NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.

PubMed Help [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2005-.

Cover of PubMed Help

PubMed Help [Internet].

Show details

XML Help for PubMed Data Providers

Created: ; Last Update: August 7, 2014.

Publishers of journals indexed in MEDLINE are encouraged to submit citation and abstract data electronically for inclusion in PubMed. Electronic submissions ensure that citations and abstracts are available to the public within 48 hours of uploading a properly formatted XML file, and meets 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 & 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? Get started at the Data Provider Quick Start.

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

Data Provider Quick Start

XML

FTP and File Submission

Corrections and Loader Reports

LinkOut

  • How do I create links to the issues of my journal?

Frequently Asked Questions from Publishers

XML

How do I know if my journal is indexed in MEDLINE/PubMed?

There are a number of ways to determine if your journal is indexed in MEDLINE/PubMed. Search for your journal in the NLM Catalog and look for the “Current Indexing Status” field.

NLM also provides the following journal lists that are available by FTP:

Journals included in PubMed:Journals included in the Entrez molecular biology databases such as Nucleotide, Protein, and Genome:Journals in PubMed and the molecular biology databases:
UncompressedUncompressedUncompressed
GNU zipGNU zipGNU zip
UNIX CompressUNIX CompressUNIX Compress
PKZIPPKZIPPKZIP

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 selection. The Journal Selection for MEDLINE fact sheet describes the journal selection policy and criteria. The fact sheet includes information about the application process.

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. To access an editable plain-text template of the Standard XML file, click here.

Once you have finished editing the tags then validate the file; save the file (click here for tips on file names) and submit the sample XML file for review.

How do I submit citation and abstract data for online-only articles?

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. NOTE: NLM strongly recommends the use of the letter "E" or “e” when paginating online-only articles. (For example, pages E1-E12.) The “E-pagination” should appear in the <FirstPage> and <LastPage> tags in the XML files. We see using the "E" as a service to the users of PubMed, as many associate "E" page numbers with this special class of journals. Online-only articles that are paginated with a single page number per article (article 1, article 2), whether in the <FirstPage> or the new <ELocationID EIdType=”pii”> tag, are often mistaken by users as single page articles, not research articles of greater substance.

Online-only articles may also have individual publication dates instead of a publication date for the complete Issue or Volume. In this case the <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 an ESSN be supplied instead of an ISSN?

An ESSN, or electronic ISSN number, can be supplied in the <Issn> tag if the ESSN exists in the NLM Catalog. 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.

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 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 submit tags for Volume and Issue Supplements?

Use the following guidelines for Supplements:

Supplement 1 for Volume 6:

 <Volume>6 Suppl 1</Volume>
<Issue></Issue> 

Issue 4, Supplement 2 for Volume 7:

<Volume>7</Volume>
<Issue>4 Suppl 2</Issue> 

Issue 4 Pt 1 for Volume 7:

<Volume>7</Volume>
<Issue>4 Pt 1</Issue> 

Issue Part 3 for Volume 7 (it has Volume 7 Part 3 on the cover):

<Volume>7</Volume>
<Issue>Pt 3</Issue>

How should the Publication Date be submitted?

The Publication Date of a printed or electronic journal should be submitted in exactly the same format as appears on the cover of the printed issue or on the Table of Contents (ToC) page of journal website. Here are some examples:

   Issue cover/ToC display:  2008 May

<PubDate> 
<Year>2008</Year> 
<Month>May</Month> 
</PubDate> 

  

Issue cover/ToC display:  Fall 2008

<PubDate> 
<Year>2008</Year> 
<Season>Fall</Season> 
</PubDate> 

  

Issue cover/ToC display:  Dec 21 2008

<PubDate> 
<Year>2008</Year> 
<Month>Dec</Month> 
<Day>21</Day> 
</PubDate> 

  

Issue cover/ToC display:  2008

<PubDate> 
<Year>2008</Year> 
</PubDate> 

   Issue cover/ToC display: Nov-Dec OR November/December OR November-December 2008

<PubDate> 
<Year>2008</Year> 
<Month>Nov-Dec</Month> 
</PubDate> 

How should I submit citations to articles in languages other than English?

Citations to non-English articles should include the vernacular title and/or a translated English title, and may include the non-English abstract. The additional language view(s) of the abstract will be links on the Abstract display, with bold text indicating the language currently displayed. Users can click the language link to view the abstract in a different language. If a citation has only a non-English abstract, PubMed will not display an abstract by default, and users can select the non-English option. See our Instructions for Non-English Languages.

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.

Here is an example of a PubMed citation with a Collective Author Name (as well as an individual Author name):

Lawrence WT; Plastic Surgery Educational Foundation DATA Committee.
Arnica.
Plast Reconstr Surg. 2003 Sep 15;112(4):1164-6. No abstract available.
PMID: 12973238 [PubMed - indexed for MEDLINE]

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

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

Can Collaborators’ 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 Project</GroupName>
<IndividualName>
<FirstName>John</FirstName>
<LastName>Smith</LastName>
</IndividualName>
<IndividualName>
<FirstName>Jane</FirstName>
<LastName>Smith</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>

Please note that 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.

