UFZ Data Infrastructure

The Helmholtz Centre for Environmental Research (UFZ) operates a set of digital infrastructures covering the research data life cycle, from collection to long-term archiving and publication. Some are general-purpose and used across research groups; others serve specific domains such as biodiversity or ecotoxicology. Below they are grouped by function rather than by owning unit. Detailed, how-to level documentation for these infrastructures is maintained in the UFZ RDM Guidelines.

UFZ's SDI (spatial.IO) combines several components into automated workflows for storing, managing and delivering geospatial (vector, raster, time-series) data:

Weber, C., Lange, R., Biskamp, B., Panda, M., Schnicke, T., & Bumberger, J. (2026). spatial.IO – An integrated cloud-ready geospatial data management system (v1.0.1). Zenodo. https://doi.org/10.5281/zenodo.10391523

• S3 storage – cloud object storage, the common backend also used by time.IO and OMERO
• GeoServer – OGC web services (WMS, WCS) including NetCDF support
• THREDDS Data Server – OPeNDAP access to gridded/raster data
• WebGIS – browser-based map viewer built on the OGC SensorThings API and PyGeoApi
• GeoNetwork – the metadata catalogue; also UFZ's entry point for connecting to external metadata federations (see below)

• time.IO – time series management: automated sensor data collection, standardized exchange protocols, quality control. Data is ultimately published via spatial.IO; PIDs are handled via the SMS.
• Sensor Management System (SMS) – manages sensor metadata and controlled vocabularies; currently the only infrastructure that captures PIDInst identifiers for instruments.
• SaQC – quality control toolkit for numerical/time-series data, used across the time series infrastructure.
• Grafana – dashboards for time series data.

• Data Management Portal (DMP) / Data Investigation Portal (DRP) – administers logger data, sample and analysis data, and cultivation data; the archive component is UFZ's route to DataCite DOI registration for research data (UFZ has been a member of the TIB DOI Consortium since 2021).
• Labspace – electronic lab notebook (ELN) with sample and inventory management, successor to eLabFTW.

• OMERO – stores, visualizes, manages and annotates microscope images and their metadata; uses S3 as its storage backend.

• BioMe – modular web platform supporting citizen science projects in biodiversity; several older UFZ biodiversity tools/projects (TMD, BiolFlor, LEGATO, ALARM) now live under it.
• BEXIS2 – manages biodiversity researchers' data across the full life cycle, from collection to sharing and publication.
• INTOB – database and web application for toxicological effects of chemicals on organisms, supporting experiment planning and execution.
• Chromeleon – connects lab measuring devices through one interface for chromatography data collection and processing.
• QualiService (external, hosted elsewhere) – archives qualitative social science research data for reuse.

• KNIME – low-code data science workflow platform.
• Galaxy – UFZ instance of the open-source scientific workflow system for accessible, reproducible computational research.
• WOMBAT – Kubernetes-based architecture for running web applications (e.g. tool front-ends built on top of other infrastructures).

Several UFZ-affiliated projects generate and structure data at larger scale and often feed into the infrastructures above:

• TERENO – long-term observatory network.
• eLTER – (Integrated) European long-term ecosystem research infrastructure.
• MOSES – mobile observation platform complementing long-term observatories for investigating highly dynamic or extreme events; includes its own Data Discovery Portal.
• MOSAIC – platform for model-based, high-resolution exploration of subsurface structures via minimally invasive methods.

Status across UFZ's infrastructures (per the PID working group inventory, 2026):

• ORCID – supported (UFZ employees can link their ORCID to the personnel service; UFZ is an institutional member of ORCID DE), but registration is voluntary and not systematically enforced across all data infrastructures.
• DataCite DOI – used for data publications via the DMP archive component.
• PIDInst – captured for instruments via the SMS only.
• IGSN (physical samples), ROR (organizations) – not yet systematically implemented; identified as gaps.
• No cross-infrastructure policy currently mandates consistent PID capture; responsibility is split across several infrastructures and, in places, unassigned.

• ODIS-Connect – ongoing project to connect UFZ's GeoNetwork to the Ocean Data and Information System (ODIS), making UFZ (meta)data findable in a global federation and serving as a blueprint for other GeoNetwork-based Helmholtz centers (e.g. HEREON) that are not yet ODIS-connected.
• Helmholtz Knowledge Graph / unHIDE – the ODIS work is explicit preparation for later harvesting of UFZ metadata into the Helmholtz-wide Knowledge Graph, which uses a related architecture.
• NFDI, HIFIS & Helmholtz Cloud – UFZ's own infrastructures are complemented by national (NFDI) and Helmholtz-wide (HIFIS/Helmholtz Cloud) services for storage, compute, collaboration and metadata (see the RDM Guidelines' infrastructure overview for the full list).