualName>
<FirstName>Mary</FirstName>
<LastName>Jones</LastName>
</IndividualName>
</Group>
<Group>
<GroupName>North American Barley Genome Project</GroupName>
<IndividualName>
<FirstName>John Jacob</FirstName>
<LastName>Han</LastName>
</IndividualName>
<IndividualName>
<FirstName>Laura</FirstName>
<LastName>Clancy</LastName>
</IndividualName>
</Group>
</GroupList>

A group name author (a collective name author, e.g., a study group name) must exist in the bibliographic citation data in order for investigator names to be supplied in the <GroupList> section. Investigator names should be listed in the order in which they appear in the full-text article.

For more information about NLM’s policy for individual authors, group or corporate authors, and investigators, please see the Authorship in MEDLINE Fact Sheet.

How should I submit citations for errata, retractions, and comments?

We encourage data providers to include the PMID, DOI, or PII of the original PubMed citation when submitting a citation for an erratum, retraction, comment, or other type of comment/correction listed below. When this information is included in the XML citation data, the link between citations will be displayed when the citation for the erratum, retraction, comment etc. becomes available in PubMed.

The accepted comment/correction types are:

ObjectType ValueDescription
Erratumcites the original article for which there is a published erratum.
Retractioncites the article(s) being retracted.
Commentcites the reference upon which the article comments.
republishedcites the first, originally published article.
Updatecites the article being updated.
Datasetcites a description of a dataset.
Reprintcites the first, originally published article.
patientsummarycites a patient summary article.
originalreportcites a scientific article associated with the patient summary.
ExpressionOfConcernForcites the original article for which there is an expression of concern

Citations for errata and retractions should have the PublicationType value “Published Erratum” or “Retraction of Publication,” as appropriate.

Sample XML:

<!DOCTYPE ArticleSet PUBLIC "-//NLM//DTD PubMed 2.7//EN" "https://dtd.nlm.nih.gov/ncbi/pubmed/in/PubMed.dtd">
<ArticleSet>
<Article>
<Journal>
<PublisherName>Public Library of Science</PublisherName>
<JournalTitle>PLoS One</JournalTitle>
<Issn>1932-6203</Issn>
<Volume>9</Volume>
<Issue>10</Issue>
<PubDate PubStatus="epublish">
<Year>2014</Year>
<Month>10</Month>
<Day>23</Day>
</PubDate>
</Journal>
<ArticleTitle>Correction: Statin Treatment in Hypercholesterolemic Men Does Not Attenuate Angiotensin II-Induced Venoconstriction</ArticleTitle>
<FirstPage LZero="save">e112205</FirstPage>
<AuthorList>
<Author>
<CollectiveName>The PLOS ONE Staff</CollectiveName>
</Author>
</AuthorList>
<PublicationType>Published Erratum</PublicationType>
<ArticleIdList>
<ArticleId IdType="doi">10.1371/journal.pone.0112205</ArticleId>
<ArticleId IdType="pii">PONE-D-14-46356</ArticleId>
</ArticleIdList>
<Abstract>This corrects the article DOI: 10.1371/journal.pone.0103909.</Abstract>
<ObjectList>
<Object Type="Erratum">
<Param Name="type">pmid</Param>
<Param Name="id">25264877</Param>
</Object>
</ObjectList>
</Article>
</ArticleSet>

Note on errata: Beginning with the publication year 2015, NLM retains the citation for an erratum notice supplied by the publisher, assigns the Publication Type “Published Erratum,” and creates a two-way link between the citation for the erratum notice and the citation for the original article, but does not assign MeSH terms. Prior to 2015, NLM did not retain publisher-supplied errata notices.

How should structured abstracts be submitted?

Submit abstract section headings in all uppercase letters followed by a colon and space, for example:

<Abstract>
BACKGROUND: Approximately 3,000 new cases of oral cancer...
</Abstract>

Common section headings are: BACKGROUND, METHODS, RESULTS, and CONCLUSIONS.

Alternatively, publishers may use the <AbstractText> element and its Label attribute to supply structured abstract section headings. The section heading should still be submitted in all uppercase letters.

<Abstract>
<AbstractText Label="OBJECTIVE">To assess the effects...</AbstractText>
<AbstractText Label="METHODS">Patients attending lung...</AbstractText>
<AbstractText Label="RESULTS">Twenty-five patients...</AbstractText>
<AbstractText Label="CONCLUSIONS">The findings suggest...</AbstractText>
</Abstract>

Can I submit author keywords?

Yes. Keyword information will be preceded by a KEYWORDS label and display below the abstract.

Keywords should be submitted in the <ObjectList> element, not as part of the abstract. Place the <ObjectList> immediately following the <Abstract>.

To submit multiple keywords, include multiple "Object" elements, one per keyword. Here is an example of the XML:

<ObjectList>
<Object Type=”keyword”>
<Param Name=”value”>GSH</Param>
</Object>
<Object Type=”keyword”>
<Param Name=”value”>Lipid peroxidation</Param>
</Object>
<Object Type=”keyword”>
<Param Name=”value”>MDA</Param>
</Object>
<Object Type=”keyword”>
<Param Name=”value”>Radiation</Param>
</Object>
</ObjectList>

How can I submit ClinicalTrials.gov and other databank accession numbers?

Use the ObjectList, Object, and Param tags to supply databank accession numbers. Following are sample XML fragments illustrating the tagging format for various databanks:

<ObjectList>
<Object Type="ClinicalTrials.gov">
<Param Name="id">NCT00000125</Param>
</Object>
</ObjectList>
<ObjectList>
<Object Type="Figshare">
<Param Name="id">10.6084/M9.FIGSHARE.1004150</Param>
</Object>
</ObjectList>
<ObjectList>
<Object Type="Dryad">
<Param Name="id">10.5061/dryad.2f050</Param>
</Object>
</ObjectList>
<ObjectList>
<Object Type="UniProtKB">
<Param Name="id">Q9H040</Param>
</Object>
</ObjectList>
<ObjectList>
<Object Type="NCBI:pubchem-substance">
<Param Name="id">251912582</Param>
</Object>
</ObjectList>
<ObjectList>
<Object Type="BioProject">
<Param Name="id">PRJNA178613</Param>
</Object>
</ObjectList>

Can I submit grant information?

Yes. The grants should be provided in the <ObjectList> as follows:

<ObjectList>
<Object Type="grant">
<Param Name="id">12345</Param>
<Param Name"grantor">Wellcome Trust</Param>
</Object>
</ObjectList>

What is an Article Identifier?

All Article Identifiers are optional. An Article Identifier can take one of two forms; a PII or a DOI.

A PII, or Publisher Item Identifier, is any internal reference identifier used in the publishing process. This identifier is assigned by the publisher.

A DOI, or Digital Object Identifier, is a number assigned by an international organization. The DOI System is a system for identifying and exchanging intellectual property in the digital environment. DOIs are issued to registrants by the DOI Registration Agency. More information about this standardized format can be obtained at http://www.doi.org/.

A DOI can be provided in two different elements: ELocationID and ArticleId. A DOI should be supplied in the standard format, e.g., 10.xxx/xxx. Do not include any leading characters like “doi:” or submit the DOI as a URL.

Article Identifiers (PII and DOI) are available for use in LinkOut, which allows providers to create links from article citations in PubMed to the full-text article hosted on the publisher websites.

How do I know if my journal is in PubMed?

To check your journal’s indexing status, search the NLM Catalog and look for the “Current Indexing Status” field.

A list of journals included in PubMed is also available by FTP.

If you cannot find your journal in the NLM Catalog or if your journal is not currently indexed, then it probably needs to apply for journal selection. The Journal Selection fact sheet describes the policy, selection criteria, and application process.

What should I do if my journal title or ISSN changes?

A change in the first five words of the title of the journal is considered a title change and will result in a new bibliographic record and the assignment of a new title abbreviation. A new ISSN should be assigned in this instance.

Also, the addition, deletion, change, or reordering of any of the first five words (not including the initial article) is considered a title change and will require a new bibliographic record and assignment of a new title abbreviation.

These are the steps for a title change:

1.

E-mail vog.hin.mln.ibcn@rehsilbup when the title has changed and a new ISSN has been assigned. Visit http://www‚Äč.issn.org for more information about applying for a new ISSN.

2.

Submit a copy of the ISSN assignment e-mail or letter from your local ISSN Centre to vog.hin.mln.ibcn@rehsilbup and mail it with a print copy of the journal with the new title and ISSN to:

National Library of Medicine

Attn: Tina Shrader

Cataloguing and Metadata Services Section

Bldg 38, Room 1N08

8600 Rockville Pike

Bethesda, MD 20894-3823

3. Wait for an e-mail confirmation from the Data Provider Support Team stating that our records have been updated and we are ready to receive data using the new title and ISSN.

What should do if my journal becomes electronic-only?

Please see the policy on indexing electronic journals and the FAQ: Indexing Requirements for Electronic Journals.

XML

How do I supply XML tagged citation and abstract data to PubMed?

The simplest way to get started is to copy the Example of a Standard XML file into a plain text editor and edit the text within each tag to fit your journal. If a tag is not used by your journal, simply delete it from your file.

