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 wiki space (confluence). Access is restricted to users.

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 to other BioMedIT use.

Available Resources

GitLab

Confluence

Confluence is a collaboration space and repository for the working- and implementation groups. To use confluence, users need a SWITCH edu-ID or valid aii credentials from a Swiss university or hospital.

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

Key server

BioMedIT provides a central Key Server where public GPG keys of BioMedIT users can be stored. Public GPG keys are required to encrypt and sign data during secure data transfers in the BioMedIT network.

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

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 data used in SPHN.

SPHN RDF Schema

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

SPHN Schema Visualization Tool

The SPHN Schema Visualization Tool generates a human-readable HTML document describing the project's RDF schema directly from the schema. It is based on pyLODE and covers detailed information about the classes, object, datatype and annotation properties and the named individuals.

SPHN Quality Control files

The SPHN data quality control contains a set of SHACL rules and statistical SPARQL queries to validate the compliance of the RDF data produced.

Quality Check Tool

The Java-based Quality Check tool facilitates the validation process of SPHN RDF data at the data provider level. Based on the SHACL file generated by the SHACLer and statistical queries in SPARQL, it generates a human-friendly report with information about data conformance to the schema and some basic statistics.

SHACLer

The SHACLer is a Python tool that extracts SHACL rules from an SPHN-compliant input ontology for facilitating data validation.

DCC Terminology Service

The DCC Terminology Service provides SPHN compatible, machine-readable versions of national (CHOP or ICD-10 GM) and international (SNOMED CT, LOINC, ATC, 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 Template Ontology

The Template Ontology helps projects to develop upon it their project-specific RDF schema. This template imports the SPHN RDF schema and other required RDF libraries as well as pre-filled basic metadata annotations. 

DCC Web Protégé

DCC Web Protégé provides an easy-to-use, web-based ontology development environment for collaborative usage. E-mail the DCC to request an account.

Semantic Web Tools

Triple store and knowledge discovery tools enabling the visualization, exploration, knowledge interference 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.

SPARQL Queries

SPARQL is the semantic web standard query language used exploring the content of a data set. A set of ‘helper’ queries are generated in SPHN for better understand and deciphering the content of SPHN-related data sets. E-mail the DCC to request access.

SPARQLer

The SPARQLer is a program that extracts example SPARQL queries for each concept from an SPHN compliant input Ontology. E-mail the DCC to request access.

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.