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Deposition in International Repositories
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Deposition in International Repositories

The Deposition in International Repositories work package contains the following tasks and components.

{% assign org_items = site.data.deliverables-wp.wp3 | where: "table", "org" %} {% if org_items.size > 0 %}

Organisational tasks

ID
Description
Status
{% for item in org_items %}
{{ item.id }}
{{ item.description }}
{{ item.status }}
{% endfor %}
{% endif %}

{% assign tec_items = site.data.deliverables-wp.wp3 | where: "table", "tec" %} {% if tec_items.size > 0 %}

Technical tasks

ID
Description
Status
{% for item in tec_items %}
{{ item.id }}
{{ item.description }}
{{ item.status }}
{% endfor %}
{% endif %}

Tasks

Deposition-1: Developing automated deposition tools for cryo-EM

To deposit biological specimen data, the European Bioinformatics Institute (EMBL-EBI) offers three central repositories relevant to Cryo-EM data. Early access to the testing version of OneDep API provides a method of depositing datasets to EMDB and PDB. OSCEM to mmCIF format converter is developed for metadata interoperability between OSCEM and OneDep PDBx/mmCIF syntax. A Web-based UI on top of SciCat allows for the upload of processed files to create OneDep depositions. Additional functionality will be added to the depositor to create depositions of raw datasets in EMPIAR.

Deposition-2: Expanding automated deposition tools for other EM disciplines

Compared to task 1 of this deliverable, there are no central repositories as those offered by EBI. We are exploring possible repositories for depositions and considering the following projects:

  • The NOMAD project lists data from EELS experiments and offers an API to interact with
  • Material Science Cloud offers an archiving solution in any format and enables integration with other services, such as built-in visualizations and workflow managers.
    During the next milestones, we will work on integrating deposition from SciCat to these repositories.