Then save the file (click here for tips on file names), validate the file; and submit the sample XML file for review.

Do online-only articles have different requirements?

Citation and abstract data for an online-only article should appear very similar to a printed article. The following are common differences:

Sometimes online-only articles do not have page numbers; instead they have a DOI. If this is the case the correct tag to use is <ELocationID> instead of the <FirstPage> tag.

Online-only articles may also have individual publication dates instead of a publication date for the complete Issue or Volume. In this case <PubDate PubStatus="epublish"> should be used with the Year, Month and Day of online publication. If an online-only article has two publications dates, individual and Issue/Volume, then the <PubDate> tag should NOT have a PubStatus attribute and the <History> tag should be used.

The following are examples of the PubMed display for online-only articles:

AAPS J. 2008 Mar 23;10(1):E1-17.

This online-only article has a Year, Month, and Day of publication (2008 Mar 23); a Volume (10); Issue (1) and has chosen to use the <FirstPage> tag (E1) & <LastPage> tag (E17).

If the XML file also included an <ELocationID> tag, then the DOI would be displayed like so:

AAPS J. 2008 Mar 23;10(1):E1-17. doi: 10.1208/aapsj1001001.

If the XML file did NOT include the <FirstPage> and <LastPage> tags, but had an <ELocationID> tag, the PubMed display would be like so (if both <ELocationID> tags are sent, both will display in the absence of the page tags):

AAPS J. 2008 Mar 23;10(1). pii: aapsj1001001. doi: 10.1208/aapsj1001001.

Here is an example of the XML:

<FirstPage></FirstPage>
<LastPage></LastPage>
<ELocationID EIdType=”doi”>10.1208/aapsj1001001</ELocationID>
<ELocationID EIdType=”pii”>aapsj1001001</ELocationID>

Also if this is the first time online-only articles have been released for the title please contact us at vog.hin.mln.ibcn@rehsilbup with the following information:

  • Full journal title
  • Electronic ISSN
  • URL
  • First volume/issue to contain online-only articles
  • Provider. If you already have an account at NCBI, enter it here. If not, enter the name of your organization.

Can I submit multiple affiliations for one author?

Yes. Please see the following example:

<Author>
<FirstName>Frank</FirstName
<LastName>Davis</LastName>
<AffiliationInfo>
<Affiliation>Department of Human Genetics, University of California, Los Angeles, California 90095, USA</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, 08544, USA</Affiliation>
</AffiliationInfo>
</Author>

How can I indicate equal contribution among authors?

Use the EqualContrib attribute of the Author element to indicate equal contribution among authors. The default value for the attribute is "N," indicating non-equal contribution. In the example below, the first two authors contributed equally.

<AuthorList>
<Author EqualContrib="Y">
<FirstName>Katherine</FirstName>
<LastName>Anderson</LastName>
<AffiliationInfo>
<Affiliation>Georgetown University</Affiliation>
</AffiliationInfo>
</Author>
<Author EqualContrib="Y">
<FirstName>Edward</FirstName>
<LastName>Scarborough</LastName>
<AffiliationInfo>
<Affiliation>Mayo Clinic</Affiliation>
</AffiliationInfo>
</Author>
<Author>
<FirstName>Joanna</FirstName>
<LastName>Kay</LastName>
<AffiliationInfo>
<Affiliation>Georgetown University</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>

Can Collective Author Names be supplied to PubMed?

Yes. A Collective Author Name, the name of the authoring committee or organization, should be included by using the <CollectiveName> tag within an <Author> tag.

Please see the following example:

<AuthorList> 
<Author>
<FirstName>W.</FirstName>
<MiddleName>Thomas</MiddleName>
<LastName>Lawrence</LastName>
</Author>
<Author>
<CollectiveName>Plastic Surgery Educational Foundation DATA Committee</CollectiveName>
</Author>
</AuthorList>

Can Single Personal Author Names be supplied to PubMed?

Yes. A Single Personal Author Name, when a person has only one name, should be included by using the EmptyYN attribute for the <FirstName> tag within an <Author> tag. The default value for the EmptyYN attribute is "N"; indicating that the <FirstName> tag should not be empty.

Here is an example of a PubMed citation with a Single Personal Author Name (as well as authors with a FirstName and LastName):

Matiullah, Rehman S, Rehman S, Mati N, Ahmad S. .

Some more new etchants for CR-39 detector.

Radiat Meas. 2005 Oct;39(5):551-5.

PMID: 16094777 [PubMed - indexed for MEDLINE]

This is the tagging for the same citation as it appears in the XML file:

<AuthorList>
<Author>
<FirstName EmptyYN="Y"></FirstName>
<MiddleName></MiddleName>
<LastName>Matiullah</LastName>
</Author>
<Author>
<FirstName EmptyYN="N">S.</FirstName>
<LastName>Rehman</LastName>
</Author>
</AuthorList>

How should I submit mathematical or chemical formulas or tables in the abstract field?

Simple formulas:

  • Chemical - do not use <sup> or <inf> in chemical formulas, for example water should be submitted as H20, carbon dioxide as CO2.
  • Mathematical - simple mathematical formulas, e.g., x2, should be submitted in UTF-8 character encoding. Please refer to the PubMed Special Character Set for preferred encodings for common special characters.

Complex formulas:

  • Submit the following in place of complex mathematical or chemical formulas or tables within the abstract:

[Formula: see text]

[Table: see text]

This text should only be used for formulas or tables that cannot be represented in any other manner.

How do I use the <History> tag?

The <History> tag is an optional tag available to publishers who want to include information about the publication history of their citations.

The <History> tag includes PubStatus attributes, which may contain only one of the following values for each date in the publication history:

<PubDate PubStatus = "received">

<PubDate PubStatus = "accepted">

<PubDate PubStatus = "revised">

<PubDate PubStatus = "aheadofprint">

<PubDate PubStatus = "epublish">

<PubDate PubStatus = "ppublish">

<PubDate PubStatus = "ecollection">

Any PubDate in History must be an exact PubDate, one that includes valid values in the <Year>, <Month> and <Day> tags.

The <History> tag plays an important part in the process of submitting Ahead of Print citations. If a citation is submitted using the "aheadofprint" attribute in the <PubDate> tag and is later replaced using the "ppublish" attribute, we recommend that the publisher "move" the Ahead of Print date to the <History> tag in the Replacement File. This will enable the citation to retain the ahead of print publish date in PubMed. For more details, see our All About Ahead of Print page.

The <PubDate PubStatus = "epublish"> can be used to tag the individual publication date of an online-only article.

Citations with PubStatus=”epublish” or PubStatus=”aheadofprint” can only be submitted for publication date years greater than or equal to 2000.

How should I submit versioned citations?

What are versions?

Revisions, scientific updates, and updates of reviews are examples of content that could be versioned. Versions are not intended for correcting specific errors in an article, for which published errata notices should continue to be used (see NLM’s Fact Sheet).

How will versions be identified?

The PMID of a versioned citation will remain constant while each version will have a unique version number assigned by PubMed. The combination of PMID and version number in the format PMID.version (e.g., (20029611.2) will be a unique identifier. All citations not versioned will be considered version 1.

There may be occasions when a specific version will be deleted. In these cases, the version number assigned to the deleted version will be skipped, and the next version of the citation will be assigned the following version number. Version numbers will not be reused.

Required data elements

The Publisher DTD contains two optional attributes to the Article tag: VersionID and VersionDate.

<!ATTLIST Article
VersionID CDATA #IMPLIED
VersionDate CDATA #IMPLIED>

VersionID is the identifier for the specific version of the article as chosen by the publisher/data provider. It has no effect on the version number assigned by PubMed. VersionID is a string and can be anything (e.g. 2, JSmithv2, 123456.2) but must be unique per PMID. Please note that VersionID is case-sensitive, and we do not remove spaces or punctuation during processing.

VersionDate is date the version was published. We recommend using a standard date format such as 2009/09/01. The data in this field will display in the [revised] notation on the citation, e.g., PublicationDate [revised VersionDate].

We recommend retaining the publication date of the original article in the PublicationDate field of subsequent versions and placing the version publication date in the VersionDate field.

How to tag a new version

To submit new version of an existing PubMed citation, create an XML file using <Replaces> tags referring to the PMID of the prior version. Assign a new VersionID and VersionDate.

Here is a sample section of an XML file showing the VersionID, VersionDate, and Replaces tagging:

<ArticleSet>
<Article VersionID="2" VersionDate="2009/10/01">
<Journal>
<PublisherName>Public Library of Science</PublisherName>
<JournalTitle>PLoS Curr</JournalTitle>
<Issn>2157-3999</Issn>
<Volume>1</Volume>
<PubDate PubStatus="epublish">
<Year>2009</Year>
<Month>9</Month>
<Day>29</Day>
</PubDate>
</Journal>
<Replaces IdType="pubmed">20029614</Replaces>
<ArticleTitle>The severity of pandemic H1N1 influenza in the United States, April-July 2009</ArticleTitle>

Correcting errors in versioned citations

A versioned citation can be updated to correct errors when in status [PubMed – as supplied by publisher]. Create a Replaces file using <Replaces> tags but use the same VersionID as in the existing version that you are replacing. Do not assign a new VersionID.

Searching and retrieving using versions

Only the most recent version of a citation will be indexed and returned in a PubMed search. The content, e.g., author names, abstract terms, from previous versions will not be included in the PubMed indices. For example, if an author name has been removed from the author list in the most recent version, a PubMed search for that author name will not retrieve the citation. The prior version(s) of a citation are accessible via links on the abstract display of the most recent version.

Search for a specific version of a citation by entering a PMID.version (e.g., 20029611.1) in the PubMed search box. To search for multiple versions of a citation at once, use a Boolean OR (e.g., 20029611.1 OR 20029611.2). Search for all versions of a citation by entering the PMID followed by .* (e.g., 20029611.*) in the PubMed search box.

Retrieve a specific version by explicitly adding the version number after the PMID in the URL, e.g., https://www.ncbi.nlm.nih.gov/pubmed/20029611.1. Only a single version can be retrieved at a time using this method.

Dates

PubMed will set the DateCreated for the new version to the date the citation is added to PubMed. Versioned citations will follow the standard Entrez Date assignment rules.

Versioning and E-utilities

E-Search will only retrieve the latest version of a citation. E-Fetch can return a PMID.version.

FTP and File Submission

What is File Transfer Protocol (FTP)?

File Transfer Protocol (FTP) is a network protocol used to upload files from one computer to another computer via a network accessed by an FTP client. Most web browsers can be used as an FTP client, but many FTP clients are available for free download.

How do I submit files via FTP?

From a standard FTP client:

1.

At a command prompt type: ftp-private.ncbi.nlm.nih.gov and press enter.

2.

Type your login name at the login prompt and press enter. (Contact us to obtain a private FTP account.)

3.

Type your password at the password prompt and press enter.

4.

You should now be logged into the FTP server. If you receive an error message, check your login information, type "bye" followed by enter, and retry steps 1-3.

5.

Type "bin" and press enter. This changes your FTP server to BINARY mode.

6.

Type the "put" command, followed by your pathname or drive and filename and press enter. (For example, "put C:\filename" or "put /home/testfiles/journalv6n3".)

7.

Type "dir" and press enter to display the files in your FTP directory.

8.

Type "bye" to disconnect from the server and close the FTP session.

From a browser window:

1.

In the URL address box type in: ftp://ftp-private.ncbi.nlm.nih.gov and press enter.

2.

From the File pull-down menu, choose "Login As".

a.

If you are using Internet Explorer 7 then click on Page and choose "Open FTP Site in Windows Explorer". In the new window go to the File pull-down menu, choose "Login As".

3.

Type in your username and password in the dialog box. The screen will display your directory with an ‘archive’ folder inside.

4.

Add new files here at the top level of the directory. DO NOT put them in the ‘archive’ folder! They will automatically be placed there after processing.

How should filenames be constructed?

File names should be unique. We do not require a specific naming convention but suggest you include journal title abbreviation, volume, and issue, e.g., AJPv36i12.xml. The file name should not contain any spaces or UTF-8 character symbols (e.g. the letter a with an acute symbol) and not exceed 32 characters. We prefer files to be submitted in plain ASCII text format. However, we can accept the compressed file formats .tar, .zip, and .gz

How do I submit a sample XML file?

1.

Create a sample file based on the PubMed DTD. (See an Example of an XML file).

2.

Contact vog.hin.mln.ibcn@rehsilbup to request FTP login information.

3.

FTP the sample file to the ftptest directory on NCBI using login information.

4.

Send a notification email to publisher@ncbi.nlm.nih.gov using the following format:

Subject: TEST: full journal title

  • FILENAME:
  • TITLE:
  • ISSN:
  • VOLUME:
  • ISSUE:
  • URL: (if any)
  • PUBLISHER: Publisher for this journal
  • PROVIDER: Provider if different from Publisher. If you already have an FTP account with NCBI, enter it here. If not, enter the name of your organization.

How do I use the Citation Validator?

Use the PubMed Citation XML File Validator to validate your XML file before uploading it.

The Citation Validator has two options: input and upload. The size of your file determines which option is better for you.

  • The input option works best for files under 30KB. If you attempt to validate a file larger than 30KB using the input option, you may see a blank screen instead of results page.
  • The upload option is best for larger files (up to 8MB) and is recommended for final validation prior to uploading the file.

The Citation Validator uses a strict syntax. Errors in one part of a file will affect how the program validates the rest of the file. The best approach is to check the lines around an error, fix the syntax errors, and validate the file again.

Some notes about the results page when using the Citation Validator:

  • Files without errors will display the citations as they will appear in PubMed.
  • Files with errors will produce an error report displaying the error message and the line number in the file where the error occurs. Click on the error message to view the segment of your file containing the error.
  • Some common errors include:
    • The presence of an incomplete entity. All entities must begin with an ampersand (&) and end with a semi-colon (;).
    • The presence of a stand-alone ampersand (&). When an ampersand is not part of an entity, it must be represented by this entity: &amp;
    • The presence of a stand-alone less than (<) or greater than (>) symbol. When less than or greater than symbols are not part of XML tags, they must be represented by the entities &lt; and &gt; respectively.
    • The presence of extraneous spaces or line breaks within XML tags.
    • The header is incorrect. The header must always be:
<!DOCTYPE ArticleSet PUBLIC "-//NLM//DTD PubMed 2.7//EN" "https://dtd.nlm.nih.gov/ncbi/pubmed/in/PubMed.dtd">
  • If you receive the message: “ISSN not found in NCBI database: ISSN= Title=”, please contact vog.hin.mln.ibcn@rehsilbup for details regarding the indexing status of the title.

The validator error messages are designed to be self-explanatory and are the same as those in the loader report, which are found here. If you are having difficulty understanding the error messages, please contact the Data Provider Support Team [vog.hin.mln.ibcn@rehsilbup].

What is the archive subdirectory for?

Files are stored in the archive subdirectory after they have been loaded into PubMed. Do not place citation files in the archive subdirectory. They will not be loaded.

May I submit an incomplete issue and then send the additional issue citations at a later date?

No. Only submit files that include the complete set of citations for an issue. Incomplete issues can result in duplicate citations and require manual operations to correct. The only exceptions to this rule are citations for articles that are published electronically in advance of the print journal (Ahead of Print articles) or articles for Online-Only journals published individually. Details on sending Ahead of Print articles are available from the Ahead of Print page.

What types of articles are accepted for PubMed?

We require the submission of research articles, editorials, case studies, letters to the editor, errata and retraction notices, and substantive narrative reports of meetings.

We ask that you do not submit data for the following items: book reviews, advertisements, announcements, software and equipment reviews, and papers to appear in forthcoming issues. In addition, do not submit individual citations for abstracts or shortened versions of presentations or papers from conference proceedings unless the full-text of the article is published.

Understanding Loader Reports

I received the Loader Report, but I cannot find my citations in PubMed.

Publisher-supplied citation data are loaded five times a day: 5am, 8:30am, 12pm, 5pm, 8pm, Monday – Saturday, and 8pm on Sunday. New citations are available in PubMed the next morning.

Occasionally, because of technical problems, indexing of new citations may take several days. Email vog.hin.mln.ibcn@rehsilbup if the citations are not retrievable in 3-5 days.

How do I interpret the PubMed Loader Report?

Below is an example of a typical Loader Report. Email vog.hin.mln.ibcn@rehsilbup if you have not received the Loader Report within one business day of submitting your file.

Journal|Year|Volume|Issue|First Page|First Author|Article ID|PubMed ID

File GSEv40i3.xml(6 articles)

Genet Sel Evol|2008|40|3|241|Doeschl-Wilson AB|g07060|18400148

Genet Sel Evol|2008|40|3|265|Lee SH|g07054|18400149

Genet Sel Evol|2008|40|3|279|Ibanez-Escriche N|g07028|18400150

Genet Sel Evol|2008|40|3|295|Tarres J|g07027|18400151

Genet Sel Evol|2008|40|3|309|Pritchard T|g07035|18400152

Genet Sel Evol|2008|40|3|321|Cinkulov M|g07062|18400153

Total processed: 6 article(s), 6 were created.

Rejected articles in a Loader Report will often be annotated with error messages. Here is a list of possible error messages:

Cannot replace Article: Article does not have "[PubMed – as supplied by publisher]" status. The <Replaces> tag can only be used if the citation is ahead of print. Please see Correcting Errors in PubMed for more information.

Cannot find article by ID. The DOI or PII listed in the <Replaces> tag IdType attribute does not exist in a PubMed citation. Please verify that the DOI or PII is accurate. If necessary remove the <Replaces> tag and reload the file to create the article rather than ‘replace’ a non-existent PubMed citation.

Article matches PMID = , which is not in " [PubMed – as supplied by publisher] " status. This message means the data is already in PubMed and cannot be modified by a Replacement file.

ISSN not found in NCBI database: ISSN= Title= . There are two actions you can take in response to this: 1) Verify the ISSN is correct; 2) Confirm that you have notified the Data Provider Support Team of any recent title changes.

Not a current MEDLINE journal: ISSN= Title= . There are two actions you can take in response to this: 1) Verify the ISSN is correct; 2) Confirm that you have notified the Data Provider Support Team of any recent title changes.