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> 

Should I submit author initials or full author names in my XML file?

Please submit author names exactly as they appear in the published article.

Full author names are searchable in PubMed using the [FAU] qualifier. See the PubMed Help for more details. Full author names can be viewed in two citation formats: XML and MEDLINE.

What information should be included in the Affiliation tag?

Please submit all affiliation information for authors, collaborators, and corporate authors published in the article.

Include the complete address information including city, state/province, and country, zip code, and email address, for example:

<Affiliation>
Division of Orthopedic Surgery, University of Wisconsin, 
312 Clinical Science Center, 600 Highland Ave., 
Madison, WI 53792, 
USA. smith@wisc.edu 
</Affiliation> 

Can I include position, degree, or honorific title in the <FirstName>, <LastName>, <MiddleName>, or <Suffix> tags?

No. Do not include titles or degrees because they will cause an incorrect author name to appear in the PubMed citation.

Can author IDs be supplied to PubMed?

Yes. PubMed accepts author ID information using the Identifier element. Identifier is an optional, possibly multiply-occurring element permissible within the Author (personal and collective) and Investigator elements. The value in the Identifier attribute Source designates the organizational authority that established the unique identifier.

We recommend data providers use one of the following organizational authorities in the Source attribute:

  • ORCID
  • ISNI
  • VIAF

Here is a sample section of an XML file using the Identifier element:

<AuthorList>
<Author>
<FirstName>John</FirstName>
<MiddleName>A</MiddleName>
<LastName>Smith</LastName>
<Affiliation>Stanford University</Affiliation>
<Identifier Source=”ORCID”>http://orcid.org/5555-5555-5555-5555</Identifier>
</Author>
</AuthorList>

How should abstract section headings 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. NLM will not perform QA on author keywords.

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 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 should be submitted with the intended characters, e.g. x2.

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 should I submit characters in Greek and other languages?

PubMed/MEDLINE has used an expanded character set since September 2010. NLM accepts for newly created MEDLINE citations any UTF-8 character in the Latin (Roman) and Greek scripts as well as mathematical and other symbols commonly found in biomedical literature. Other scripts such as Chinese, Japanese, or Korean are not supported.

Previously, NLM spelled out Greek letters, for example, replacing β (Unicode 03B2) with beta. PubMed users are now able to search for these characters either by copying and pasting the text or spelling out the letter as they always have done. Both approaches retrieve the same set of citations.

NLM will continue to standardize some characters:

  • All instances that represent a Double Quote will be translated to the straight double quote " (Unicode 0022).
  • All instances that represent a Single Quote (this includes prime and apostrophe) will be translated to the straight single quote ' (Unicode 0027).
  • Em Dash, En Dash, Hyphen, or Minus will be translated to the single dash - (Unicode 002D).

We encourage data providers to submit UTF-8 characters rather than SGML entities or Unicode character references.

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., http://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.

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 do I validate my XML file before uploading it?

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 2.6//EN" "http://www.ncbi.nlm.nih.gov/corehtml/query/static/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].

Does PubMed provide a citation matching service?

A citation matching service is available for publishers to obtain the PMIDs of the references in their articles and link these references back to PubMed.

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. You can also download different FTP clients depending on your needs.

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".

  • 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.

Note: If you receive a server error please try again 30 minutes later.

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.sgml. 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 with my citation data?

1.

Create a sample file based on the PubMed DTD. (See an Example of an XML file and an editable plain-text template of the Standard 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 letter to publisher@ncbi.nlm.nih.gov using the following format:

To: vog.hin.mln.ibcn@rehsilbup

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.

Note: Use a separate email notification for each journal title submitted for review.

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, and letters to the editor.

We ask that you do not submit data for the following items: book reviews, advertisements, announcements, erratum notices, 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. In most instances, NLM does create a single citation to cover a group of meeting abstracts or shortened versions of conference proceedings; for example, see PMIDs 12526142, 12516608, and 12516600.

Corrections and Loader Reports

How do I determine if a PMID has been deleted?

For a list of all PMIDs that have been deleted since October 2004 click here:

ftp://ftp.ncbi.nlm.nih.gov/pubmed/deleted_pmids.txt

This plain text file is updated every night at 10 PM EST. If a PMID is restored to PubMed, it will be removed from the file during the nightly update.

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, erratum notices, 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.

3.

The citation was identified as an incomplete issue. Data Providers who submit citations electronically to NLM for PubMed are required to upload citations to all articles in an issue on the same day unless otherwise specified. For example Ahead of Print citations are not required to be uploaded as a complete issue.

How do I correct an error in electronically submitted data?

An error found in a PubMed record can be corrected, but whether the correction can be made by the data provider depends on the publication status of the citation in question and whether the error also occurred in the original version of the article (print or online). Please see Correcting Errors in PubMed for more information.

