File Submission Specifications: Delivery
On This Page:
1. 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 |
|
jour-vol-pg.ext | biotes-01-100.xml |
| PDF of Article |
|
jour-vol-pg.ext | biotes-01-100.pdf |
| Figures and Graphics |
|
jour-vol-pg-typ.ext |
biotes-01-100-g001.tif
biotes-01-100-g002.tif biotes-01-100-i002.eps biotes-01-100-e001.png |
| Supplementary Material |
|
jour-vol-pg-typ.ext |
biotes-01-100-s001.mpg
biotes-01-100-s002.doc biotes-01-100-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.
2. Naming ZIP 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 |
jour-vol-issue.ext | biotes-10-01.zip |
| Article-based
delivery package |
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.
- 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).
3. Revised or Corrected ZIP Files
Naming Revisions
- The name of the replacement article data files (.xml, .pdf, .tif, etc.) must be identical to the original (replaced) file names.
- Add the suffix .r1, .r2, .r3, and so on, to indicate the sequence of replacement to the file package name.
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.
- 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:
- You send the original files for “Biological Testing” volume 15,
issue 1 in a zip file named:
biotes-15-01.zip - Three days later, you send a revised XML file for one article, in a zip file
named:
biotes-15-01.r1.zip - Later that same day, you send replacement files for the same issue, in a zip
file named:
biotes-15-01.r2.zip - The next week, you make more corrections, and submit:
biotes-15-01.r3.zip
4. ZIP File Delivery
- Do not send files as attachments to an email message.
- To transfer ZIP files via FTP, write to pmc@ncbi.nlm.nih.gov 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)
- Address the email to: pmc@ncbi.nlm.nih.gov.
- When corrections involve 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 the US Department of Energy Guide to Bulk Data Transfer over a WAN.