Article matches PMID= To update use <Replaces> tag. Please refer to Instructions for Replacement Files for more information.

Cannot replace Article: PMID does not exist. NLM has deleted the PMID or you have provided an invalid PMID. Please refer to the "How do I determine if a PMID has been deleted?" question.

Wrong provider. Verify that you have received Approval from the Data Provider Support Team.

Partial match. Submitted citation matched an existing PubMed citation. Volume, issue, page and Article Id matched but there are differences in the author, title, or publication date tags.

Invalid Year / Invalid Month / Invalid Day. The message will specify whether the invalid date appeared in the PubDate tag within <Journal> or the PubDate tag within <History>. <Year> can only contain a 4-digit number between 1966 and the current year. <Month> can only contain the numbers 1-12, the month (in English) or the first three letters of the English months. NOTE: The only PubStatus attribute that allows for a dual month in <Month> is ppublish. <Day> can only contain the numbers 1-31.

Month tag is missing or empty; Day tag is present.

ISSN tag is missing or empty.

Both Volume and Issue tags are missing or empty. A valid file must contain a value in the Volume tag or the Issue tag, or both.

Replaces tag has invalid symbols or is empty. <Replaces> tag cannot be empty. Please refer to the Instructions for Replacement Files for more information.

FirstPage tag is missing or empty. In a <PubDate PubStatus ="ppublish" article the <FirstPage> tag cannot be empty.

FirstPage tag is missing or empty; LastPage is present. If an article is only one page in length the value should appear in the <FirstPage> tag not the <LastPage> tag.

FirstPage / LastPage tag has invalid symbols. Invalid symbols are anything other than letters or numbers.

Unknown Language. See our list of accepted language codes (Table 1).

Table 1: . The following is a subset of the ISO 639 standard for language codes.

Table 1:

The following is a subset of the ISO 639 standard for language codes.

FirstName / LastName / CollectiveName tag is missing or empty. Message will specify which Author tag the error occurred in. (Author 1, Author 2, etc.) If either the FirstName or LastName tag is present and contains text both must be present and contain text. If neither the FirstName nor LastName tag is present then the CollectiveName tag must be present and contain text.

FirstName / LastName contains invalid characters. Message will specify which Author tag the error occurred in. (Author 1, Author 2, etc.). The following are invalid characters:

! " # $ % & @ ( ) * + / ; : ` < = > ? ^ { | } [ \ ]

Ahead-of-print Article must have "pii" or "doi". See All About Ahead of Print for more details

Invalid Ahead of Print date. Ahead of Print files cannot have an electronic publication date greater than eighteen (18) months prior to the date of uploading to PubMed.

Cannot replace Article: Replacement file must use the original ArticleIds

Cannot replace Article: ArticleIds do not match. Contact LinkOut to change ArticleIds.

Bibliographic data does not match.

Non-indexable content: the citation was identified as being content not indexed for MEDLINE.

A rejected article or file will not necessarily produce an error message in the loader report. Some common errors that do not produce them are:

  • The presence of an incomplete entity. All entities must begin with an ampersand (&) and end with a semi-colon (;).
  • The presence of a stand-alone ampersand (&). When an ampersand is not part of an entity it must be represented by this entity: &amp;
  • The presence of a stand-alone less than (<) or greater than (>) symbol. When less than or greater than symbols are not part of XML tags they must be represented by the entities &lt; and &gt; respectively.
  • The presence of extraneous spaces and/or line breaks within XML tags.
  • The file or an article within the file was not formatted in accordance with PubMed specifications. Additional information on the required XML format is available in the PubMed DTD.

How do I determine if a PMID has been deleted?

For a list of all publisher-supplied citations that have ever been deleted, click here: ftp://ftp.ncbi.nlm.nih.gov/pubmed/deleted.pmids.gz

Citations are deleted from PubMed for one or more of the following reasons:

1.

The citation was verified as a duplicate citation.

2.

The NLM Indexing staff determined the citation was "non-indexable" material. The following are a few examples of "non-indexable" material: book reviews, advertisements, announcements, society calendars, software and equipment reviews, papers to appear in forthcoming issues, forwards, table of contents, and citations for articles not printed/published in full. Short reports, news items, letters and editorials are also subject to deletion.

PubMed XML Tagged Format

The XML tags are listed below followed by descriptions. This format is required for submission of citation and abstract data to PubMed. Only journals that are already approved for inclusion in PubMed should be submitted.

We encourage data providers to submit citation data in UTF-8 character encoding. For any special characters, we recommend referencing the PubMed Special Character Set to ensure that the appropriate encoding is used.

Links to the journal website, if available, may be submitted using LinkOut.

Section Contents

XML Tag Descriptions

The following is a glossary of the tags defined in the PubMed DTD. Click on each of the tag names below for more information. You can also view an Example of a Standard XML File.

Data Tags (R = Required, O = Optional O/R = Optional or Required). Tag names are case sensitive. Required tags must be included; optional tags must be included only if the data requested appears in the print or electronic article. Optional or Required tags are dependent on the use of other tags.

File Header (R)

The file header is the first line of the XML file that tells us the DTD information. It must appear in the PubMed XML files exactly as:

<!DOCTYPE ArticleSet PUBLIC "-//NLM//DTD PubMed 2.7//EN"
"https://dtd.nlm.nih.gov/ncbi/pubmed/in/PubMed.dtd">

You will be notified if this header changes.

ArticleSet (R)

This tag should enclose an entire set of articles in an issue or volume of a given journal.

Article (R)

Each article must be enclosed in these tags. Do not submit data for the following items: book reviews, advertisements, announcements, software and equipment reviews, and papers to appear in forthcoming issues. In addition, do not submit individual citations for abstracts or shortened versions of presentations or papers from conference proceedings unless the full-text of the article is published.

Journal (R)

Citation information about the journal issue is contained within this tag in the file.

PublisherName (R)

The publisher name.

JournalTitle (R)

The NLM Title Abbreviation for the journal. If you do not know the abbreviation, see the NLM Catalog.

Issn (R)

The ISSN or ESSN of the journal. An ESSN can be supplied if it exists in the journal’s NLM Catalog record. If you do not see the ESSN number in the Catalog, please write to vog.hin.mln.ibcn@rehsilbup, and we will have the number added to our records. Note that the ESSN must be a registered number.

Volume (O/R)

The volume name or number of the journal, including any supplement information, e.g., 12 Suppl 2, 514 (Pt 2), 19 Suppl A, etc. This tag is Required if the Issue tag is not present.

Issue (O/R)

The issue number, e.g., 4 Suppl 2, 6 Pt 2, 7-8, etc. This tag is Required if the Volume tag is not present.

PubDate (R)

The publication date information must be enclosed in the following tags. NOTE: Print or Electronic publication dates should accurately reflect the date format on the article. The PubDate tag includes the PubStatus attribute, which may contain only one of the following values:

  • ppublish - print-format (default value). With this value the PubDate must contain a Year tag and it could also contain a Month, Season, and/or Day tag. The tags used depend on how the date appears on the article.
  • epublish - electronic-format. With this value the PubDate must contain a Year, Month and Day tag that gives the exact date the article was publicly available in the final version.
  • aheadofprint - electronic-format without final citation information; to be followed later by a version with final citation information. With this value the PubDate must contain a Year, Month and Day tag that gives the exact date the article was first made publicly available. This PubStatus value plays an important part in the process of submitting Ahead of Print citations.

If the PubStaus attribute is not present it will default to ppublish.

Year (R)

The 4-digit year of publication. This tag must only contain a 4-digit year greater than or equal to 1966.

Month (O/R)

The month of publication. This tag may only contain the numbers 1-12, the month (in English) or the first three letters of the English months. NOTE: The only PubStatus attribute that allows for a dual month in <Month> is ppublish. This tag is Required if the Day tag is present.

Season (O)

The season of publication (do not use if a Month is available); ex: Winter, Spring, Summer, Fall.

Day (O)

The day of publication. This tag may only contain the numbers 1-31.

Replaces (O)

The identifier of the article that this one replaces. Do not use this tag for new articles. The <Replaces> tag can be used to update an Ahead of Print citation, or to correct an error in citations with [PubMed - as supplied by publisher] status. The Replaces tag includes the IdType attribute, which may contain only one of the following values:

  • pubmed - PubMed Unique Identifier (PMID) (default value)
  • pii - controlled publisher identifier
  • doi - Digital Object Identifier

See our Instructions for Replacement Files for more details.

ArticleTitle (O)

The article title, in English, if published in English or translated to English in the journal. Do not submit this tag if the published title is not in English or is not translated to English in the journal. See VernacularTitle.

VernacularTitle (O)

The article title in the original language, if not in English. Used only for Latin based alphabets. See our Instructions for Non-English Languages.

FirstPage (O/R)

The first page on which the article appears. If an article appears in more than one language with consecutive pagination, pagination should be inclusive of all texts. This tag is Required if ELocationID is not present.

LastPage (O)

The last page on which the article appears. If an article appears on one page, this is the same as FirstPage. If an article appears on non-consecutive pages this tag should still contain the last page on which the article appears. If an article appears in more than one language in the same issue, pagination should be inclusive of all the texts.

