OpenEM Depositor of EM data to International Repositories

This repository provides a depositor app backend on top of SciCat frontend that allows users to seamlessly deposit their data to OneDep system. OneDep covers depositions to PDB end EMDB.

This depositor is designed for Swiss OpenEm project and supports only depositions to OneDep that are experimentally based on methods covered by Electron Microscopes.

Files necessary for a deposition:

OneDep defines an obligatory set of files required to create a deposition based on the specific method. Subsequently, same files are necessary for this depositor too.
Additionally, the user can provide an extra file with metadata that will be accepted by the depositor and appended to the deposition. This metadata file must be in json format and follow the OSC-EM schema supported by OpenEM. Once provided, this metadata will be automatically converted to mmCIF format accepted by OneDep. If deposition is destined to PDB, a new mmCIF file will be created containing both metadata and coordinates model provided by the user. For EMDB depositions a brand new mmCIF file will be created.

In OneDep user needs to manually provide the pixel spacing. Here user is not required to do it, as the headers definition of .mrc files provide this information.

pixel_spacing_{x/y/z} = cell_dimensions_{x/y/z} / sampling_unit_cell_{x/y/z}

Running a depositor

Running the container using Docker Compose

The Depositor service can be run in a docker container and be deployed using docker compose.

docker compose up -d

You would need to set an environmental variable SCICAT_FRONTEND_URL to allow the Depositor calls from your frontend. You can set this variable with .env file. Depositor is pre-configured to run on port 8080.

Depositor is using the SciCat frontend. SciCat Project promotes using a central environment for development - SciCatLive, which significantly simplifies the set up. There, frontend is configured to run on localhost:4200 port, but this can be changed. In this case the CORS setting of depositor need to be changed as well.

** From the frontend perspective only datasets, that have an OpenEm keyword, will get an access to the depositor backend and UI. **

REST API.definition based on OpenAPI v3.0 specs are available at /docs/index.html, once service is running.

Limitations

• depositions/onedep/config.go defined the base URL, to which requests will be sent to create deposition, add files and files metadata. Currently only a test server for OneDep is used. Once, the API is rolled out in the production (https://deposit-pdbe.wwpdb.org/deposition/ in Europe), this will then be changed.
• Additional Endpoint will be implemented to create deposition in EMPIAR for raw datasets. This is expected by March 2025, as described on our Project Timeline.
• Authorization with ORCID Id is not supported yet, requires a jwt token that needs to be created by user.