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

Citations are usually indexed by noon of the next day. Occasionally, because of technical problems, indexing of new citations may take several days. Email vog.hin.mln.ibcn@rehsilbup if the articles 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.

 

Total processed: # article(s), # were created, # were replaced, # were rejected.

The report contains the filename (XGEv133i2.xml), followed by the number of citations in the file. This is followed by a listing of citations created with each citation containing the following fields: MEDLINE Title Abbreviation, Year, Volume, Issue, First Page, First Listed Author, Article ID (if present in the file), and PubMed Identifier (PMID). Following the batch of articles is a "Total processed" message indicating the number of citations processed from the uploaded file and the number created, replaced, and/or rejected.

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 currently in the "[PubMed – as supplied by publisher]" status. 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 2013. <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.

Abstract is too short. The text within the <Abstract> tags must be more than 50 characters in length. If the Article does not have an abstract then the <Abstract> tag should be left empty. The phrase "No Abstract Available" is not necessary in XML files.

Unknown Language. See our list of accepted language codes.

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

Table

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 can not 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.

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.  

Can the PubMed Loader Report be sent via FTP instead of email?

No. You may want to designate a special email address (or addresses) for the processing of your automatic Loader Reports.

LinkOut

PubMed XML Tagged Format

The XML tags are listed below followed by descriptions. Additional information on XML tagged format is available at the following websites: W3Schools, XML.com, and OASIS.

This format is required for submission of citation and abstract data to PubMed. Other formats are not accepted. Only journals that are already approved for inclusion in PubMed/MEDLINE should be submitted. See the Data Provider Quick Start for more information about journals indexed for MEDLINE.

If you wish to have non-ASCII characters in your citations you must use standard SGML entity names. It is not possible to keep a separate translation table for each publisher, given the number of possible non-ASCII characters.

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 2.6//EN"
"http://www.ncbi.nlm.nih.gov/corehtml/query/static/PubMed.dtd">

You will be notified if this header ever 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, erratum notices, 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. In most instances, NLM does create a single citation to cover a group of meeting abstracts or shortened versions of conference proceedings; for example, see PMIDs 18213900, 18062069, and 17956175.

Journal (R)

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

PublisherName (R)

The publisher name.

JournalTitle (R)

The MEDLINE abbreviation for the journal title. If you do not know the abbreviation, see the NLM Catalog.

Issn (R)

The ISSN or ESSN of the journal.

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., 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. This tag frequently contains special characters that need to be represented by SGML entities.

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

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.

See How do I submit citation and abstract data for Online-only articles? for more details.

Language (O)

The language in which the article is published. This should be chosen from the language codes 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 Authors’ 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". NOTE: This tag sometimes contains special characters that need to be represented by SGML entities.

MiddleName (O)

The Authors’ full middle name, or initial if the full name is not available. Multiple names are allowed in this tag. NOTE: This tag sometimes contains special characters that need to be represented by SGML entities.

LastName (O/R)

The Authors’ last name. This tag is Required if the FirstName tag is present. NOTE: This tag sometimes contains special characters that need to be represented by SGML entities.

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. NOTE: This tag sometimes contains special characters that need to be represented by SGML entities.

Affiliation (O)

The institution(s) that the Author is affiliated with. If a given article contains affiliations, this tag must be submitted. You should submit affiliations for each Author. These data should be provided as a simple string within the <Affiliation> </Affiliation> tags. The body of the affiliation should include the following data, if available, separated by commas: division of the institution, institution name, city, state, postal or zip code, country (use USA for the United States) followed by a period, then a space followed by the e-mail address which itself should not end in a period. Do not include the word 'e-mail'. NOTE: This tag sometimes contains special characters that need to be represented by SGML entities.

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. We recommend data providers use one of the following organizational authorities in the Source attribute: ORCID, ISNI, VIAF.

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. Do not use all upper case letters. 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 only available PublicationTypes are REVIEW, LETTER or EDITORIAL. The default value, JOURNAL ARTICLE, will be added to citations if this tag is left blank or an invalid PublicationType is used. Note: 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 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

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. All abstracts should be at least 50 characters in length. The PubMed DTD does not allow text formatting tags such as line breaks, italics, or bold. Do not include citation information in the Abstract tag. NOTE: This tag sometimes contains special characters that need to be represented by SGML entities.

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 for the language of the abstract, e.g., <OtherAbstract Language=”fr”>.

CopyrightInformation (O)

The Copyright information associated with this article. NOTE: This tag sometimes contains special characters that need to be represented by SGML entities.

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.

Keyword
SwissProt
Omim
PIR
PDB
ISRCTN
UniProtKB
UniParc
UniRef
UniMES
EudraCT
ANZCTR
ReBec
ChiCTR
CRiS
CTRI
RPCEC
DRKS
IRCT
JPRN
NTR
PACTR
SLCTR
GDB
Dryad
Figshare
BioProject
DDBJ/EMBL/GenBank
NCBI:protein
NCBI:nucleotide
NCBI:structure
NCBI:genome
NCBI:gensat
NCBI:geo
NCBI:homologene
NCBI:popset
NCBI:pubchem-bioassay
NCBI:pubchem-compound
NCBI:pubchem-substance
NCBI:refseq
NCBI:snp
NCBI:taxonomy
NCBI:unigene
NCBI:unists
NCBI:dbgap
NCBI:dbvar
NCBI:genbank
NCBI:sra

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

Follow the links for more information about each tag.