ELocationID (O/R)

The Electronic Location Identifier is used when an article does not have a FirstPage value OR to include the online location of the article. This tag is Required if FirstPage is not present. The ELocationID tag includes the EIdType attribute, which may contain only one of the following values:

  • pii - controlled publisher identifier
  • doi - Digital Object Identifier

The DOI will be displayed on the citation, alongside the journal, issue, and pagination information, and it should be supplied in the standard format, e.g., 10.xxx/xxx. Do not include any leading characters like “doi:” or submit the DOI as a URL.

Language (O)

The language in which the article is published. This should be chosen from the language codes (Table 1) in ISO 639. If unspecified, EN (English) is assumed. If an article appears in more than one language in the same issue, submit multiple language tags listed in the order in which the texts appear in the journal, not in the alphabetical order of the symbols. If one of the languages is English, enter EN first. See our Instructions for Non-English Languages.

AuthorList (O/R)

The author information must be enclosed in these tags. If a given article has one or more authors, this tag must be submitted. Authors should be listed in the same order as in the article, and author name format should accurately reflect the article. Do not use all upper case letters. This tag is Required if the Author tag is present.

Author (R)

Information about a single Author must begin with this tag.

FirstName (O/R)

The Author’s full first name is required if it appears in the print or online version of the journal. First initial is acceptable if full name is not available. This tag is Required if the LastName tag is present. To represent a Single Personal Author Name use the FirstName EmptyYN attribute value "Y".

MiddleName (O)

The Author’s full middle name, or initial if the full name is not available. Multiple names are allowed in this tag.

LastName (O/R)

The Author’s last name. This tag is Required if the FirstName tag is present.

Suffix (O)

The Author's suffix, if any, e.g. "Jr", "Sr", "II", "IV". Do not include honorific titles, e.g. "M.D.", "Ph.D.".

CollectiveName (O)

The name of the authoring committee or organization. CollectiveName can be used instead of or in addition to a personal name. A collective author name should be included by using the CollectiveName tag within an Author tag.

Affiliation (O)

The institution(s) that the author is affiliated with. You should submit affiliations for each author, collaborator and corporate author published in the article. Include the following data, if available: division of the institution, institution name, city, state, postal or zip code, country, e-mail address. Do not include the word 'e-mail'. Instructions for tagging authors with multiple affiliations is available here.

Identifier (O)

An author (personal or collective) or investigator’s author ID. The value in the Identifier attribute Source designates the organizational authority that established the unique identifier, e.g., ORCID. Please submit ORCID in the format: XXXX-XXXX-XXXX-XXXX.

GroupList (O/R)

Group information should be enclosed in these tags. If a given article has one or more Groups, this tag must be submitted. Groups should be listed in the same order as in the printed article, and Group name format should accurately reflect the article. This tag is Required if the tag Group is present.

Group (R)

Information about a single Group must begin with this tag.

GroupName (R)

The name of the authoring committee or organization.

IndividualName (O)

The name of individual members belonging to the authoring committee or organization. The name should be tagged with the FirstName, MiddleName, LastName, Suffix, and Affiliation tags.

PublicationType (O)

Used to identify the type of article. The available PublicationTypes are:

  • Addresses
  • Bibliography
  • Case Reports
  • Classical Article
  • Clinical Conference
  • Clinical Trial
  • Congresses
  • Consensus Development Conference
  • Consensus Development Conference, NIH
  • Corrected and Republished Article
  • Editorial
  • Festschrift
  • Guideline
  • Interview
  • Journal Article
  • Lectures
  • Letter
  • Meta-Analysis
  • News
  • Newspaper Article
  • Observational Study
  • Patient Education Handout
  • Practice Guideline
  • Published Erratum
  • Retraction of Publication
  • Review
  • Video-Audio Media
  • Webcasts

The default value, Journal Article, will be added to citations if this tag is left blank or an invalid PublicationType is used. Please submit only one PublicationType per citation.

ArticleIdList (O/R)

The list of Article Identifiers. This tag is Required if ArticleId is present.

ArticleId (R)

The Article Identifier. The ArticleId tag includes the IdType attribute, which may include only one of the following values for each identifier:

  • pii - controlled publisher identifier (default value)
  • doi - Digital Object Identifier

DOI in ArticleId is used to generate LinkOut links to the full-text and will also display at bottom of the citation.

DOI should be supplied in the standard format, e.g., 10.xxx/xxx. Do not include any leading characters like “doi:” or submit the DOI as a URL.

Click here for more information about Article Identifiers.

History (O)

The history of a publication (e.g., received, accepted, revised, published, ahead of print). Publishers may supply PubDates and PubStatus in History using the PubDate format detailed above. History PubDate is optional; however the PubDate within Journal, outlined above, is required. The History PubDate tag includes the PubStatus attribute, which may contain only one of the following values for each date in the publication history:

  • received - date manuscript received for review
  • accepted - accepted for publication
  • revised - article revised by publisher or author
  • aheadofprint - published electronically prior to final publication
  • epublish – published electronically
  • ppublish – published in print
  • ecollection – used for electronic-only journals that publish individual articles and later collect them into an “issue” date, typically called an eCollection.

The <History> tag plays an important part in the process of submitting Replacement Files for Ahead of Print citations.

Abstract (O)

The article’s abstract. Include all text as a single ASCII paragraph. Headings of structured abstracts, e.g., OBJECTIVE, DESIGN, etc. should be capitalized and end with a colon, followed by a space before the text, or tagged with the AbstractText element. Do not include citation information in the Abstract tag.

AbstractText (O)

This element can be used to submit structured abstract section headings. It can be placed within the Abstract or OtherAbstract elements and should have a Label attribute containing the structured abstract section heading.

OtherAbstract (O)

This tag can contain the article’s non-English abstract. OtherAbstract has a Language attribute, which should contain the two- or three-letter code (Table 1) for the language of the abstract, e.g., <OtherAbstract Language=”fr”>.

CopyrightInformation (O)

The Copyright information associated with this article.

CoiStatement (O)

The Conflict of Interest statement associated with this article.

ObjectList (O)

This tag contains a list of <Object>s and <Param>s.

Object (O)

The Object tag includes the Type attribute, which may include only one of the following values for each identifier. Sample XML for tagging database accession numbers is available here.

  • Keyword
  • Comment
  • Dataset
  • Erratum
  • Originalreport
  • Partialretraction
  • Patientsummary
  • Reprint
  • Republished
  • Retraction
  • Update
  • ANZCTR
  • BioProject
  • ClinicalTrials.gov
  • CRiS
  • CTRI
  • ChiCTR
  • DRKS
  • Dryad
  • EudraCT
  • Figshare
  • GDB
  • IRCT
  • ISRCTN
  • JapicCTI
  • JMACCT
  • JPRN
  • NTR
  • Omim
  • PACTR
  • PDB
  • PIR
  • RPCEC
  • ReBec
  • SLCTR
  • SwissProt
  • TCTR
  • UMINCTR
  • UniMES
  • UniParc
  • UniProtKB
  • UniRef
  • NCBI:dbgap
  • NCBI:dbvar
  • NCBI:genbank
  • NCBI:genome
  • NCBI:gensat
  • NCBI:geo
  • NCBI:homologene
  • NCBI:nucleotide
  • NCBI:popset
  • NCBI:protein
  • NCBI:pubchem-bioassay
  • NCBI:pubchem-compound
  • NCBI:pubchem-substance
  • NCBI:refseq
  • NCBI:snp
  • NCBI:sra
  • NCBI:structure
  • NCBI:taxonomy
  • NCBI:unigene
  • NCBI:unists

Param (O)

The Param tag includes the Name attribute, which may only include the below for the following values for each identifier:

