The PMC FTP Service may be used to download the source files for any article in the PMC Open Access Subset, associate PMC articles with identifiers such as: PubMed IDs, DOIs, Manuscript IDs, ISSN, etc., and can used as a source for data mining.

Source files from the PMC Open Access Subset

This FTP service may be used to download the source files for any article in the PMC Open Access Subset. The source files for an article may include:

1. A .nxml file, which is XML for the full text of the article, encoded in the NLM Journal Archiving and Interchange DTD.
2. A PDF file of the article.
3. Image files from the article, and graphics for display versions of mathematical equations or chemical schemes.
4. Supplementary data, such as background research data or videos.

The URL to access the FTP site is ftp://ftp.ncbi.nlm.nih.gov/pub/pmc

All the source files for an article are packaged in a single .tar.gz file. The FTP site has a two-level-deep folder (directory) structure. Folder names are randomly generated and the .tar.gz file for an article is randomly assigned to a second-level folder.

Finding Data in the File List (file_list.txt)

The file_list.txt file in the main FTP folder is an index of all the articles available from the site. The file is located at ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/file_list.txt. Each entry in the list consists of:

• The fully qualified name of the .tar.gz file for an article.
• The article citation:
  • journal title abbreviation
  • publication date
  • volume
  • issue
• The PMC accession number:
  • a unique, persistent ID for the article that can be used to display it in PMC

Sample entries: 08/dc/PLoS_Biol-2-9-490026.tar.gz PLoS Biol. 2004 Sep; 2(9):e259 pmcA490026 65/25/Nucleic_Acids_Res-33-7-1079965.tar.gz Nucleic Acids Res. 2005; 33(7):2129-2140 pmcA1079965

To display an article in PMC: Use the accession number, drop the "pmcA" prefix and append the rest of the number to the base URL: http://www.pubmedcentral.gov/articlerender.fcgi?artid= For example: To display PLoS Biol. 2004 Sep; 2(9):e259. Accession number: pmcA490026 (From the sample entries above) Use:  http://www.pubmedcentral.gov/articlerender.fcgi?artid=490026

To find an article from PMC on the FTP site: Copy the accession number (artid) from the PubMed Central URL by highlighting it in your browser's address bar and copying to the clipboard. Open the file file_list.txt, use the “find on this page” function (ctrl f), and paste (ctrl v) the artid into the “find on this page” dialogue box.

Obtaining DOIs and PubMed IDs for Articles in PMC

Use PMC-ids.csv.gz to associate PMC articles with a PMC ID, a PubMed ID, and the corresponding DOI.

PMC-ids.csv.gz is a comma separated file with the following fields:

• Journal Title
• ISSN
• Electronic ISSN
• Publication Year
• Volume
• Issue
• Page
• DOI (if available)
• PMC ID
• PubMed ID (if available)
• Manuscript ID (if available)

If the information is not available, entries will contain an empty space.

Format: Journal Title,ISSN,eISSN,Year,Volume,Issue,Page,DOI,PMCID,PMID,Manuscript Id Sample entries: Breast Cancer Res,1465-5411,1465-542X,2000,3,1,55, ,PMC13900,11250746, Breast Cancer Res,1465-5411,1465-542X,2000,3,1,61, ,PMC13901,11250747, Proc Natl Acad Sci U S A,0027-8424,1091-6490,2001,98,5,2132,10.1073/pnas.031581098,PMC30104,11226204, Proc Natl Acad Sci U S A,0027-8424,1091-6490,2001,98,5,2138,10.1073/pnas.051502898,PMC30105,11226205,

XML for Data Mining via FTP

The file articles.tar.gz contains XML (and only XML) files for ALL PMC open access articles. This was created for users who need PMC XML for data mining and processing purposes, but do not need PDFs, images, or supplementary data.

Suggested FTP Client Configuration

After a series of experiments using ftp clients with NCBI's ftp server, we've found that the configuration of ftp clients can seriously affect performance.

NCBI recommends setting the TCP buffer size to 32Mb.

For more information on FTP configuration, please see the US Department of Energy's Guide to Bulk Data Transfer over a WAN.

The contents of the PMC FTP site is normally updated once a day.

If you have questions or comments about the PMC FTP site, please write to oai@ncbi.nlm.nih.gov.