Frequently-asked questions about EMPIAR


How do I download?

  • You can either download data using a web interface or via a command line interface
  • To download via the web interface:
  • Instructions on downloading via a command line interface can be found here

How do I download data using a command line interface?

  • Download using ftp command:
    As an example, to download EMPIAR-10009, use:
    $ ftp -i 
    Name ( anonymous
    ftp> cd pub/empiar/archive/10009/data
    250 Directory successfully changed.
    ftp> mget *
  • Download using rsync command:
    As an example, to download EMPIAR-10009, use:
    rsync -avz  10009
  • Download using Aspera ascp command:
    AsperaConnect or aspera cli must be installed in your computer. We have prepared the account "emp_ext" with the password"empiar-pdbj" to download EMPIAR by Aspera. As an example, to download EMPIAR-10009, use a following command.

    Linux (AsperaConnect)
    ascp -QT -k3 -l 200M -P33001 -i ~/.aspera/connect/etc/asperaweb_id_dsa.openssh 10009 
    *Input password: empiar-pdbj

    Linux (aspera cli):
    ascp -QT -k3 -l 200M -P33001 -i ~/.aspera/cli/etc/asperaweb_id_dsa.openssh 10009 
    *Input password: empiar-pdbj

    ascp  -QT -k3 -l 200M -P33001 -i "/Users/<replace_your_username_here>/Applications/Aspera" 10009 
    *Input password: empiar-pdbj

Do you have a small data set for testing downloads?

How are ORCIDs used in EMPIAR?

ORCID iDs are shown on entry pages for every author that has provided us with such during the deposition process. This allows a quick and easy way to access the list of the author's publications from Europe PMC search or directly from the author's ORCID profile page.

EMPIAR has now integrated ORCID into the deposition system. The user can sign in into the system using their ORCID account. This would automatically populate such user profile fields and ORCID iD, first and last names and email. Also, the user can automatically populate the deposition information fields using ORCID sign in with THOR project integration in EMPIAR.

What formats does EMPIAR support?

We provide image data in the formats in which they are uploaded. We recommend the use of common formats in the field including MRC, MRCS, TIFF, DM4, IMAGIC, SPIDER, MRC FEI and RAW FEI.

How do I deposit data to EMPIAR?

Send the media to Osaka or use the online deposition system in EBI. Start by checking the EMPIAR-PDBj page and online depotision manual.

How do I cite EMPIAR entries?

Please cite the original publication and cite the EMPIAR entry using the guidelines provided here

How do I cite EMPIAR?

We recommend that you follow the guidelines provided here

Can I selectively download files and directories for an entry?

Yes, EMPIAR entry pages offer three options - Aspera, download of a tarball via http, and download of individual files via ftp. The file browsers on the EMPIAR entry pages allow you to select files and sub-directories to be downloaded via Aspera or http. Aspera is the recommended option and can be used for any size of download. Please note that the download will be an as-is structure of the selected files and directories and not an archive (tar-ball)! The http download option will create a tarball that can be downloaded. This option only works for tarballs < 1.5GB. You can also download individual files (but not sub-directories) using Ftp (select "Browse Ftp").

Having trouble with transferring data?

Our web transfer interface has the target rate set to 200 000 Kbps and the policy to adaptive. Similarly, the command line displayed above. In case you are having issues with transferring data, it might help to reduce the target rate.

To do so, please use the command line transfer and change the value of '-l' parameter. For example: ascp -QT -l 10M -P33001 -i ~/.aspera/connect/etc/asperaweb_id_dsa.openssh testset

Please get in touch if the issue persists.