<!DOCTYPE ArticleSet PUBLIC "-//NLM//DTD PubMed 2.6//EN"
"http://www.ncbi.nlm.nih.gov/corehtml/query/static/PubMed.dtd">
<ArticleSet>
     <Article>
        <Journal>
            <PublisherName>Nature Publishing Group</PublisherName>
            <JournalTitle>Nature Chemical Biology</JournalTitle>
            <Issn>1552-4450</Issn>
            <Volume>4</Volume>
            <Issue>2</Issue>
            <PubDate PubStatus="ppublish">
                <Year>2008</Year>
                <Month>February</Month>
            </PubDate>
        </Journal>
        <ArticleTitle>High-content single-cell drug screening with
phosphospecific flow cytometry</ArticleTitle>
        <FirstPage>132</FirstPage>
        <LastPage>142</LastPage> 
  <ELocationID EIdType="pii">nchembio.2007.59</ELocationID> 
  <ELocationID EIdType="doi">10.1038/nchembio.2007.59</ELocationID>
        <Language>EN</Language>
        <AuthorList>
            <Author>
                <FirstName>Peter</FirstName> 
                <MiddleName>O</MiddleName>
                <LastName>Krutzik</LastName> 
          <Suffix>Jr</Suffix>
                <Affiliation>
Department of Microbiology and Immunology,
Baxter Laboratory in Genetic Pharmacology, Stanford University, 
269 Campus Drive, Stanford, California 94305, USA. 
                </Affiliation>
            </Author>
            <Author>
                <FirstName>Janelle M</FirstName>
                <LastName>Crane</LastName>
            </Author>
            <Author>
                <CollectiveName>Cancer Genome Project</CollectiveName>
            </Author>            
            <Author>
                <FirstName>Matthew R</FirstName>
                <LastName>Clutter</LastName>
            </Author>
            <Author>
                <FirstName>Garry P</FirstName>
                <LastName>Nolan</LastName>
            </Author>
            <Author>
                <CollectiveName>North American Barley
Genome Project</CollectiveName>
            </Author>            
        </AuthorList>
        <GroupList>
           <Group>
              <GroupName>Cancer Genome Project</GroupName>
                 <IndividualName>
                    <FirstName>John</FirstName>
                    <LastName>Smith</LastName>
                 </IndividualName>
                 <IndividualName>
                    <FirstName>Jane</FirstName>
                    <LastName>Smith</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>
        <ArticleIdList>
            <ArticleId IdType="pii">nchembio.2007.59</ArticleId>
            <ArticleId IdType="doi">10.1038/nchembio.2007.59</ArticleId>
        </ArticleIdList>
        <History>
            <PubDate PubStatus="received">
                <Year>2007</Year>
                <Month>06</Month>
                <Day>15</Day>
            </PubDate>
            <PubDate PubStatus="accepted">
                <Year>2007</Year>
                <Month>10</Month>
                <Day>30</Day>
            </PubDate>
            <PubDate PubStatus="aheadofprint">
                <Year>2007</Year>
                <Month>December</Month>
                <Day>23</Day>
            </PubDate>
        </History>
        <Abstract>
Drug screening is often limited to cell-free assays involving
purified enzymes, but it is arguably best applied against systems
that represent disease states or complex physiological cellular
networks. Here, we describe a high-content, cell-based drug
discovery platform based on phosphospecific flow cytometry, 
or phosphoflow, that enabled screening for inhibitors against
multiple endogenous kinase signaling pathways in heterogeneous
primary cell populations at the single-cell level. From a library
of small-molecule natural products, we identified pathway-selective
inhibitors of Jak-Stat and MAP kinase signaling. Dose-response
experiments in primary cells confirmed pathway selectivity, 
but importantly also revealed differential inhibition of cell
types and new druggability trends across multiple compounds. 
Lead compound selectivity was confirmed in vivo in mice. Phosphoflow
therefore provides a unique platform that can be applied throughout
the drug discovery process, from early compound screening to in
vivo testing and clinical monitoring of drug efficacy.
        </Abstract>
        <ObjectList>
            <Object Type="NCBI:pubchem-substance">
                <Param Name="id">46391334</Param>
            </Object>
            <Object Type="NCBI:pubchem-substance">
                <Param Name="id">46391335</Param>
            </Object>
            <Object Type="NCBI:pubchem-substance">
                <Param Name="id">46391336</Param>
            </Object>
         </ObjectList>
    </Article> 
    <Article>     
        <Journal>
            <PublisherName>Nature Publishing Group</PublisherName>
            <JournalTitle>Nature Chemical Biology</JournalTitle>
            <Issn>1552-4450</Issn>
            <Volume>4</Volume>
            <Issue>2</Issue>
            <PubDate PubStatus="ppublish">
                <Year>2008</Year>
                <Month>February</Month>
            </PubDate>
        </Journal>
        <ArticleTitle>Site selectivity of platinum
anticancer therapeutics</ArticleTitle> 
        <FirstPage>110</FirstPage>
        <LastPage>112</LastPage>
        <Language>EN</Language>
        <AuthorList>
            <Author>
                <FirstName>Bin</FirstName>
                <LastName>Wu</LastName>
                <Affiliation>
Division of Structural and Computational Biology,
School of Biological Sciences, Nanyang Technological University,
60 Nanyang Drive,Singapore 637551, Singapore. 
                </Affiliation>
            </Author>
            <Author>
                <FirstName>Peter</FirstName>
                <LastName>Dr&amp;ouml;ge</LastName>
            </Author>
            <Author>
                <FirstName>Curt A</FirstName>
                <LastName>Davey</LastName>
            </Author>
        </AuthorList>
        <ArticleIdList>
            <ArticleId IdType="pii">nchembio.2007.58</ArticleId>
            <ArticleId IdType="doi">10.1038/nchembio.2007.58</ArticleId>
        </ArticleIdList>
        <History>
            <PubDate PubStatus="received">
                <Year>2007</Year>
                <Month>06</Month>
                <Day>07</Day>
            </PubDate>
            <PubDate PubStatus="accepted">
                <Year>2007</Year>
                <Month>10</Month>
                <Day>26</Day>
            </PubDate>
            <PubDate PubStatus="aheadofprint">
                <Year>2007</Year>
                <Month>December</Month>
                <Day>23</Day>
            </PubDate>
        </History>
        <Abstract>
X-ray crystallographic and biochemical investigation
of the reaction of cisplatin and oxaliplatin with nucleosome core
particle and naked DNA reveals that histone octamer association can
modulate DNA platination. Adduct formation also occurs at specific
histone methionine residues, which could serve as a nuclear platinum
reservoir influencing adduct transfer to DNA. Our findings suggest
that the nucleosome center may provide a favorable target for the
design of improved platinum anticancer drugs. </Abstract>
</Article>
</ArticleSet>

