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) with substance amounts and lab test (LOINC) with lab results and units (according to UCUM). Overall, the system includes over 700 Mio data points from currently over 700 000 patients, who signed the general consent.

Access Criteria

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

Access requirements:

The user's institution has signed an agreement with SIB. Currently, the five Swiss university hospitals and the Universities of Basel, Bern, Geneva, Zurich, Lausanne, EPFL and ETH Zurich are part of the network. Additional institutions (e.g. further Swiss universities) have the possibility to join the consortium (contact the DCC for more details).
Users have a SWITCH edu-ID account with their employing institution linked in their profile (though SWITCHaai). USB users need to contact their local IT to manually set up the authentication through SWITCHaai via SWITCH edu-ID
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 local implementation at the hospital side is taken care of by the FQS WG. 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 after the first Monday of each month. During this time, the system will be offline.

Watch our demonstration of the system here.

FAQ User Guide

1. How to change the link type between the search criteria from AND to OR and vice versa?

Links between search criteria are easy to handle when you create a new node for each search criteria. All nodes are linked with AND. Within a node, all codes you have selected for this criterion are linked with OR by default, as shown in the following screenshot.

You can switch the type of link within a node from OR to AND by editing the node and setting the connector with the “Set type of Connector” buttons, as shown in the following screenshot.

2. How can I link nodes using an OR statement?

For queries with alternative features that span different data types, you can create a node within a node, and all criteria will be linked with OR. The following example shows a query for patients diagnosed with either “Postviral fatigue syndrome” OR “Malaise and fatigue” OR who have taken either an amantadine-containing drug OR a modafinil-containing drug.

To find out how many patients were diagnosed with either "Postviral fatigue syndrome" OR "Malaise and fatigue" AND were taking either an amantadine-containing drug OR a modafinil-containing drug, a separate query would be required, as shown in the screenshot below.

3. Why do I see more than one entry when searching for a medication such as acetylsalicylic acid?

The FQS uses ATC-coded data to indicate which medications a patient has taken. However, the ATC classification does not contain unique identifiers for substances. If you want to search for patients treated with a specific substance, you may need to add multiple ATC codes to your query.

For example, for acetylsalicylic acid, multiple ATC codes need to be added to the query to find all patients treated with this substance. The integrated terminology server offers the possibility to search for the name of the substance and to add the different ATC codes to the selection for the query.

The "Select All" button allows you to add the ATC codes to your query in one step (see example below). This functionality works the same way for all data types. It should be noted that depending on the terminology content, it may be necessary to search for multiple synonyms.

4. How can I set a time restriction?

If you want to retrieve results for a specific time period, e.g. all patients with Sepsis due to streptococcus between 01.01.2019 and 31.12.2020, you can use the Time Range function. You can set the Time in relation to screening or as absolute time frames using the Time by date picker setting. You can set the Time Range once on the Node and it will apply to all ICD10 codes specified under that node. The hourglass icon next to the search criteria indicates that a time range has been set. The Time Range function can be used for all data types such as diagnoses, procedures, medications, and lab tests.

5. Can I get some basic statistics of the patients in my search?

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

Contact the DCC

SPHN Federated Query System

Access Criteria

Software and Data Architecture

Regular Data Loads

FAQ User Guide

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