What is the difference between EMDB and EMPIAR?
The final 3D reconstruction from a single-particle, electron tomography or electron diffraction experiment can be deposited to EMDB. Image data related to EMDB entries, e.g., micrographs, particle-stacks and tilt-series can be deposited to EMPIAR. EMPIAR also supports the following experimental methods (taking image data and final reconstructions where available):
- 3D Scanning Electron Microscopy (3DSEM)
- Soft X-ray Tomography (SXT)
- 2D EM image data from integrative/hybrid modelling experiments
For these experimental methods we require that the data set is directly related to a publication or is a part of a community initiative, e.g. as benchmarking data.
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:
- Navigate to https://empiar.org using any one of the following browsers: Firefox, Chrome, Internet Explorer or Opera
- To use the web interface you will need to install Aspera Connect and a web browser plugin. If you have not already done so you will be presented with a link which will take you to the Aspera Connect installation site
- Once you have installed Aspera Connect and the browser plugin, you can download any of the datasets shown in the table by clicking on the corresponding download icon shown in column 1
- Instructions on downloading via a command line interface can be found here
- Instructions on downloading via Globus can be found here
- Instructions on downloading via ftp can be found here
How do I install the Aspera Connect client?
- Download Aspera Connect for the correct operating system
- On a Linux machine, you will either download a shell script or a .tar.gz file. If you have dowloaded the .sh file, download and excecute it. If you downloaded a .tar.gz file then unzip/untar the package and follow install instructions.
How do I download data using a command line interface?
- The Aspera copy command is installed by default in the ~/.aspera/connect/bin directory on Linux machines and in the ~/Applications/Aspera\ Connect.app/Contents/Resources directory on Macs. You will find the ascp program in this directory
- Download and install the Aspera Connect client if you have not done so already
- As an example, to download EMPIAR-10009, use:
Linux: ./ascp -QT -l 200M -P33001 -i ~/.aspera/connect/etc/asperaweb_id_dsa.openssh firstname.lastname@example.org:/10009 ~/Destination/path/10009
Mac: ./ascp -QT -l 200M -P33001 -i "/Users/<replace_your_username_here>/Applications/Aspera Connect.app/Contents/Resources/asperaweb_id_dsa.openssh" email@example.com:/10009 ~/Destination/path/10009
- By using the flag -k3 you can ensure that the source and destination files are compared based on full checksum when resuming partially transferred (incomplete) files. Note that computing full checksums of large files takes time, and heavily utilizes the CPU.
While this would increase the reliability of the transfer, please note that this could also reduce the overall speed of the transfer. A example of the command then would be:
Linux: ./ascp -QT -k3 -l 200M -P33001 -i ~/.aspera/connect/etc/asperaweb_id_dsa.openssh firstname.lastname@example.org:/10009 ~/Destination/path/10009
Mac: ./ascp -QT -k3 -l 200M -P33001 -i "/Users/<replace_your_username_here>/Applications/Aspera Connect.app/Contents/Resources/asperaweb_id_dsa.openssh" email@example.com:/10009 ~/Destination/path/10009
Do you have a small data set for testing downloads?
- The 58MB data set "test" is available for this purpose
- You can use the web interface or the command line interface (Linux: ascp -QT -l 200M -P33001 -i ~/.aspera/connect/etc/asperaweb_id_dsa.openssh firstname.lastname@example.org:/test testset)
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 user profile fields like 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, RAW FEI and BIG DATA VIEWER HDF5.
Under what license is EMPIAR data available?
All data in EMPIAR is freely and publicly available to the global community under the CC0 license (https://creativecommons.org/share-your-work/public-domain/cc0/).
How do I deposit data to EMPIAR?
What happens to my data after submission and when will it be released?
Pressing the "Submit" button sends the deposition for review by the EMPIAR annotation team. They will communicate with the depositor regarding any issues and may choose to unlock the deposition if complementary details or data are required. Once this process is completed, the entry will be released to the public following the instructions provided by the depositor.
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").
Can I upload/download data via Globus?
Yes! To download data use endpoint:
What is EMPIAR data model?
EMPIAR schema is described here. It consists of the main empiar.xsd XML schema file and additional requirements in empiar.sch in Schematron format.
Having trouble with transferring data?
Make sure that your Firewall does not block your transfer.
For Globus ensure that hx-gridftp-*.ebi.ac.uk addresses are whitelisted.
For Aspera you might need to modify the rules to accommodate the following:
permit TCP outbound to 220.127.116.11 on port 33001
permit UDP outbound to 18.104.22.168 on port 33001
permit UDP inbound from 22.214.171.124 on port 33001
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 email@example.com:/test testset
How do I contact EMPIAR team?
Send us a message!