  • id - Accession Number
  • value

Example of a Standard XML file

<!DOCTYPE ArticleSet PUBLIC "-//NLM//DTD PubMed 2.7//EN" "https://dtd.nlm.nih.gov/ncbi/pubmed/in/PubMed.dtd">
<ArticleSet>
<Article>
<Journal>
<PublisherName>American Society for Clinical Pathology
</PublisherName>
<JournalTitle>Am J Clin Pathol</JournalTitle>
<Issn>1943-7722</Issn>
<Volume>143</Volume>
<Issue>3</Issue>
<PubDate PubStatus="ppublish">
<Year>2015</Year>
<Month>03</Month>
</PubDate>
</Journal>
<ArticleTitle>A Modified Lynch Syndrome Screening Algorithm in
Colon Cancer: BRAF Immunohistochemistry Is Efficacious and Cost
Beneficial.</ArticleTitle>
<FirstPage>336</FirstPage>
<LastPage>343</LastPage>
<ELocationID EIdType="doi">10.1309/AJCP4D7RXOBHLKGJ</ELocationID>
<Language>EN</Language>
<AuthorList>
<Author>
<FirstName>Rachel</FirstName>
<MiddleName>M</MiddleName>
<LastName>Roth</LastName>
<Affiliation>Department of Pathology, The Ohio State
University Wexner Medical Center, Columbus</Affiliation>
</Author>
<Author>
<FirstName>Heather</FirstName>
<LastName>Hampel</LastName>
<Affiliation>Department of Human Genetics, The Ohio State
University Wexner Medical Center, Columbus</Affiliation>
</Author>
<Author>
<FirstName>Christina A</FirstName>
<LastName>Arnold</LastName>
<AffiliationInfo>
<Affiliation>Department of Pathology, The Ohio State
University Wexner Medical Center, Columbus</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>Department of Microbiology, The Ohio State
University Wexner Medical Center, Columbus</Affiliation>
</AffiliationInfo>
</Author>
<Author>
<FirstName>Martha</FirstName>
<MiddleName>M</MiddleName>
<LastName>Yearsley</LastName>
<Affiliation>Department of Pathology, The Ohio State
University Wexner Medical Center, Columbus</Affiliation>
</Author>
<Author>
<FirstName>William L</FirstName>
<LastName>Marsh</LastName>
<Affiliation>Department of Pathology, The Ohio State
University Wexner Medical Center, Columbus</Affiliation>
</Author>
<Author>
<FirstName>Wendy L</FirstName>
<LastName>Frankel</LastName>
<AffiliationInfo>
<Affiliation>Department of Pathology, The Ohio State
University Wexner Medical Center, Columbus</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>Department of Human Genetics, The Ohio State
University Wexner Medical Center, Columbus</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<PublicationType>Journal Article</PublicationType>
<ArticleIdList>
<ArticleId IdType="pii">j143/3/336</ArticleId>
<ArticleId IdType="doi">110.1309/AJCP4D7RXOBHLKGJ</ArticleId>
</ArticleIdList>
<History>
<PubDate PubStatus="received">
<Year>2014</Year>
<Month>09</Month>
<Day>30</Day>
</PubDate>
<PubDate PubStatus="accepted">
<Year>2014</Year>
<Month>10</Month>
<Day>14</Day>
</PubDate>
<PubDate PubStatus="aheadofprint">
<Year>2015</Year>
<Month>01</Month>
<Day>17</Day>
</PubDate>
</History>
<Abstract>
<AbstractText Label="OBJECTIVES">Somatic BRAF mutation in
colon cancer essentially excludes Lynch syndrome. We compared
BRAF V600E immunohistochemistry (IHC) with BRAF mutation in
core, biopsy, and whole-section slides to determine whether
IHC is similar and to assess the cost-benefit of IHC.
</AbstractText>
<AbstractText Label="METHODS">Resection cases (2009-2013)
with absent MLH1 and PMS2 and prior BRAF mutation polymerase
chain reaction results were chosen (n = 57). To mimic biopsy
specimens, tissue microarrays (TMAs) were constructed. In
addition, available biopsies performed prior to the resection
were available in 15 cases. BRAF V600E IHC was performed and
graded on TMAs, available biopsy specimens, and whole-section
slides. Mutation status was compared with IHC, and cost
benefit analysis was performed.</AbstractText>
<AbstractText Label="RESULTS">BRAF V600E IHC was similar in
TMAs, biopsy specimens, and whole-section slides, with only
four (7%) showing discordance between IHC and mutation
status. Using BRAF V600E IHC in our Lynch syndrome screening
algorithm, we found a 10% cost savings compared with
mutational analysis.</AbstractText>
<AbstractText Label="CONCLUSIONS">BRAF V600E IHC was
concordant between TMAs, biopsy specimens, and whole-section
slides, suggesting biopsy specimens are as useful as whole
sections. IHC remained cost beneficial compared with
mutational analysis, even though more patients needed
additional molecular testing to exclude Lynch
syndrome.</AbstractText>
</Abstract>
<CopyrightInformation>Copyright© by the American Society for
Clinical Pathology</CopyrightInformation>
<CoiStatement>The authors of this article and the planning
committee members and staff have no relevant financial
relationships with commercial interests to disclose.
</CoiStatement>
<ObjectList>
<Object Type="keyword">
<Param Name="value">BRAF</Param>
</Object>
<Object Type="keyword">
<Param Name="value">MLH1</Param>
</Object>
<Object Type="keyword">
<Param Name="value">Immunohistochemistry</Param>
</Object>
<Object Type="keyword">
<Param Name="value">Cost-benefit analysis</Param>
</Object>
</ObjectList>
</Article>
</ArticleSet>

Example of a Non-English XML file

<!DOCTYPE ArticleSet PUBLIC "-//NLM//DTD PubMed 2.7//EN"
"https://dtd.nlm.nih.gov/ncbi/pubmed/in/PubMed.dtd">
<ArticleSet>
<Article>
<Journal>
<PublisherName>Public Health Agency of Canada</PublisherName>
<JournalTitle>Chronic Dis Inj Can</JournalTitle>
<Issn>1925-6523</Issn>
<Volume>33</Volume>
<Issue>4</Issue>
<PubDate PubStatus="ppublish">
<Year>2013</Year>
<Month>Sep</Month>
</PubDate>
</Journal>
<ArticleTitle>Improved estimation of the health and economic burden
of chronic disease risk factors in Manitoba.</ArticleTitle>
<FirstPage>236</FirstPage>
<LastPage>246</LastPage>
<Language>EN</Language>
<Language>FR</Language>
<AuthorList>
<Author>
<FirstName>H</FirstName>
<LastName>Krueger</LastName>
<AffiliationInfo>
<Affiliation>School of Population and Public Health, University
of British Columbia, Vancouver, British Columbia,
Canada.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>H. Krueger &amp; Associates Inc., Delta, British
Columbia, Canada.</Affiliation>
</AffiliationInfo>
</Author>
<Author>
<FirstName>D</FirstName>
<LastName>Williams</LastName>
<Affiliation>H. Krueger &amp; Associates Inc., Delta, British
Columbia, Canada.</Affiliation>
</Author>
<Author>
<FirstName>A E</FirstName>
<LastName>Ready</LastName>
<Affiliation>Faculty of Kinesiology and Recreation Management,
University of Manitoba, Winnipeg, Manitoba,
Canada.</Affiliation>
</Author>
<Author>
<FirstName>L</FirstName>
<LastName>Trenaman</LastName>
<Affiliation>H. Krueger &amp; Associates Inc., Delta, British
Columbia, Canada</Affiliation>
</Author>
<Author>
<FirstName>D</FirstName>
<LastName>Turner</LastName>
<AffiliationInfo>
<Affiliation>Department of Community Health Sciences,
University of Manitoba, Winnipeg, Manitoba,
Canada.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>CancerCare Manitoba, Winnipeg, Manitoba,
Canada.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<PublicationType>Journal Article</PublicationType>
<Abstract>
<AbstractText Label="INTRODUCTION">There are analytic challenges involved with estimating the aggregate burden of multiple risk factors (RFs) in a population. We describe a methodology to account for overlapping RFs in some sub-populations, a phenomenon that leads to "double-counting" the diseases and economic burden generated by those factors.</AbstractText>
<AbstractText Label="METHODS">Our method uses an efficient approach to accurately analyze the aggregate economic burden of chronic disease across a multifactorial system. In addition, it involves considering the effect of body weight as a continuous or polytomous exposure that ranges from no excess weight through overweight to obesity. We then apply this method to smoking, physical inactivity and overweight/obesity in Manitoba, a province of Canada.</AbstractText>
<AbstractText Label="RESULTS">The annual aggregate economic burden of the RFs in Manitoba in 2008 is about $1.6 billion ($557 million for smoking, $299 million for physical inactivity and $747 million for overweight/obesity). The total burden represents a 12.6% downward adjustment to account for the effect of multiple RFs in some individuals in the population.</AbstractText>
<AbstractText Label="CONCLUSIONS">An improved estimate of the aggregate economic burden of multiple RFs in a given population can assist in prioritizing and gaining support for primary prevention initiatives.</AbstractText>
</Abstract>
<OtherAbstract Language="fr">
<AbstractText Label="TITRE">Meilleure estimation du fardeau que représentent les facteurs de risque de maladie chronique pour la santé et l’économie au Manitoba.</AbstractText>
<AbstractText Label="INTRODUCTION">L’estimation du fardeau global que représentent les facteurs de risque multiples au sein d’une population présente certains défis d’ordre analytique. Nous décrivons une méthodologie permettant de tenir compte des facteurs de risque se chevauchant dans certaines sous-populations et entraînant un « double compte » des maladies et du fardeau économique qu’ils engendrent.</AbstractText>
<AbstractText Label="MÉTHODOLOGIE">Notre démarche permet d’analyser avec précision le fardeau économique global des maladies chroniques dans un cadre multifactoriel tout en tenant compte de l’incidence du poids en tant qu’exposition continue ou polytomique (allant de l’absence d’excédent de poids au surpoids et à l’obésité). Nous appliquons cette méthode au tabagisme, à l’inactivité physique et au surpoids et à l’obésité à la province du Manitoba (Canada).</AbstractText>
<AbstractText Label="RÉSULTATS">En 2008, le fardeau économique global annuel des facteurs de risque au Manitoba était d’environ 1,6 milliard de dollars (557 millions pour le tabagisme, 299 millions pour l’inactivité physique et 747 millions pour le surpoids et l’obésité). Le fardeau total représente un rajustement à la baisse de 12,6% lorsqu’on tient compte de l’effet des facteurs de risque multiples chez certaines personnes.</AbstractText>
<AbstractText Label="CONCLUSION">Une meilleure estimation du fardeau économique global des facteurs de risque multiples au sein d’une population peut faciliter l’établissement des priorités et améliorer le soutien aux initiatives de prevention primaire. </AbstractText>
</OtherAbstract>
<ObjectList>
<Object Type="keyword">
<Param Name="value">population attributable fraction</Param>
</Object>
<Object Type="keyword">
<Param Name="value">risk factors</Param>
</Object>
<Object Type="keyword">
<Param Name="value">obesity</Param>
</Object>
<Object Type="keyword">
<Param Name="value">physical inactivity</Param>
</Object>
<Object Type="keyword">
<Param Name="value">tobacco smoking</Param>
</Object>
<Object Type="keyword">
<Param Name="value">chronic disease</Param>
</Object>
</ObjectList>
</Article>
</ArticleSet>

