Research Data Management
Increasingly larger amounts of research data are being collected and archiving, curation, and reuse is becoming more and more important. Here you can find an overview of research data management platforms and consulting services available at Charité.
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Research Data Management at Charité
In order to support researchers with structured research data management (RDM), Charité offers platforms for certain data types: SODAR for OMICS data, OMERO for microscopy data, and the Virtual Research Environment (VRE) primarily for imaging data, but not restricted to it. In addition, Charité is currently in the process of establishing generic RDM services: The infrastructures and services for handling research data support, their structured storage and documentation as well as their later reuse. IT-related RDM services are additionally offered by Team Science-IT within the IT department, and high-performance computing is offered by the HPC IT Team of the BIH.
Generic Research Data Management Services (under development)
Structured RDM addresses questions of e.g. documentation, data formats, and quality assurance. In addition, the so-called FAIR principles are central to the later reusability of the data. Personal data require additional measures regarding data access, consent etc. Additionally, in the context of grant applications it is increasingly required to address all of these RDM questions, often in the form of a data management plan.
Currently, plans are being made regarding which RDM service structures are to be established to address aforementioned requirements. These shall complement existing infrastructures for certain data types and usage. A central RDM service could offer consulting, qualification formats, and online information. Currently, such a service is not in place yet, but there is the possibility of consulting by the BIH QUEST Center, subject to availability, as well as a limited offer of seminars and online information. In addition, a survey on RDM needs and further RDM activities are planned within a BUA-funded project.
- Consulting on all RDM-related questions (subject to availability)
- possibly redirection of requests to other departments and infrastructures with RDM-related services
- Qualification formats (RDM, Open Data, sharing sensitive data)
- Online information, e.g. FAQ Open Data, FAQ Data Management Plans (DMP)
- Presentations on RDM and Open Data in institutes and research groups upon request
- Collection of RDM requirements, which then contribute to further planning
OMERO image data management
OMERO Plus is a client-server platform for the management and analysis of microscopy and other imaging data. The system offers a secure, central repository which users can use to process their imaging data from the initial microscopy image to export or publication. The platform currently supports more than 150 image formats (OME Bio-Formats Library), including all commercially available microscopy imaging modalities.
The OMERO Plus platform enables users to display, share (internally), analyze and manage their microscopy imaging data. The platform also supports collaborations with external partners. OMERO Plus also includes PathViewer, an interactive visualization, analysis and annotation tool specifically tailored for the digital pathology workflow.
Gaining access to OMERO at Charité:
An OMERO user account may be requested via Open IRIS (user must first log in to Open IRIS).
- Individual OMERO accounts
- OMERO groups for research groups
Please note: Each user must be assigned to a research group (i.e. OMERO group). This will require confirmation by the head of the working/research group (sent automatically by OpenIRIS). - Click here to open an account (you must first log in to OpenIRIS!)
- PathViewer for digital pathology workflows
- High content screening workflows
- Data backup and archiving
- Dr. Harald Stachelscheid / t: +49 30 450 539 428
- PD Dr. Philipp Mergenthaler / t: +49 30 450 560 020
Charité Science IT:
Dr. Peter Brunecker / t: +49 30 450 543 038
User support, training, and onboarding
Robyn Brackin-Helmers (AMBIO)
Handbooks, training materials and instructional videos
Additional learning materials
Virtual Research Environment (VRE)
- web portal
- segregated Green Room zone to capture and pre-process sensitive data
- analytics workbench tools for processing, analyzing, and visualizing datasets, automated ingestion of data from hospital-based data capture sources
- project-specific Data Warehouse for ingestion and query of structured datasets
- a metadata repository and graph database for capture and query of metadata and lineage tracking
- support for ontologies and automated extraction
- indexing of standard metadata fields to make data findable
System for Omics Data Access and Retrieval (SODAR)
SODAR (System for Omics Data Access and Retrieval) has been developed by CUBI to provide easy and safe access to omics data, and its meta data, processing results, and logs. SODAR is a great help in organizing data and empowering users to manage access to their data and meta data curation. The main features of SODAR include web and command line interfaces for biomedical and computational users.
The local SODAR instance is reachable from internal networks only (Charite VPN access requires “Zusatzantrag B”). Most data sets within SODAR are private. Access to a private project requires approval by the PI (or consortium) in charge of the data.
SODAR has been selected as the omics data management solution for numerous large collaborative research projects including:
- Terminate-NB (Cancer Genomics)
- Translate NAMSE Berlin (Rare Disease Genetics)
- NUM-OrganoStrat (Single Cell Transcriptomics)
- BIH Clinical Single Cell Pipeline (Single Cell)
- MSTARS (Diverse Mass Spectrometry Technologies)
- SFB 1444 (Functional Genomics)
- Beyond the Exome (Genomics)
- BeLOVE (Multiomics)
and also hosts 100+ smaller single PI projects. The total capacity includes PBs of available storage space. SODAR follows the FAIR principles and uses community standards (Elixir) for metadata modelling.
Medical Data Integration Center (MeDIC)
In the Data Integration Centers (DICs) of the German university hospitals, the technical and organizational foundations are laid for the cross-institutional use of data for research purposes. The Medical Data Integration Center (MeDIC) at Charité was established under the umbrella of the Medical Informatics Initiative (MII) as part of the HiGHmed consortium. Its operation is currently funded by the Network University Medicine (NUM).
The goal of Charité’s MeDIC is to improve the availability of routine healthcare data for cross-site and local research purposes in close collaboration with the Health Data Platform (HDP). For this purpose, healthcare data of the Charité are integrated in the MeDIC and mapped to the national core data set of the MII using open interoperability standards. For cross-site data use, the MeDIC is connected to the structures of the HiGHmed consortium as well as the MII (Research Data Portal for Health).
In addition to the MeDIC, BIH and Charité have established governance structures according to the MII specifications. These include a Data Use & Access Committee, which reviews requests for data use, and an independent Trust Center, which is responsible for pseudonymization and consent management. The MII Broad Consent forms another important component.
The MeDIC focusses on providing data according to the specifications and regulations of the MII and participating in local and national use cases:
- Provision of the national core data set of the MII.
- Participate in national use cases and projects within the scope of the MII and the NUM.
- Provide additional services in collaboration with the HDP
Local requests for data use can be submitted via the Use & Access Committee (Charité intranet). For multi-site projects, please use the Research Data Portal for Health.
Dr. Peter Brunecker
+49 30 450 543 038
Prof. Dr. Fabian Prasser
+49 30 450 528 781