BioMedIT and SPHN DCC Tools and Resources

BioMedIT provides a number of in-house, commercial, and open-source tools and services to its users. Below you will find information on these along with links to the relevant platforms. Should you have any questions to these, please contact BioMedIT.

BioMedIT Central Tools and Services

Work instructions and SOPs for BioMedIT

BioMedIT hosts a full repository of documentation on the BioMedIT Git Wiki.

BioMedIT Data Management Solutions

BioMedIT nodes also provide standard data management solutions on-demand basis for the research projects based on OpenBis, LabKey, SLIMS etc. Please contact BioMedIT or your assigned BioMedIT node for more details. 

BioMedIT Secure HPC service

BioMedIT secure HPC service enables researchers to connect secure (HPC) clusters in the BioMedIT nodes directly from their home organizations to execute compute or memory intensive workflows leveraging the large CPU, memory and GPU resources of the nodes. BioMedIT secure HPC service is setup in an access-controlled, private environment offering network isolation, data isolation and computational resources isolation ensuring high standards of data security. Please E-mail BioMedIT or your assigned BioMedIT node for more details on this service. 

BioMedIT Secure Remote Desktop service

BioMedIT secure remote desktop service enables researchers to connect to a remote server in the BioMedIT nodes from their home organisation using a web browser. Please E-mail BioMedIT or your assigned BioMedIT node for more details.

Code repository service (Git)

The BioMedIT Code Repository Service (based on Git), is accessible to registered BioMedIT users to create, collaborate and share their application codes with other BioMedIT users.

Available Resources


Confluence Cloud

Confluence is a collaboration space and repository for the working- and implementation groups, projects and iniatives.

Available Resources

Access Confluence Cloud

Container registry

Provides a secure, easy-to-use registry for hosting, vulnerabilities scanning and sharing of OCI compatible container images. E-mail BioMedIT to request access.

Available Resources

Container registry

Legal Agreements for use in BioMedIT

The SPHN Data Coordination Centre has produced a set of templates for legal agreements for data transfers and cross institutional collaboration within the scope of BioMedIT.

BioMedIT Portal

The single point of entry into the BioMedIT environment allowing access to central services, node services, user management for collaborative projects and data transfer request management.


sett is BioMedIT's bespoke secure encyption and transfer tool. This tool allows users to package and move their data around the BioMedIT network in a safe and legal manner.

Scientific Tools and Services

SPHN Dataset

The SPHN Dataset contains the main concept definitions for clinical and genomic data used in SPHN.


The SPHN RDF Schema enables the semantic encoding of clinical routine data in a FAIR (findable, accessible, interoperable, and reusable) format, using other existing standard ontologies. 

SPHN Schema Forge

SPHN provides a set of tools to enable schema visualization, quality control, automatic SPARQL query generation, etc. Setup and installation of these tools are a time consuming process, which is why we developed an easy-to-use web service enabling users to get all files from a single application. This web service includes the following tools: Dataset2RDF, SHACLer, SPHN Schema Visualization Tool, SPARQLer.


SPHN Dataset Template

SPHN provides the Dataset Template, a template to extend the SPHN Dataset, that can be used to design project specific concepts in Excel. This file can be used as input for the SPHN Schema Forge to get your project-specific RDF Schema.

SPHN Quality Control Files

The SPHN data quality control files contain a set of SHACL rules (e.g.validity of classes and properties. cardinalities and timeframe) and statistical SPARQL queries (e.g. counting instances or providing min and max values for quantities and datetimes) to validate the compliance of the RDF data produced.


SPHN Mock Data Generator

SPHN provides the Mock Data Generator, an open-source tool for generating mock data for a given SPHN RDF Schema. This tool facilitates the generation of large amounts of mock data in RDF which can be used for testing of tools, SPARQL queries, and validation. E-mail the DCC for more details.


DCC Terminology Service

The DCC Terminology Service provides SPHN compatible, machine-readable versions of national (CHOP or ICD-10 GM) and international (e.g. SNOMED CT, LOINC, ATC, SO, GENO, HGNC, UCUM) terminologies and classifications in RDF format. They are available directly in the individual project spaces on the BioMedIT nodes or for download through the BioMedIT Portal (via SWITCH edu-ID). E-mail the DCC for more details.

SPHN Schema Scope

Schema Scope is an interactive tool to explore the RDF Schema and its properties, allowing to explore individual concepts in their context. Please note that the visualization may not reflect the full details of an individual concept in every case to improve accessibility. Please consult the concept documentation for full details of individual concepts. E-mail the DCC for more details.



SPHN Schema Scope online

Semantic Web Tools

Triple store and knowledge discovery tools enabling the visualization, exploration, knowledge inference and querying of specific data in RDF on a local instance. 

These tools are available on request in BioMedIT project spaces. E-mail the DCC for more details.

SPHN Connector

The SPHN Connector is a tool developed to facilitate the creation of valid SPHN-compliant graph data based on relational, semantically described data from data-providing institutions.The connector creates an input interface based on an RDF Schema conforming to the SPHN Semantic Interoperability Framework. The ingested data is converted into RDF, validated to check its conformity with the schema, and de-identified.


SPHN Data Management Plan (DMP) Guidelines

Funding agencies commonly require researchers to submit a data management plan (DMP) when writing research proposals. The SPHN DMP guidelines offer general recommendations for the use of sensitive biomedical data to help researchers to plan the entire life cycle of their data, with particular focus on SPHN-funded projects using health-related data for research purposes, and data processing on the BioMedIT infrastructure.

available resources

SPHN DMP Guidelines

Maelstrom catalogue

The Swiss Cohort consortia is a network of Swiss Cohorts available on the internationally renowned Maelstrom metadata catalogue.

SPHN Federated Query System

The SPHN Federated Query System allows researchers to assess, whether and where patients or patient data potentially suitable for a specific research question exists at Swiss University Hospitals.

We use cookies to help give you the best experience while browsing our website and to collect visitor statistics. By using the BioMedIT website, we assume that you agree to their use.
Read our privacy statement.