Example of a Non-English XML file

<!DOCTYPE ArticleSet PUBLIC "-//NLM//DTD PubMed 2.6//EN"
"http://www.ncbi.nlm.nih.gov/corehtml/query/static/PubMed.dtd">
<ArticleSet> 
    <Article>     
        <Journal>
            <PublisherName>T&#252;rkiye Sinir ve Ruh
Sa&#287;l&#305;&#287;&#305; Derne&#287;i</PublisherName>
            <JournalTitle>Turk Psikiyatri Derg</JournalTitle>
            <Issn>1300-2163</Issn>
            <Volume>18</Volume>
            <Issue>1</Issue>
            <PubDate PubStatus="ppublish">
                <Year>2007</Year>
                <Season>Spring</Season>
            </PubDate>
        </Journal>
        <ArticleTitle>Case Report: Comorbid Anorexia Nervosa and
Schizophrenia in a
        Male Patient</ArticleTitle>
        <VernacularTitle>Olgu Sunumu: Bir Erkek Hastada
        Anoreksiya Nervoza ve &#350;izofreni
        E&#351;hastalan&#305;m&#305;</VernacularTitle>
        <FirstPage>87</FirstPage>
        <LastPage>91</LastPage>
        <Language>TR</Language>
        <AuthorList>
            <Author>
                <FirstName>Buket</FirstName>
                <LastName>Cinemre</LastName>
            </Author>
            <Author>
                <FirstName>Burak</FirstName>
                <LastName>Kulaks&#305;zo&#287;lu</LastName>
            </Author>
        </AuthorList> 
        <PublicationType>Journal Article</PublicationType>
        <ArticleIdList>
            <ArticleId IdType="pii">570</ArticleId>
        </ArticleIdList>
        <Abstract> Anorexia nervosa is a rare psychiatric disorder
        and epidemiological studies have shown a female to male
        ratio of 10:1, suggesting it is a disorder predominantly
        seen among females. The prevalence of anorexia nervosa
        comorbid with other psychiatric disorders has been reported
        to be quite high. Whereas depression and anxiety 
        disorders are the most common comorbid diagnoses in anorexic
        patients, the dual-diagnosis of anorexia and schizophrenia
        is a relatively rare condition. Based generally on the
        observations from single case reports or case series, 
        several explanations have been made about the
        co-occurrence ofanorexia and schizophrenia. Herein, 
        we present a male patient who developed schizophrenia
        after an anorexic period of 4 years that began when he
        was 14 years old with the decision to lose weight, which
        then progressed to a pattern of disordered eating and body
        image. This case is rare because the patient is male and
        has a comorbid diagnosis of anorexia nervosa and schizophrenia.
        To the best of our knowledge, there is only one previous
        case report in the literature describing a male anorexic
        patient comorbid schizophrenia. In this case presentation,
        the diagnosis of anorexia nervosa in males is addressed,
        the definition and significance of sub-threshold cases
        are discussed, and the comorbidity of anorexia nervosa
        and schizophrenia are reviewed in light of the literature.
        </Abstract>
    </Article> 
</ArticleSet>

