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Metadata Standards
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Metadata Standards

The Metadata Standards work package contains the following tasks and components.

{% assign org_items = site.data.deliverables-wp.wp1 | 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.wp1 | 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

Metadata-Standards-1: Community consensus and commitment to data collection standards

  • Established the Open Standards Community for EM
  • Workshop 22-23 Feb 2024 with participants from facilities, software developers and repository curators.
  • Schema is now available for EM metadata. During the next milestones, metadata required for processing will be included by our collaborators and support for Material Sciences will be extended.
  • Schema terms are defined with respect to existing ontologies where available: CryoEM ontology, PDBx/mmCIF dictionary, Helmholtz EM Glossary, NeXus-FAIRmat NXem format.
  • Tools available for major instrument manufacturers and formats (Thermo Fisher EPU and SerialEM)
  • Ontologies are also coordinated with the PREMISE project

Metadata-Standards-2: Ensure streamlined and automatic metadata harvesting at all ETH sites

Metadata extraction tools for life sciences (LS-Metadata Reader) and material science (Metadata-Extractor)

Metadata-Standards-3: SciCat Dataset Ingestor

  • Fast data transfer using Globus (PSI) and S3 (ETHZ) to the archiver systems is available
  • Web-based UI for data ingestion is supported by SciCat/ GUI application. Instrument metadata is automatically extracted while user enters sample metadata and authorship
  • SciCat CLI was updated to a new version of SciCat backend