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Data Provider Journal Submission FAQs

Last Updated: April 25, 2007

FTP and File Submission


XML


Corrections and Loader Reports


LinkOut

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


FTP and File Submission

What are the procedures I need to follow for indexing my journal in MEDLINE?

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 submit files via FTP?

From a standard FTP client:

  1. At a command prompt type: ftp-private.ncbi.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. At the command prompt type: ftp://ftp-private.ncbi.nih.gov and press enter.
  2. From 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.

For more information on submitting files, see our page Submitting Citation Data via FTP .

How should filenames be constructed?

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. a with an accute symbol) and not exceed 32 characters.

How do I submit a sample XML file with my citation data?

  1. Create a sample file based on the PubMed DTD.
  2. Contact publisher@ncbi.nlm.nih.gov 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: publisher@ncbi.nlm.nih.gov

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 account at NCBI enter it here. If not, enter the name of your organization.

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

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.

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 in this documentation. Details on submitting articles for Online-Only journals can be found in the document Properly Coding Print, Electronic and Ahead of Print Articles

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.

XML

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 Abstract section headings be submitted?

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

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

What information should be included in the Affiliation field?

Submit the complete address information including city, state/province, 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>

Affiliation data for the first author only will be displayed in PubMed.

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 page of journal website. Here are some examples:

   Issue cover display:  1999 May

   Submit:  <PubDate>
                      <Year>1999</Year>
                      <Month>May</Month>
                  </PubDate>

   Issue cover display:  Fall 2001

   Submit:  <PubDate>
                      <Year>2001</Year>
                      <Season>Fall</Season>
                  </PubDate>

   Issue cover display:  Dec 21 2001

   Submit:  <PubDate>
                      <Year>2001</Year>
                      <Month>Dec</Month>
                      <Day>21</Day>
                  </PubDate>

   Issue cover display:  2001

   Submit:  <PubDate>
                     <Year>2001</Year>
                 </PubDate>

   Issue cover display: Nov-Dec OR November/December OR November-December 2003

   Submit:  <PubDate>
                    <Year>2003</Year>
                    <Month>Nov-Dec</Month>
                    </PubDate>

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 interpretation by the processing program.

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

Citations to non-English articles should include the vernacular title and a translated English title. Only English abstracts are included in PubMed. Do not submit an abstract if an English language abstract is not published with the journal article. See our Instructions for Non-English Languages.

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 <sup> or <inf>, for example sin(x<sup>2</sup>/2).

Complex formulas:

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

[Formula: see text]
[Table: see text]

What is anArticle 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 Identification, 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/.

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.

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 Fourndation 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 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>
<Author>
<FirstName EmptyYN="N">S.</FirstName>
<LastName>Rehman</LastName>
</Author>
<Author>
<FirstName EmptyYN="N">N.</FirstName>
<LastName>Mati</LastName>
</Author>
<Author>
<FirstName EmptyYN="N">S.</FirstName>
<LastName>Ahmad</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 printed article.

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

Can an ESSN be supplied instead of an ISSN?

An ESSN, or electronic ISSN number, can be supplied in the <Issn> tags if the ESSN resides in our NLM Catalog. If you do not see the ESSN number in the database, please write to publisher@ncbi.nlm.nih.gov and we will have the number added to our records. Note that the ESSN must be a registered number.

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">

Any PubDate in History must be an exact PubDate, one that includes completed tags for Year, Month and Day.

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 electronic publish date in PubMed. For more details, see our All About Ahead of Print page.

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

If this is the first time Online-only articles have been released for the title then contact us at publisher@ncbi.nlm.nih.gov 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.

Also read our Properly Coding Print, Electronic and Ahead of Print Articles documentation.

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 of course 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 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 our Correcting Errors in PubMed page 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. Contact us at publisher@ncbi.nlm.nih.gov 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. Contact us at publisher@ncbi.nlm.nih.gov 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 XGEv133i2.xml (7 articles, data format - ncbi) :


 

J Exp Psychol Gen|2004|133|2|139|Rothermund K|2004-14313-001|15149248
J Exp Psychol Gen|2004|133|2|166|Sloutsky VM|2004-14313-002|15149249
J Exp Psychol Gen|2004|133|2|189|Kane MJ|2004-14313-003|15149250
J Exp Psychol Gen|2004|133|2|218|Logan GD|2004-14313-004|15149251
J Exp Psychol Gen|2004|133|2|237|Sedek G|2004-14313-005|15149252
J Exp Psychol Gen|2004|133|2|261|Rinkenauer G|2004-14313-006|15149253
J Exp Psychol Gen|2004|133|2|283|Balota DA|2004-14313-007|15149254
 

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

The report contains the filename (XGEv133i2.xml), followed by the number of articles in the file. This is followed by a listing of articles created with each article 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 articles 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 our Correcting Errors in PubMed documentation for more information.

Article matches PMID = , which is not in “[PubMed – as supplied by publisher]” status This message means the data is already in PubMed and it can not 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 the Instructions for Replacement Files documentation for more information.

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

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 4-digit ranging between 1966 and 2010. <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 documentation 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.

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 our page “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

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

To create links you must participate in LinkOut.  LinkOut is a feature of Entrez where third parties provide information to link specific Entrez records to relevant Web-accessible online resources such as full-text publications, molecular biology databases, consumer health information, research tools, and more.  Typically, publishers or full-text providers use LinkOut to provide links from PubMed citations to their full-text journals available on the Web.

See the LinkOut documentation for additional information.

Go back to Information for Publishers re: XML Tagged Data