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, the BUA-funded CARDS project develops RDM services within the Berlin University Alliance (BUA). This includes data management planning, electronic lab notebooks, and RDM courses. The Charité-led part of the project will offer data stewardship services to Clusters of Excellence based at BUA institutions.
Services
- Consulting on all RDM-related questions (subject to availability)
- possibly redirection of requests to other departments and infrastructures with RDM-related services
- Online information, e.g. FAQ Open Data, FAQ Data Management Plans (DMP), DMP Template for Charité Researchers
- Presentations on RDM and Open Data in institutes and research groups upon request
- Collection of RDM requirements, which then contribute to further planning
Contact
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).
Service
- 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!)
Equipment
- OMERO+
- PathViewer for digital pathology workflows
- High content screening workflows
- Data backup and archiving
Contact
Project coordination
- Dr. Harald Stachelscheid / t: +49 30 450 539 428
- PD Dr. Philipp Mergenthaler / t: +49 30 450 560 020
Technical infrastructure
-
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)
Features included
- 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
Contact
+49 30 450 560 005
Further information
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.
Resource
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.
Contact
+49 30 450 543 601
Medical Data Integration Center (MeDIC)
In the data integration centers (DIZ) of the university hospitals, the technical and organizational prerequisites for the cross-site use of care and research data for scientific purposes were created. Charité's Medical Data Integration Center (MeDIC) was set up as part of the Medical Informatics Initiative (MII) as part of the HiGHmed consortium. Its operation is currently being funded as the NUM-DIZ infrastructure as part of the University Medicine Network (NUM).
In close cooperation with the structures of the Charité Health Data Platform and the Berlin Institute for Health Research at the Charité (BIH), the Charité MeDIC has integrated different types of data, such as laboratory and medication data, and makes these available in standardized form in the form of the MII National Core Data Set (KDS) for scientific evaluations. This data can also be used across locations via the MII's national platform, in particular the Research Data Portal for Health (FDPG), whereby data protection and the informational self-determination of patients are of central importance. The aim is both to optimize patient care and to promote translation between research and patient care. In addition to the MeDIC, Charité and BIH have established governance structures in accordance with the MII guidelines. These include the establishment of a so-called Use & Access Committee, which examines applications for data use, the implementation of pseudonymization procedures and the obtaining of broad consent from the MII.
Services
MeDIC's services focus on providing data in accordance with the specifications and regulations of the Medical Informatics Initiative (MII) and the Network of University Medicine (NUM) and facilitating data utilization projects. In addition, we operate interfaces to national and international platforms and offer other services, including project-specific services.
Data utilization
- Advice on questions regarding data use and applications
- Feasibility studies for data utilization projects
- Data extraction, data preparation and pseudonymization
- Provision of data for local and national research projects
- Carrying out statistical evaluations as part of distributed evaluations
- Federated data analysis with DataSHIELD
Data indexing
- Expansion of the local dataset based on the national core dataset
- Implementation of data quality checks and improvements
- Standardization of data using interoperability standards (e.g. HL7 FHIR, SNOMED, LOINC) together with the Core Unit eHealth and
Project-specific services and data management
- Implementation of project-specific requirements, for example for data collection, in particular by the expansion and networking team
- Operation of an openEHR Clinical Data Repository together with the Center for Digital Health
- Provision of ATLAS and i2b2 instances together with the Medical Informatics working group
- Offering additional services, such as the provision of virtual analysis rooms or project-specific data slices, in collaboration with the Health Data Platform
Networking
- Connection of the MeDIC to the research data portal for health
- Connection to the OHDSI and EHDEN network in collaboration with the Medical Informatics Working Group
An overview of other cooperating institutions, institutes and clinics can be found here. Information on access and how to contact us can be found here.
Contact
Operational Lead
Dr. Peter Brunecker
+49 30 450 543 038
Scientific Lead
Prof. Dr. Fabian Prasser
+49 30 450 528 781