SPHN Federated Query System

Information retrieval systems enabling researchers to query for specific clinical information of patients have so far been limited to individual clinics or single hospitals. With the new Federated Query System (FQS), established in the realm of the Swiss Personalized Health Network (SPHN), it is now possible to search for fully anonymized clinical information across all five university hospitals, while allowing the hospitals to retain full control over their data.

The SPHN federated query system (FQS) allows queries on anonymized and nationally harmonized data coded in national or international terminologies. Researchers can assess whether and where patients or patient data potentially suitable for a specific research question exist at one or several of the Swiss University Hospitals (UHs). The system enables researchers to verify the feasibility of their project by running simple queries against a subset of clinical data of all UHs. Additionally, it allows designing and optimizing inclusion and exclusion criteria for study protocols without transferring any patient data.

These queries may include demographic information (age and gender), diagnosis (ICD-10), procedures (CHOP), medication (ATC) and lab test (LOINC) and lab results with units (according to UCUM). Overall, the system includes over 70 Mio data points from currently 450 000 patients, who signed the general consent.


Watch the following video to learn more about the SPHN Federated Query System and how to use it.

Access Criteria

The FQS is accessible for authorized users through the BioMedIT portal (find instructions here).

Access requirements:

  • Their institution has signed an agreement with SIB. In a first pilot phase starting 16 November 2021, the five Swiss university hospitals are part of this network. Additional institutions (e.g. Swiss universities) will have the possibility to join the consortium at a later time point.
  • Users have a SWITCH edu-ID account with their employing institution linked in their profile (though SWITCHaai). As authentication through SWITCHaai via SWITCH edu-ID is unfortunately not currently possible for USB employees, USB researchers will have access to the SPHN FQS from the beginning of 2022.
  • Each user has individually agreed to abide by the FQS Acceptable Use Policy.

Software and Data Architecture

The FQS is a federated distributed query system based on a customized version of the Patient Network Explorer (PNEx) software product developed by Clinerion. The data follows the same semantic standards as the SPHN semantic interoperability framework, so feasibility studies for research projects and real-world data provision are aligned in terms of semantic data standards.

Regular Data Loads

New anonymized data are loaded into the FQS on a regular basis, which means that the number of eligible patients in a given query may change over time as the total number of data points increases. The new data is loaded on the first Tuesday and Wednesday of each month. During this time, the system or individual sites may be offline or fluctuating numbers may be observed. We therefore recommend not to use the system during this time.

FAQ User Guide

Please send us an email if you have any question or feedback regarding the SPHN FQS.

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