PubMed

Submitting Citation Data via FTP

Citation information must be provided to NLM via FTP.   To obtain an FTP account with NCBI, please send an e-mail to publisher@ncbi.nlm.nih.gov.  Publishers must submit sample records to NLM before participation begins. Only journals approved for inclusion will be accepted.

How to 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. (See how to obtain ftp account from NCBI.)
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.

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.

FTP procedure when testing a journal

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:

FTP procedure once a journal is approved for inclusion in PubMed

1. FTP the text file to NCBI, using the name and password sent to you. If you have lost your password, please send an e-mail.
2. All entries for a journal issue must be sent in the same file.
3. The file is read, parsed and added to PubMed. If the journal is in MEDLINE, the citation information is sent to the appropriate offices at the NLM for further processing, including the addition of MeSH terms.
4. If the file processed without error, it moved from the FTP directory to the archive subdirectory (folder) in your private account.  These files are retained for your reference purposes.  A Loader Report will be sent to you within 1-2 days of uploading the file.  If an error occurred in loading we will also send you an e-mail.

Important Notes on Files and File Names

• It is not necessary to send notification emails to the publisher team when uploading issues of journals that have been approved for XML delivery.
• All file names must be unique.  We do not require a specific naming convention but suggest you include journal title abbreviation, volume and issue, e.g., AJPv36i12.xml.
• The file name should not contain any spaces, 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
• If you think that a file you have sent us is bad, or if articles are missing from the file, consult our Correcting Errors in PubMed page.