Example of an Ahead of Print XML file

<!DOCTYPE ArticleSet PUBLIC "-//NLM//DTD PubMed 2.7//EN"
"https://dtd.nlm.nih.gov/ncbi/pubmed/in/PubMed.dtd">
<ArticleSet>
<Article>
<Journal>
<PublisherName>Lancet Publishing Group</PublisherName>
<JournalTitle>Lancet</JournalTitle>
<Issn>1474-547X</Issn>
<Volume/>
<Issue/>
<PubDate PubStatus="aheadofprint">
<Year>2015</Year>
<Month>Feb</Month>
<Day>13</Day>
</PubDate>
</Journal>
<ArticleTitle>Hepatitis C.</ArticleTitle>
<FirstPage/>
<LastPage/>
<ELocationID EIdType="doi">10.1016/S0140-6736(14)62401-
6</ELocationID>
<ELocationID EIdType="pii">S0140-6736(14)62401-6</ELocationID>
<Language>EN</Language>
<AuthorList>
<Author>
<FirstName>Daniel P</FirstName>
<LastName>Webster</LastName>
<Affiliation>Department of Virology, Royal Free London NHS
Foundation Trust, London, UK.</Affiliation>
</Author>
<Author>
<FirstName>Paul</FirstName>
<MiddleName>P</MiddleName>
<LastName>Klenerman</LastName>
<Affiliation>National Institute for Health Research (NIHR)
Biomedical Research Centre and Nuffield Department of
Medicine, University of Oxford, Oxford,UK.</Affiliation>
</Author>
<Author>
<FirstName>Geoffrey M</FirstName>
<LastName>Dusheiko</LastName>
<Affiliation>Institute of Liver and Digestive Health,
University College London, London, UK.</Affiliation>
</Author>
</AuthorList>
<PublicationType>REVIEW</PublicationType>
<ArticleIdList>
<ArticleId IdType="pii">S0140-6736(14)62401-6</ArticleId>
<ArticleId IdType="doi">10.1016/S0140-6736(14)62401-
6</ArticleId>
</ArticleIdList>
<Abstract>Hepatitis C virus (HCV) infection is a major health problem worldwide. The effects of chronic infection include cirrhosis, end-stage liver disease, and hepatocellular carcinoma. As a result of shared routes of transmission, co-infection with HIV is a substantial problem, and individuals infected with both viruses have poorer outcomes than do peers infected with one virus. No effective vaccine exists, although persistent HCV infection is potentially curable. The standard of care has been subcutaneous interferon alfa and oral ribavirin for 24-72 weeks. This treatment results in a sustained virological response in around 50% of individuals, and is complicated by clinically significant adverse events. In the past 10 years, advances in HCV cell culture have enabled an improved understanding of HCV virology, which has led to development of many new direct-acting antiviral drugs that target key components of virus replication. These direct-acting drugs allow for simplified and shortened treatments for HCV that can be given as oral regimens with increased tolerability and efficacy than interferon and ribavirin. Remaining obstacles include access to appropriate care and treatment, and development of a vaccine. </Abstract>
</Article>
</ArticleSet>

Example of a Replaces XML file

<!DOCTYPE ArticleSet PUBLIC "-//NLM//DTD PubMed 2.7//EN"
"https://dtd.nlm.nih.gov/ncbi/pubmed/in/PubMed.dtd">
<ArticleSet>
<Article>
<Journal>
<PublisherName>Sage Publications</PublisherName>
<JournalTitle>Am J Hosp Palliat Care</JournalTitle>
<Issn>1938-2715</Issn>
<Volume>31</Volume>
<Issue>2</Issue>
<PubDate PubStatus="ppublish">
<Year>2014</Year>
<Month>Mar</Month>
</PubDate>
</Journal>
<Replaces IdType="doi">10.1177/1049909113482745</Replaces>
<ArticleTitle>Neuromodulation and palliative
medicine.</ArticleTitle>
<FirstPage>211</FirstPage>
<LastPage>219</LastPage>
<ELocationID EIdType="doi">10.1177/1049909113482745</ELocationID>
<Language>EN</Language>
<AuthorList>
<Author>
<FirstName>Howard S</FirstName>
<LastName>Smith</LastName>
<Affiliation>Department of Anesthesiology, Albany Medical
College, Albany, NY, USA.</Affiliation>
</Author>
<Author>
<FirstName>Julie G</FirstName>
<LastName>Pilitsis</LastName>
<AffiliationInfo>
<Affiliation>Center for Neuropharmacology and Neuroscience,
Albany Medical College, Albany, NY USA.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>Division of Neurosurgery, Albany Medical Center,
Albany, NY USA.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<PublicationType>JOURNAL ARTICLE</PublicationType>
<ArticleIdList>
<ArticleId IdType="pii">1049909113482745</ArticleId>
<ArticleId IdType="doi">10.1177/1049909113482745</ArticleId>
</ArticleIdList>
<History>
<PubDate PubStatus = "aheadofprint">
<Year>2013</Year>
<Month>3</Month>
<Day>26</Day>
</PubDate>
</History>
<Abstract>The palliative care population is generally vulnerable to experiencing medication-induced adverse effects and drug-drug interactions. Neuromodulation may offer particular advantages over systemic medications in this population. Spinal cord stimulation and peripheral nerve stimulation have long been utilized in efforts to provide analgesia for various painful conditions. More recently, deep brain stimulation/motor cortex stimulation has anecdotally been utilized for certain intractable pain states. Although brain electrical stimulation has not been adequately trialed or in some cases even tried at all for management of a variety of symptoms, it is conceivable that in the future it may be a potential therapeutic option in efforts to palliate various severe refractory symptoms (eg, intractable pain, nausea, dyspnea, delirium).</Abstract>
<ObjectList>
<Object Type="keyword">
<Param Name="value">brain</Param>
</Object>
<Object Type="keyword">
<Param Name="value">dyspnea</Param>
</Object>
<Object Type="keyword">
<Param Name="value">electrical</Param>
</Object>
<Object Type="keyword">
<Param Name="value">nausea</Param>
</Object>
<Object Type="keyword">
<Param Name="value">neuromodulation</Param>
</Object>
<Object Type="keyword">
<Param Name="value">pain</Param>
</Object>
<Object Type="keyword">
<Param Name="value">palliative care</Param>
</Object>
<Object Type="keyword">
<Param Name="value">stimulation</Param>
</Object>
</ObjectList>
</Article>
</ArticleSet>

Instructions for articles published in Non-English Languages

Here is an example of a non-English language citation:

Image publisherhelp-Image001.jpg

The [brackets] around the article title and the text "French" indicate the full-text of the article is in a language other than English. The French article title can be viewed by selecting the XML display for this citation in PubMed.

Publishers may submit abstracts in languages other than English. The non-English abstract text should be submitted within the <OtherAbstract> element. The Language attribute should contain the two- or three-letter code for the language of the abstract.

<OtherAbstract Language="it">Unroofed coronary sinus comprende un insieme di anomalie cardiache in cui la parete comune fra seno coronarico e atrio sinistro e parzialmente o completamente assente. La maggior parte dei casi e associata a un ritorno venoso sistemico anomalo, come la persistenza della vena cava superiore sinistra. La diagnosi di questa anomalia e importante per la prognosi del paziente, ma e spesso difficoltosa a causa dei segni clinici aspecifici. Qui illustriamo un caso di assenza completa del tetto del seno coronarico associato a persistenza della vena cava superiore sinistra, riscontrato durante un esame di tomografia computerizzata effettuato per ipertensione polmonare.</OtherAbstract>

Publishers submitting files for articles published in non-English languages often have specific questions about how to construct their XML files. Here are some guidelines for the submission of non-English articles. We also have a sample XML file for this type of article.

Tags involved

  • The <Language> tag should contain the two- or three-letter code for the language the article is in. If unspecified, EN (English) is the default code. See our list of Language Tag Codes (Table 1), a subset of the ISO 639 standard for language codes.
  • The <ArticleTitle> tag should contain the article title, in English, if published in English or translated to English in the journal. Do not fill this tag if the published title is not in English or is not translated to English in the journal.
  • The <VernacularTitle> should contain the article title in the original language, if not in English. It is used only for Latin based alphabets; articles in non-Latin alphabets should leave this tag blank.
  • The <OtherAbstract> should contain the non-English abstract text, if available.