Example of an Ahead of Print XML file

<!DOCTYPE ArticleSet PUBLIC "-//NLM//DTD PubMed 2.6//EN"
"http://www.ncbi.nlm.nih.gov/corehtml/query/static/PubMed.dtd">
<ArticleSet> 
    <Article>     
        <Journal>
            <PublisherName>AMERICAN SOCIETY FOR BIOCHEMISTRY AND
            MOLECULAR BIOLOGY</PublisherName> 
         <JournalTitle>J Biol Chem</JournalTitle> 
         <Issn>0021-9258</Issn> 
         <Volume></Volume> 
         <Issue></Issue> 
         <PubDate PubStatus = "aheadofprint"> 
           <Year>2008</Year> 
           <Month>December</Month> 
           <Day>3</Day> 
         </PubDate> 
       </Journal> 
       <ArticleTitle>Inhibition of Hepatitis C Virus NS2/3
       Processing by NS4A Peptides</ArticleTitle>
        <FirstPage></FirstPage>
        <LastPage></LastPage>
        <ELocationID EIdType="doi">
        10.1967/s002449910026
        </ELocationID>
        <Language>EN</Language>
        <AuthorList>
            <Author>
                <FirstName>John</FirstName> 
                <MiddleName>Jacob</MiddleName>
                <LastName>Smith</LastName> 
                <Suffix>Sr</Suffix>
         </Author> 
       </AuthorList> 
       <PublicationType>NEWS</PublicationType> 
       <ArticleIdList> 
         <ArticleId IdType="pii">s002449910026</ArticleId> 
         <ArticleId IdType="doi">10.1967/s002449910026</ArticleId> 
       </ArticleIdList> 
       <History> 
         <PubDate PubStatus="received"> 
           <Year>2007</Year> 
           <Month>November</Month> 
           <Day>20</Day> 
         </PubDate> 
         <PubDate PubStatus="accepted"> 
           <Year>2007</Year> 
           <Month>November</Month> 
           <Day>29</Day> 
         </PubDate> 
       </History> 
     </Article> 
     </ArticleSet>

Example of a Replaces XML file

<!DOCTYPE ArticleSet PUBLIC "-//NLM//DTD PubMed 2.6//EN"
"http://www.ncbi.nlm.nih.gov/corehtml/query/static/PubMed.dtd">
<ArticleSet> 
    <Article>     
        <Journal>
            <PublisherName>AMERICAN SOCIETY FOR BIOCHEMISTRY
AND MOLECULAR BIOLOGY</PublisherName> 
         <JournalTitle>J Biol Chem</JournalTitle> 
         <Issn>0021-9258</Issn> 
         <Volume>32</Volume>
         <Issue>1 Pt 2</Issue> 
         <PubDate PubStatus = "ppublish"> 
           <Year>2009</Year> 
           <Month>Jan-Feb</Month> 
         </PubDate> 
       </Journal> 
       <Replaces IdType="pubmed">10660634</Replaces> 
       <ArticleTitle>
       Inhibition of Hepatitis C Virus NS2/3
       Processingby NS4A Peptides
       </ArticleTitle> 
       <FirstPage>234</FirstPage> 
       <LastPage>234</LastPage> 
       <Language>EN</Language> 
        <AuthorList>
            <Author>
                <FirstName>John</FirstName> 
                <MiddleName>Jacob</MiddleName>
                <LastName>Smith</LastName> 
                <Suffix>Sr</Suffix>
         </Author> 
       </AuthorList> 
       <PublicationType>NEWS</PublicationType> 
       <ArticleIdList> 
         <ArticleId IdType="pii">s002449910026</ArticleId> 
         <ArticleId IdType="doi">10.1967/s002449910026</ArticleId>
       </ArticleIdList> 
       <History> 
        <PubDate PubStatus="received"> 
           <Year>2008</Year> 
           <Month>November</Month> 
           <Day>20</Day> 
         </PubDate> 
         <PubDate PubStatus="accepted"> 
           <Year>2008</Year> 
           <Month>November</Month> 
           <Day>29</Day> 
         </PubDate> 
         <PubDate PubStatus = "aheadofprint"> 
           <Year>2008</Year> 
           <Month>December</Month> 
           <Day>3</Day> 
         </PubDate> 
       </History> 
     </Article> 
     </ArticleSet>

SGML Data Entities for PubMed Submissions

Here is a list of commonly used SGML entities that can be used in XML files uploaded to PubMed. For each entity listed we have provided the hexadecimal UNICODE value, the translation as it will appear in PubMed, and the meaning. Though they are not listed, we also accept the decimal UNICODE values for the entities listed here. This is not a comprehensive list of accepted characters.

When creating your XML file, please keep in mind the following:

  • If it is possible to use an ASCII character to represent an entity, please use the ASCII character. For example, general punctuation such as quotation marks, colons, and number signs may be created with keyboard characters. Note that there are three exceptions to this rule: We require you to use an SGML entity instead of ASCII when creating an ampersand (&) [use &amp;], a less than symbol (<) [use &lt;], and a greater than symbol (>) [use &gt;] Where these three occur in tag names or entities, simply use the ASCII characters. For example:

                     Entities:
                     &uuml; NOT &amp;uuml;
                     &apos; NOT &amp;apos;

                     Tag Names:
                     <Month> NOT &lt;Month&gt;

                     Text:
                     [P &lt; 0.01] NOT [P < 0.01]

Image

Table

ISO Latin-1

Image

Table

ISO Latin-2

Image

Table

Publishing

Image

Table

General Technical

Image

Table

Fractions, Super/Subscripts, Punctuation

Image

Table

Greek Letters

Image

Table

Monotoniko Greek

Image

Table

Greek Symbols

Image

Table

Alternative Greek Symbols

Image

Table

Relations

Image

Table

Negated Relations

Image

Table

Arrows

Image

Table

Binary Operators

Image

Table

Added Math Symbols - Operators

Image

Table

Added Math Symbols - Relations

Image

Table

Russian Cyrillic

Image

Table

Non-Russian Cyrillic

Image

Table

Box and Line Drawing

Correcting Errors in PubMed

An error found in a PubMed record can be corrected, but whether the correction can be made by the publisher depends on the publication status of the citation in question and whether the error also occurred in the original version of the article (print or online).

Publishers can correct errors ONLY if the citation has the publication status [PubMed - as supplied by publisher]. Citations with the publication status [PubMed - in process], [PubMed - Indexed for MEDLINE], [PubMed] and [PubMed - OLDMEDLINE] can ONLY be corrected by NLM staff.

Errors that also appeared in the original version of the article cannot be corrected until an Erratum is issued in an upcoming issue of the journal. Please see NLM's Errata, Retraction, Duplicate Publication, and Comment Policy Fact Sheet for more information.

Correction Procedures for the different Publication Status Tags

All PubMed citations display a Publication Status Tag. There are five possible Publication Status Tags:

[PubMed - as supplied by publisher]

Image correct_pub.jpg

Citations in this stage appear exactly as the publisher provided them. Errors can be corrected by sending a revised file using the <Replaces> tags. Please see our Instructions for Replacement Files for details.

[PubMed - in process]

Image correct_process.jpg

Citations in this stage are in the process of data review at the NLM. Errors cannot be corrected with a Replacement File. If the error in the citation is correct in the print/online version of the article, it will likely be revised by NLM Indexers during this stage. Please allow a few months for the completed citation to appear in the database.

[PubMed - Indexed for MEDLINE]

Image correct_med.jpg

Citations in this stage have moved completely through the indexing process at NLM. Citation data has been quality assured and MeSH subject headings have been added to the records. Any errors found in citations at this stage should be reported to NLM's Customer Service department at vog.hin.mln@vrestsuc. Please use the Request for Correction format below when composing your message to Customer Service.

[PubMed]

Image correct_pubmed.jpg

See [PubMed - Indexed for MEDLINE] for correction procedures

[PubMed - OLDMEDLINE]

Image correct_old.jpg

See [PubMed - Indexed for MEDLINE] for correction procedures

See PubMed Help PubMed Citation Status Subsets for more information.

Correcting/Adding ArticleIds

Please read LinkOut Help Additional Information about Linking page for instructions on how to edit or add ArticleIds (PII or DOI) for the purpose of linking from PubMed to the full-text article.

Request for Correction Format

Please use this format when submitting a request for correction to vog.hin.mln@vrestsuc

To: vog.hin.mln@vrestsuc

Subject: REQUEST FOR CORRECTION

  • PMID:
  • TITLE:
  • ISSN:
  • VOLUME:
  • ISSUE:
  • URL: (if any)
  • PUBLISHER: Publisher for this journal
  • PROVIDER: XML data provider for this journal
  • TEXT: Current text
  • CORRECTION: Revised text
  • NOTE: Additional notes

Instructions for articles published in Non-English Languages

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

Image french.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>

Alternatively, publishers may indicate the availability of non-English abstracts on an external website without supplying the non-English abstract text to PubMed. This information will appear in brackets on the Abstract display, e.g., [Abstract available in French from the publisher]. Like the previous example, the Language attribute should contain the two- or three-letter code for the language of the abstract. Please see sample XML tagging below for a citation with a French abstract available at an external website.

