Article and Package Naming Delivery Specifications

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Naming Article Data Files

  • Names of image files and supplemental data files must match the names referenced in the XML file.
  • All file names must be unique within a volume.
  • XML and PDF base file names must match exactly.
  • “Zero-fill” volume and page numbers so that the same number of digits exists in every file.
  • Article Data Files should be packaged in a zip file. See Naming ZIP File Packages for guidance on how to name packages of article data files.
  • The name of any replacement article data files (.xml, .pdf, .tif, etc.) must be identical to the original (replaced) file names.
  • File names should not contain spaces.
File Use File Type Naming Scheme Examples
“Biological Testing” Vol. 10, Issue 01
Article XML Code XML jour-vol-pg.ext biotes-10-100.xml
PDF of Article PDF jour-vol-pg.ext biotes-10-100.pdf
Figures and Graphics TIFF EPS PNG jour-vol-pg-typ.ext biotes-10-100-g001.tif
biotes-10-100-g002.tif
biotes-10-100-i002.eps
biotes-10-100-e001.png
Supplementary Material MPG DOC CSV jour-vol-pg-typ.ext biotes-10-100-s001.mpg
biotes-10-100-s002.doc
biotes-10-100-s003.csv
  • jour is an identifier such as the alphanumeric journal abbreviation or ISSN.
  • vol identifies a specific journal volume.
  • pg is the first page of the article.
    • For articles that start on the same page, to make the file names unique, add a sequence letter (-a, -b, -c) to the end of the page number. Use sequence letter -a for the first article that starts on that page.
    • For electronic journals that assign each article a unique article sequence number (e-ID) in place of pagination, use this e-ID as the "first page".
  • typ is optional, and identifies one of the following:
    • -g figure graphic + alphanumeric identifier
    • -i inline graphic + alphanumeric identifier
    • -e equation + alphanumeric identifier
    • -s supplementary data file + alphanumeric identifier
  • ext is the lowercase file type extension.

Naming Compressed File Packages

Terms:

  • Collection-based: a publishing model in which an entire collection of articles is published and deposited at the same time, as a group, and typically has a single issue or volume.
  • Article-based: a publishing model in which articles are published and deposited individually, either as part of a volume or issue, or simply submitted article-by-article.

Accepted formats

  • PMC accepts .zip, .tar, .gz, and .tgz.
  • PMC does not accept bzip2 compressed .zip files.
  • PMC recommends using compression software that supports the Zip 2.0 standard file format.
  • If using WinZip PMC recommends using the Maximum (portable) compression option for compatability.
File Use File Type Naming Scheme Example
“Biological Testing” Vol. 10, Issue 01
(Article DOI: 10.000/bt.12345)
Collection-based
delivery package
ZIP
 ZIP
jour-vol-issue.ext biotes-10-01.zip
Article-based
delivery package
ZIP
 ZIP
jour-vol-issue-artid.ext biotes-10-01-bt.12345.zip
  • Article data files should be packaged in a .zip, .tar, .gz, or .tgz for delivery. PMC does NOT accept .rar packages.
  • PMC only supports a single level of file decompression. If there are nested compressed files within the compressed package, they will not be decompressed; they instead will be treated as unique supplementary files that must be referred to from within the XML.
  • Naming MUST be consistent across every submission.
  • jour is an alphanumeric identifier such as a journal abbreviation.
  • ext is the lowercase file extension .zip, .tar, .gz, or .tgz.
  • If articles are not organized into issues, the issue may be omitted from the package file name.
  • If the article is from a supplement, include the supplement number (as "suppl1", "suppl2", etc.) in the package name, in place of the issue.
  • For Article-based submission, artid is a unique identifier such as a DOI suffix. In the example the DOI is (10.000/bt.12345).
  • For Collection-based submission, include all files for an issue in the file package. Do not create separate subdirectories for each article inside the package.
  • Submit all article data files in the same package file, or create a separate package file for each class of files (XML, PDFs, Images, Supplemental Material).

Revised or Corrected File Packages

Naming Revision or Correction Packages

  • For each revision package sent to PMC, add a suffix .r1, .r2, .r3, and so on, to the file package name. This suffix indicates the sequence of replacements.
  • The names of the replacement article data files compressed in the package (XML, PDF, image files, etc.) must be identical to the original (replaced) file names.

Contents of Revision Packages

  • For journals in the evaluation stage: Please resubmit the entire set of files, which were previously submitted.
  • For journals that have passed the evaluation stage and are in production: Please resubmit only the files that have been modified, along with their corresponding XML files. Do NOT change the file names of the resupplied files, only change the package name to indicate a revision (see "Naming Revisions or Correction Packages" above.)
  • If submitting replacement files for multiple issues at the same time, use a separate package for each issue. Do not combine files for different issues or journals in the same package.

Example:

  1. You send the original files for “Biological Testing” volume 15, issue 1 in a zip file named:
    biotes-15-01.zip
  2. Three days later, you send a revised XML file for one article, in a zip file named:
    biotes-15-01.r1.zip
  3. Later that same day, you send replacement files for the same issue, in a zip file named:
    biotes-15-01.r2.zip
  4. The next week, you make more corrections, and submit:
    biotes-15-01.r3.zip

Package Delivery

  • Do not send files as attachments to an email message.
  • To transfer compressed files (zip, tar, gz, tgz) via FTP, write to your current PMC contact for an account on the PMC FTP site.
  • Send an email notification for each submission including:
    • Journal title
    • Volume
    • Issue
    • ZIP filename(s) and size(s)
  • When corrections involve citation information, such as author, title, volume, issue, doi, or publication date, please explicitly include what has been changed in the email notification.

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 NCBI's FTP README page..

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Last updated: Mon, 26 Oct 2015