Rules to Remember

  • When constructing XML files for citations published in non-English languages it is important to use the final/published version of the article as the authority on what citation data should be included in the file. If English translations for titles or abstracts are not in the article, do not include them.
  • Author Names and Vernacular Titles frequently contain special characters.
  • If the full text of an article appears in more than one language in the same issue, submit multiple language tags listed in the order in which the texts appear in the journal, not in the alphabetical order of the symbols. If one of the languages is English, enter EN first. For example, an article which appears full-text in both Chinese and English should be coded as:
<Language>EN</Language>                     <Language>ZH</Language>
  • If the full text of an article appears in one language, but the abstract appears in two or more languages, the <Language> tag should contain only the code for the language of the full-text article.
  • For articles that are published in multiple languages, the PubMed citation will display the various languages when the full translations are available at the original time of publication. An unlimited number of languages may display. PubMed data providers are responsible for including all appropriate languages as part of the XML citation data submitted to PubMed.

Some examples:

If the article contains...Your XML file should contain...
a title in Japanese characters and a title in Englishthe English title in the <ArticleTitle> tags and empty <VernacularTitle> tags
author names in Chinese characters onlyempty <Author> tags
Russian transliterated names and affiliationstransliterated names in the <Author> tags and affiliations in the <Affiliation> tags; however, you should check the transliterations against NLM's System of Transliteration and make changes if necessary.
an English abstract, but article title and author names in Cyrillic onlythe English abstract and transliterated Cyrillic in <ArticleTitle> and <Author> tags.

Indexing English Editions of Journals

It is customary for journals to be indexed from the original language of publication. The language to be indexed is approved by the Literature Selection Technical Review Committee at the time a journal is accepted for MEDLINE indexing.

For non-English MEDLINE journals that create a separately published English edition after being accepted for indexing, the English edition may be indexed in lieu of the non-English edition upon request from the publisher and approval by the Index Section. Content and coverage of the English edition must match the content and coverage of the language originally indexed.

Submit requests to index English editions of non-English MEDLINE journals to Deborah Ozga, Head, Index Section (vog.hin.liam@dagzo).

All About Ahead of Print

Publishers authorized to submit XML data to PubMed have the option of submitting citations prior to their publication in final or print format. This option is used for those publications in which the date of an article's electronic publishing predates publication in the journal issue or volume. When articles are first made available on a website (publishers’ or other), the publisher or provider sends the same citation data made available to the public for inclusion in PubMed.

Often these types of citations contain partial citation information--for example, they might contain an article title and full abstract, but not contain a volume, issue, or page number. This information is expected to be filled in by a Replaces XML file after the issue or volume has been finalized or printed. These incomplete citation records hold an [Epub ahead of print] status until updated data is sent to PubMed. See our Ahead of Print File Example and the Replacement File that updates it.

IMPORTANT: The Ahead of Print (AOP) mechanism must not be used for an article if its eventual publication is uncertain. In the rare case where an AOP citation is retracted, the citation information should remain on the publisher website. See our Ahead of Print Withdrawn policy

Here's an example of an AOP citation in PubMed:

Image publisherhelp-Image002.jpg

The notation [Epub ahead of print] labels this citation as incomplete. Note it does not display a volume number or issue number or page numbers, only a publication date.

Here's the same citation after being updated with a Replacement File:

Image publisherhelp-Image003.jpg

Steps for creating an Ahead of Print file

  • Construct an XML file according to the PubMed DTD, including all available citation information.
  • If Volume, Issue, FirstPage and LastPage are not known, these tags should be blank.
  • Add the electronic publication date to the <PubDate> tag, along with the PubStatus="aheadofprint" attribute. The electronic publication date must be an exact date, one that includes completed tags for Year, Month and Day. Articles using the "aheadofprint" PubStatus attribute that do not contain exact publication dates will be rejected from loading to PubMed. NOTE: The electronic publication date cannot be greater than 18 months prior to the month of uploading to PubMed.
  • Be sure to include an ArticleId in the file along with the appropriate ArticleId IdType attribute ("pii" or "doi"). This is REQUIRED of all AOP submissions. Click for more information about Article Identifiers.
  • Check your file for errors and preview the PubMed Abstract display using the PubMed Citation File Validator
  • FTP the AOP file to your private FTP account, placing it at the top of the directory.
  • Wait for a Loader Report confirming the loading of the AOP file. If the file loaded successfully, PMIDs will appear for each citation submitted.
  • Save the Loader Report until you are ready to update the citations; you may use the PMIDs for in the Replacement File.
  • When you are ready to update your AOP citations, follow our Instructions for Replacement Files.

Points to Remember

  • Please notify the Data Provider Support Team [vog.hin.mln.ibcn@rehsilbup] if you intend to begin using the Ahead of Print function. Once you begin sending AOP files, it is not necessary to notify us before each new delivery.
  • You can check your original AOP citations in PubMed using the query "pubstatusaheadofprint". For example, the search string Arch Microbiol[jour] AND 2015:2020[dp] AND pubstatusaheadofprint will retrieve all AOP citations with the journal title and dates indicated.
  • Citations in AOP status can be updated/revised as many times as necessary prior to the submission of the final Replacement file. Simply follow the steps above, but add the <Replaces> tag and keep the PubDate PubStatus attribute as "aheadofprint".

Instructions for Replacement Files

Updating Ahead of Print citations

Data providers may submit Replaces files to update an Ahead of Print (AOP) citation. The AOP citation will be replaced in its entirety.

AOP citations eventually become "published" citations by way of the publisher sending a Replacement XML file with completed citation information. These replacement files must use the PubStatus attribute value "ppublish" or "epublish" in the <PubDate> tag in order to replace the AOP citation.

Take the following steps to update an AOP citation:

  • Update the AOP citation file, adding the finalized citation information.
  • Add the final publication date to the <PubDate> tag, along with the PubStatus="ppublish" or "epublish" attribute. The publication date must be exactly as it appears on the finalized article.
  • "Move" the existing PubDate with PubStatus="aheadofprint" attribute to the <History> tag. This will enable the citation to retain the AOP publishing date in PubMed.
  • Add a single <Replaces> tag to each <Article> to be updated. The <Replaces> tags should be placed after the <Journal> tags and before the <ArticleTitle> tags, and should contain the IdType attribute with one of the following values: "pubmed" (default), "pii", "doi" of the citation to be updated.
  • Verify that the ArticleIdList (pii or doi) in the Replacement File matches the ArticleIdList in the AOP citation in PubMed. If these numbers do not match, the citation will not be updated.
  • Check the file for errors and preview the PubMed Abstract display using the PubMed Citation XML File Validator.
  • FTP the Replacement File to your private FTP account, placing it at the top of the directory.
  • Wait for a Loader Report confirming the loading of the Replacement File. Following the batch of articles is a "Total processed" message indicating the number of articles processed from the uploaded file and the number created, replaced, and rejected.

To correct an error in an AOP citation without changing its publication status:

1.

Correct the AOP citation file.

2.

Leave the PubStatus attribute as "aheadofprint".

3.

Add a single Replaces tag to the citation in which the error occurred. The Replaces tags should be placed after the Journal tags and before the ArticleTitle tags, and should contain the IdType attribute with one of the following values: "pubmed" (default), "pii", "doi" of the citation to be corrected.

4.

FTP the Replacement File to your private FTP account, placing it at the top of the directory.

5.

Wait for a Loader Report confirming the loading of the Replacement File. Following the batch of articles is a "Total processed" message indicating the number of articles processed from the uploaded file and the number created, replaced, and rejected.

Updating citations in any other status

We also accept Replaces files to update data in the following fields, regardless of the citation’s status in PubMed:

  • AuthorList (includes Author, Affiliation, Identifier)
  • InvestigatorList (includes Investigator, Affiliation, Identifier)
  • Pagination
  • ELocationID
  • OtherAbstract
  • PII
  • DOI

Although the update is targeted, the Replaces file should still be valid XML. Our loader will compare the content of the above fields in the Replaces file with the existing PubMed citation and only modify the content if it is different.

Ahead of Print Withdrawn Policy

On rare occasions a publisher may need to remove an Ahead of Print (AOP) article from a journal’s website. There are a variety of reasons for this type of withdrawal: plagiarism, copyright infringements, duplicate publication in another journal. PubMed understands that these circumstances cannot always be prevented before AOP citation data is uploaded to PubMed. Thus we have designed the following policy:

If an AOP article is removed completely from the journal’s website, the publisher should have a Replacement file uploaded to PubMed. The Replacement file should use the following format:

The text "WITHDRAWN:" (without quotation marks) should appear at the beginning of the original article title in the <ArticleTitle> tag.

The text "Ahead of Print article withdrawn by publisher." (without quotation marks) should be added at the beginning of the original text within the <Abstract> tag. If desired the original abstract text may be completely replaced with the above text. For additional reference, see our Instructions for Replacement Files.

Here's an example:

Image publisherhelp-Image004.jpg

If an AOP article is replaced on the journal’s website with a Retraction or Withdrawn Notice then the publisher should have a Replacement file uploaded to PubMed. The Replacement file should match the text of the Retraction or Withdrawn Notice on the journal's website.

Here's an example:

Image publisherhelp-Image005.jpg

Table 2:

Table 2:

Slavic Transliteration (1995)

Bookshelf ID: NBK3828