<OtherAbstract Language="fr">Abstract available from the publisher.</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, 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. <ArticleTitle> and <Author> tags left blank in your XML file submission will be filled by the appropriate NLM staff when the citations are indexed for MEDLINE.
  • Author Names and Vernacular Titles frequently contain special characters. Use of UTF-8 characters is encouraged.
  • 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.
  • Articles in non-Latin alphabets can include transliterated author names. However, these names may be changed by Indexers based on NLM's System of Transliteration.
Image

Table

Slavic Transliteration (1995)

Some examples:

If the article contains... Your XML file should contain...
a title in Japanese characters and a title in English the English title in the <ArticleTitle> tags and empty <VernacularTitle> tags
author names in Chinese characters only empty <Author> tags
Russian transliterated names and affiliations transliterated 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 only the 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 aop.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 rep_aop.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. For example: if the Ahead of Print file is uploaded in the month of June 2005 then the electronic publication date within the file cannot be prior to December 2003.
  • 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 XML 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 2008:2020[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

Replacement Files can be used for two purposes: updating an Ahead of Print (AOP) citation or correcting a citation currently in [PubMed - as supplied by publisher] status.

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. See "How should the Publication Date be submitted?"
  • "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. The PubMed ID (PMID) can be located in the Loader Report or by searching for the article in PubMed.
  • 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.

For additional reference, see our Ahead of Print File Example and the Replacement File that updates it.

Error Correction Replacement File

Citations with the Publication Status Tag [PubMed - as supplied by publisher] can be corrected by uploading a revised file with <Replaces> tags.

Please note that the following steps are not effective if the citation with error has a Publication Status Tag other than [PubMed - as supplied by publisher]. See Correcting Errors in PubMed for more details.

These steps are also not appropriate if the error appeared in the original version of the article (whether print or online). Errors that were published in the original version must be corrected by issuing an Erratum; please see NLM's Errata, Retraction, Duplicate Publication, and Comment Policy Fact Sheet for more information.

Suppose an error existed in the following PubMed citation as a result of an error in the original XML file:

Image repl_ex.jpg

Take the following steps to correct the PubMed citation:

  • Correct the citation in the original file and delete the rest of the file.
  • Add <Replaces> tags 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", "pii", "doi" of the citation to be corrected.

    In the example above, the additional tag could look like this:

    <Replaces IdType="pubmed">17273292</Replaces>

    OR like this:

    <Replaces IdType="doi"> 10.1624/105812402X88669</Replaces>
  • Upload the Replacement File to your private ftp account.
  • Send an email to vog.hin.mln.ibcn@rehsilbup to notify us of the uploading of a Replacement File for error correction.
  • Wait for a new Loader Report confirming the loading of the Replacement File. If the file loaded successfully, the original PMID should appear on the new citation batch.
  • View revised citations in PubMed 1-2 days after receiving the Loader Report. If error does not appear to be corrected, contact vog.hin.mln.ibcn@rehsilbup

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 ret_aop.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 ret_aop_abs.jpg

Frequently Asked Questions from Publishers

How do I get my journal into PubMed?

Please see NLM’s Journal Selection Fact Sheet for details.

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: Wilma Bass

Bldg 38, Room 1N08

Catalogue Section

8600 Rockville Pike

Bethesda, MD 20894

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.

Why are my author replies not in PubMed?

Frequently, a published letter that NLM considers a comment will be immediately followed by a response written by the author(s) of the original article.

Author replies to commenting letters are cited separately and linked to the commenting letter and to the original article. Author responses published with "Reply," "Author Reply," or a similar non-distinctive title will have their titles amended to include the PMID of the commenting letter in the format "Author Reply: To PMID 12345678."

Please note: for journals with a publication date of 2012 or earlier, author replies were not cited separately but had their pagination included in the pagination of the commenting letter. For more details, please refer to the NLM Fact Sheet.

Requirements for electronic-only journals indexed for MEDLINE

NLM updated its policy regarding electronic journals indexed in MEDLINE in 2011. Initially, the updated policy applies to electronic-only journals approved for inclusion in MEDLINE and journals currently indexed in MEDLINE that have switched or will switch to an electronic-only publishing model.

There are 3 required conditions that electronic-only journals must meet in order to be indexed in MEDLINE:

1.

Provide NLM with XML-tagged data of its bibliographic citations.

2.

Provide robust current access to all its content under a license allowing efficient support of NLM operations, onsite services, and interlibrary loan.

3.

Have an acceptable arrangement for permanent preservation of, and access to, the published content.

The preferred means for a journal to satisfy conditions 2 and 3 is to deposit all its content in PMC under a full participation agreement.

If a journal chooses not to participate in PMC, it may satisfy conditions 2 and 3 by doing both of the following:

1.

Provide NLM with immediate access to its content at a publisher or third-party site under a license that allows efficient support of NLM operations, onsite services, and interlibrary loan (without delivery method or geographic restrictions).

2.

Promptly deposit tagged, full-text content in a certified third-party repository able to provide robust access to NLM and NIH if there is a trigger event. See the CRL Certification and Assessment of Digital Repositories page for the current list of certified repositories.

Additional information on the policy is available from the FAQ: MEDLINE Indexing Requirements for Electronic Journals.

Bookshelf ID: NBK3828