XML

• How do I get started?
• Do online-only articles have different requirements?
• Can I submit multiple affiliations for one author?
• How should I submit citations for articles in languages other than English?
• How can I indicate equal contribution among authors?
• Can Collective Author Names be supplied to PubMed?
• Can Single Personal Author Names be supplied to PubMed?
• How should I submit mathematical or chemical formulas or tables in the Abstract tag?
• How do I use the  tag?
• How should I submit versioned citations?

FTP and File Submission

• What is File Transfer Protocol (FTP)?
• How do I submit files via FTP?
• How should filenames be constructed?
• How do I submit a sample XML file?
• How do I use the Citation Validator?
• What is the archive subdirectory for?
• May I submit an incomplete issue and then send the additional issue citations at a later date?
• What types of articles are accepted for PubMed?

Understanding Loader Reports

• I received the Loader Report, but I cannot find my citations in PubMed.
• How do I interpret the PubMed Loader Report?
• How do I determine if a PMID has been deleted?

FAQs

Correcting Errors in PubMed

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

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

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

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

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

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

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

Can Collaborator Names be supplied to PubMed?

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

Cancer Genome Center


North American Barley Genome Project




Cancer Genome Center

John
Smith


Mary
Jones



North American Barley Genome Project

John Jacob
Han


Laura
Clancy

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 section. Investigator names should be listed in the order in which they appear in the full-text article.

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

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

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

The accepted comment/correction types are:

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

Sample XML:

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

How should structured abstracts be submitted?

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

BACKGROUND: Approximately 3,000 new cases of oral cancer...

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

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

To assess the effects...
Patients attending lung...
Twenty-five patients...
The findings suggest...

Can I submit author keywords?

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

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

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

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

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

Can I submit grant information?

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

What is an Article Identifier?

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

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

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

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

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

How do I know if my journal is in PubMed?

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

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

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

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

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

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

These are the steps for a title change:

1.

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

2.

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

National Library of Medicine

Attn: Tina Shrader

Cataloguing and Metadata Services Section

Bldg 38, Room 1N08

8600 Rockville Pike

Bethesda, MD 20894-3823

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

What should do if my journal becomes electronic-only?

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

XML

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

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

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

Do online-only articles have different requirements?

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

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

Online-only articles may also have individual publication dates instead of a publication date for the complete Issue or Volume. In this case  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  tag should NOT have a PubStatus attribute and the  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  tag (E1) &  tag (E17).

If the XML file also included an  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  and  tags, but had an  tag, the PubMed display would be like so (if both  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:

10.1208/aapsj1001001 
aapsj1001001 

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

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

Can I submit multiple affiliations for one author?

Yes. Please see the following example:

FrankDavis

Department of Human Genetics, University of California, Los Angeles, California 90095, USA


Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, 08544, USA

How can I indicate equal contribution among authors?

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

Katherine
Anderson

Georgetown University



Edward
Scarborough

Mayo Clinic



Joanna
Kay

Georgetown University


 

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 tag within an tag.

Please see the following example:

 
 
W. 
Thomas 
Lawrence 
 
 
Plastic Surgery Educational Foundation DATA Committee 
 
 

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 tag within an tag. The default value for the EmptyYN attribute is "N"; indicating that the 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:

Matiullah


S.
Rehman

 

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

Simple formulas:

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

Complex formulas:

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

[Formula: see text]

[Table: see text]

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

How do I use the tag?

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

The  tag includes PubStatus attributes, which may contain only one of the following values for each datein the publication history:

Any PubDate in History must be an exact PubDate, one that includes valid values in the ,  and  tags.

The  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 tag and is later replaced using the "ppublish" attribute, we recommend that the publisher "move" the Ahead of Print date to the 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 can be used to tag the individual publication date of an online-only article.

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

How should I submit versioned citations?

What are versions?

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

How will versions be identified?

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

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

Required data elements

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

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

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

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

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

How to tag a new version

To submit new version of an existing PubMed citation, create an XML file using 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: