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====== 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 [[https://rdm.pages.ufz.de/guidelines/|UFZ RDM Guidelines]].

===== Spatial Data Infrastructure (SDI) =====

UFZ's SDI ([[https://doi.org/10.5281/zenodo.10391523|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 Series & Sensor Data Infrastructure =====

  * **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.

===== Sample, Lab & Archiving Infrastructure =====

  * **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.

===== Imaging Data Infrastructure =====

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

===== Domain-specific Research Data Platforms =====

  * **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.

===== Analysis & Workflow Tools =====

  * **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).

===== Research Infrastructures & Long-term Observatories =====

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.

===== Persistent Identifiers & Metadata Integration =====

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.

===== Connections Beyond UFZ =====

  * **ODIS-Connect** – ongoing project to connect UFZ's GeoNetwork to the [[https://odis.org/|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' [[https://rdm.pages.ufz.de/guidelines/RDM-infrastructures/infrastructures.md|infrastructure overview]] for the full list).