STCS Data Center
About us
The STCS Data Center (DC) is the central point of contact for data-related services within the STCS. We provide support throughout the research data lifecycle, from study planning and data collection to data management, analysis, and research outputs.
Our services include:
Data support:
- Add-on data collection
Support for collecting additional data beyond the information already available in STCS databases, including the definition of data requirements and collection processes. - Database queries
Extraction of data from STCS database according to predefined research questions, study criteria, and data specifications. - Data management
Support with data cleaning, validation, structuring, documentation, and quality control to ensure that research datasets are consistent and fit for purpose. - Analysis dataset preparation
Processing and preparation of analysis-ready datasets, including data extraction, transformation, derivation of variables, and quality checks.
Project support:
- Project and data analysis planning
Consultation during study planning to define data requirements, identify appropriate data sources, and develop an analysis strategy. - Statistical analysis
Statistical consultation and support throughout the research process, from selecting appropriate methods to performing analyses and interpreting results. Learn more about the stastistical support we provide here. - Budget planning for Data Center support
Estimation of the resources and costs associated with data-related services, including data extraction, management, analysis, and other Data Center activities. - CRF review and production
Support in designing, reviewing, and producing Case Report Forms (CRFs), with a focus on data quality, completeness, and suitability for downstream analysis. - Manuscript preparation
Support with the preparation of tables, figures, data summaries, and methodological descriptions for scientific publications.
Bio-sample support:
- Sample size calculation
Statistical support to determine the required sample size based on the study design, expected effects, variability, and statistical power. - Bio-sample management
Support for the management and documentation of bio-sample-related data and processes including sample tracking and linkage with clinical or research data where applicable.
Technical development:
- Web application development
Development and maintenance of web-based applications to support research data collection, management, workflows, and study-specific processes. Learn more below.
How to request support:
Are you already an STCS user?
Please access our web applications here and submit your project and/or data-related requests here. Only available for STCS users (you will have to log in).
Not yet an STCS user?
Please register here to access internal documents, submit project proposals and STCS requests, and quickly access all STCS digital applications and other user resources.
Not an STCS user but have a question?
If you have any other queries - please submit a contact message here.
Do you want to collaborate?
Please contact us if you are interested in collaborating or would like to learn more about any of these applications.
STCS digital solutions
Several in-house web applications have been developed to support the STCS. More information about our data environment and each individual application is provided below.
Please be aware that:
- Rights to access applications are granted by STCS administrators upon request.
- Some applications require you to sign in with your hospital credentials.
- Certain applications can only be accessed while connected to the hospital network.
- Please contact us in case you need access to one of the applications and you are unable to do so.
- Codebook
- 3LC
- DQC and Analytics
- STCS Universe
- CHIL
- SePP
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Codebook
The Codebook contains the 3LC metadata description and provides a structured overview of all 3LC variables, including their definitions, labels, and values, along with version control.
It serves as a key resource for researchers, enabling them to easily identify and understand available variables. This supports the selection and request of relevant data for research projects.
Codebook: browse the STCS metadata
The Codebook describes all 3LC metadata and provides a structured overview of all 3LC variables, including their definitions, labels, values, and version history.
Codebook is publicly available to browse.
To be redirected click here.
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3LC
3LC is the STCS in-house Clinical Data Management System (CDMS), built by the Application Development and Data Integration unit at the Data Center to standardize the collection, quality control, and secure storage of clinical data from all solid organ transplant recipients in Switzerland. Since 2008, Swiss law has mandated that every transplant recipient be enrolled in long-term follow-up, and 3LC captures this data across the full patient journey: from baseline recipient, donor, and transplant characteristics through longitudinal outcomes such as biopsies, rejection episodes, complications, graft function, and patient-reported quality of life. All data are pseudonymized, with strict access controls, and are made available for approved research only after the necessary ethical and regulatory requirements are met.
3LC was developed with Django framework since early 2020 and replaced the STCS's previous system in January 2023 following a major changeover that included revising eCRFs, migrating and validating all historical data from 2008–2022, redesigning the front-end UX, and training local data managers at all six Swiss transplant centers. The platform is now used nationwide and, hosted in partnership with sciCORE, combines robust data protection with a scalable infrastructure built specifically for transplantation medicine. The successful set up of 3LC gives the STCS a reliable foundation for future research and quality assurance, with a data model flexible enough to extend beyond transplantation into other clinical research applications.
3LC: access the STCS Clinical Data Management System
3LC is used to collect, manage, and securely store the clinical data of all STCS patients.
Only local data managers, DC members and investigators have access to 3LC.
To be redirected click here.
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3LC data quality checks (DQC) and Analytics
Superset is a business intelligence and data visualization platform and has been used to provide a centralized view of all data within the 3LC ecosystem. It enables the DC users to explore key metrics, monitor performance, and gain actionable insights through interactive dashboards and analytics that are also made available in the 3LC Analytics’ section.
In addition to reporting and visualization, Superset is used to set up a powerful data query management tool designed to identify, track, and monitor data inconsistencies across the 3LC platform - 3LC DQC. Queries are developed and validated by data managers at the DC in the Stage environment before being deployed to the Production (PROD) environment, ensuring accuracy and reliability.
Once deployed, Local Data Managers can efficiently review, investigate, and resolve identified issues. Queries run continuously in real time, providing ongoing data quality monitoring and enabling the immediate detection of newly introduced inconsistencies.
Investigate the 3LC data quality checks and analytics
Superset is behind the 3LC data visualization, reporting and query platform.
Only 3LC users can access this platform.
To be redirected click here.
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STCS Universe
STCS Universe is our central research project management platform, designed to support researchers throughout the project lifecycle. It enables investigators to submit letters of intent and project proposals, monitor the evaluation, review the progress of submitted studies awaiting the Scientific Committee decision. The platform is the main working area of all Scientific Committee members with specific sections for statistical and medical reviewers.
The platform also supports the activities of the Patient Advisory Board, allowing members to create, manage, and publish lay summaries to facilitate the communication of research findings to a broader audience.
STCS working groups are able to manage their group projects and publications and support researchers in their field of expertise. In addition, STCS Universe serves as a repository for all project publications, providing a centralized location for accessing and managing scientific outputs.
The platform also provides a streamlined process for submitting data and statistical support requests to the STCS DC directly.
STCS universe: project management area
Submit and manage your letters of intent, research projects, lay summaries, publications and data requests on STCS Universe.
All investigators can have access to the STCS Universe.
To be redirected click here.
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CHIL (Cohort Hospital Integration Layer)
CHIL was developed as part of the Cohort Demonstrator project funded by SPHN (learn more here) and provides seamless access to clinical data through direct integration with the hospital’s Clinical Data Warehouse (CDWH).
Its integrated patient management system enables efficient management of study participants, allowing users to update personal information, manage hospital appointments, and organize associated tasks with ease. By maintaining a secure and reliable link to each corresponding hospital patient, CHIL ensures straightforward retrieval of study data directly from the hospital data warehouse.
CHIL also functions as a powerful CDWH exploration and browsing platform. Medical personnel and researchers can query clinical data with ease, from simple requests—such as identifying patients with elevated creatinine levels—to more advanced analyses, such as finding patients with multiple diagnoses.
At the core of the platform is a self-service system for querying the CDWH, involving a querying system designed to be accessible to users of all technical backgrounds. Advanced users can write queries directly in Cypher and SQL, while non-technical users can build queries visually through an intuitive drag-and-drop interface, with the system automatically generating the underlying query. Alternatively, users can interact with Carry, CHIL’s AI-powered assistant, which guides them through the query design using natural language.
CHIL operates in two secure environments:
- Inside the hospital network: Full access to patient data is available in a secure environment protected by the hospital’s firewall.
- Outside the hospital network: Access is limited to pseudonymized data, ensuring compliance with data protection requirements.
Retrieved data can be transferred seamlessly to the cohort database through a dedicated API integration, enabling efficient downstream analysis and research workflows.
We are committed to making CHIL available to a broader community of users and collaborators. Our initial focus is on partnerships with teams at University Hospital Basel, but we welcome interest from other groups as well. Please get in touch if you would like to learn more about CHIL and potential collaboration opportunities.
CHIL: explore clinical data
Visit CHIL to securely access and explore hospital clinical data, manage study participants, and build queries through an intuitive interface.
Only autorized investigators can access CHIL.
To be redirected click here.
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SEcure Patient Portal (SePP)
SePP (Secure Patient Portal) is a secure online platform that enables patients to access, review, and complete pending clinical questionnaires at their convenience. Once submitted, responses are transmitted directly to the care team using end-to-end encryption, ensuring that sensitive health information remains protected and patients' identities are never exposed.
With SePP, patients can complete clinical questionnaires anytime, anywhere, while maintaining the highest standards of privacy, confidentiality, and data security.
SePP is currently in development, and we aim to launch the platform by the end of the year.
Our data environment
At the center of our digital environment is 3LC, our Clinical Data Management System, which stores the patient data collected by the STCS.
Data is entered into 3LC through different channels:
- CHIL automatically extracts data from the hospital systems.
- Local data managers (LDMs) can enter data manually.
- Patients will be able to enter their own data directly through SePP (coming soon).
Once collected, the data can be requested by researchers for use in approved research projects. STCS Universe is used to manage the entire project lifecycle, from project submission, data requests to project management.
Several tools are connected to 3LC:
- Codebook provides the metadata and definitions describing the data stored in 3LC.
- Superset is used for data quality checks, monitoring, and analytics.
See below a representation of our data environment:
