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Testing, traceability, and isolation actions are a central strategy defined by the World Health Organization to contain the COVID-19 pandemic. In this sense, the countries have had difficulties in counting the number of people infected with SARS-CoV-2. Errors in reporting results are a common factor, as well as the lack of interoperability between laboratories and governments. Approaches aimed at sending spreadsheets via email expose patients’ privacy and have increased the probability of errors due to retyping, which generates a delay in the notification of results.
This study aims to design and develop an interoperable platform to report polymerase chain reaction (PCR) SARS-CoV-2 tests from laboratories to the Chilean government.
The methodology to design and develop the interoperable platform was comprised of six well-structured stages: (1) creation of a minimum data set for PCR SARS-CoV-2 tests, (2) modeling processes and end points where institutions interchange information, (3) standards and interoperability design, (4) software development, (5) software testing, and (6) software implementation.
The interoperable Fast Healthcare Interoperability Resources (FHIR) platform to report PCR SARS-CoV-2 tests from laboratories to the Chilean government was successfully implemented. The platform was designed, developed, tested, and implemented following a structured methodology. The platform’s performance to 1000 requests resulted in a response time of 240 milliseconds, throughput of 28.3 requests per second, and process management time of 131 milliseconds. The security was assured through a private network exclusive to the Ministry of Health to ensure confidentiality and integrity. The authorization and authentication of laboratories were implemented with a JavaScript Object Notation Web Token. All the PCR SARS-CoV-2 tests were accessible through an application programming interface gateway with valid credentials and the right access control list.
The platform was implemented and is currently being used by UC Christus Laboratory. The platform is secure. It was tested adequately for confidentiality, secure authorization, authentication, and message integrity. This platform simplifies the reporting of PCR SARS-CoV-2 tests and reduces the time and probability of mistakes in counting positive cases. The interoperable solution with FHIR is working successfully and is open for the community, laboratories, and any institution that needs to report PCR SARS-CoV-2 tests.
The COVID-19 pandemic has caused an unprecedented public health crisis. When this issue occurs, technology can effectively support institutions by facilitating the immediate widespread distribution of information in real time [
The COVID-19 pandemic is especially challenging for laboratories tasked with rapid and reliable testing of an increased number of PCR tests [
Chile has strengthened its testing capacity by creating a national network of diagnostic laboratories that includes more than 100 authorized centers in the country [
On the other hand, the government implemented a web platform to receive the PCR results. The process of transferring these results is still by spreadsheets via email, which is, in most cases, entered manually due to the lack of interoperability between health information systems.
Despite the effort, Chile did not account for 31,412 patients who were infected due to the lack of interoperability between systems (laboratory and government) and using spreadsheets and email as a formal mechanism for notifying PCR test results [
During the COVID-19 situation, modern health care systems significantly depend on teamwork and communication. The meaningful information exchange within laboratories is needed to provide information when and where required, facilitate quicker and more effective decision making, reduce repeated work, and improve safety with fewer errors [
In Chile, the interoperability between health care information systems has been difficult. The public and private institutions have not established consensus in the absence of a government strategy that regulates the interoperability’s policies in the health sector. The lack of defined standards and terminologies and a public-private health system regulatory framework have blocked an interconnected health network from functioning.
In this context, the National Center of Health Information Systems (CENS, acronym in Spanish), in collaboration with private and public laboratories, signaled the need to advance to the national strategy of interoperability. This alliance’s focus was connecting laboratories and the government with standards, which would solve the problems associated with health care systems’ interoperability. This contribution was centered on visualizing the need to share information through standards and demonstrating the feasibility and associated benefits with a specific use case.
For reporting PCR SARS-CoV-2 tests from laboratories and to advance a proposal for interoperability between health information systems, this paper proposes a platform designed and developed by CENS with a focus on safely expediting the delivery of the PCR SARS-CoV-2 tests from different laboratories to the Chilean government, avoiding data entry mistakes. We intend to accelerate the emerging interoperability agenda, presenting tangible and transferable results to the national and international community. The platform proposed a solution designed and developed with the international standards set by Health Level 7 (HL7) Fast Healthcare Interoperability Resources (FHIR) [
FHIR is an extensive international standard of interoperability that uses lightweight and modern web principles [
The methodology to design and develop the interoperable platform had six well-structured stages (
Creation of minimum data set
Build the minimum data set to build the polymerase chain reaction SARS-CoV-2 report
Modeling process
Designs the model of the laboratory process for sharing data with the Chilean government
Standards and interoperability design
Matches with the minimum data set and Fast Healthcare Interoperability Resources (FHIR)
Software development
Designs and develops the software solution using the HAPI FHIR libraries to create end points, resources, and messages
Software testing
Tests of the functional and nonfunctional requirements for the interoperable platform
Software implementation
Pilot software implementation by considering all the documentation and sharing real data between institutions
This methodology was proposed to develop interoperability projects. The methodology complements any methodology for developing software. Three initial phases (first level: interoperability design) were established focusing on data, processes, and standards. The first phase was the creation (and consensus) of a minimum data set to be exchanged. Phase two modeled and formalized the process, which considers obtaining the data and detecting the exchange points. With these inputs, it is now possible to select the appropriate standard and match it (whether it be messaging, resources, or documents) with the HL7 standards. This first level shows the importance of good design for interoperability with the data, process, and standards previous to developing software [
The three final phases (second level: software developing) were oriented to include methodologies for developing software, considering developing, testing, and implementing stages. In this development, the platform was created using agile software methods that support the incremental and iterative approaches for developing robust and interoperable health care information systems [
To create the interoperable platform, two full-time computer engineers and the CENS interoperability area leader worked on the platform. They took 2 months to develop the prototype (July to August 2020) and 1 month to make modifications during the pilot application (September). In October 2020, the pilot application was implemented for one laboratory (UC Christus) that sends PCR SARS-CoV-2 results to the local department of health services (Servicio de Salud Metropolitano Sur Oriente).
The first stage to communicate the results between laboratories and the Chilean government was constructing a minimum data set to share the information (
Methodology to design and develop an interoperable software solution. Six well-defined stages with its products and standards involved. BPMN: Business Process Model and Notation; FHIR: Fast Healthcare Interoperability Resources; HL7: Health Level 7.
The modeling of the process is an essential component for interoperable development [
Once the minimum data set was defined, the process modeled, and the end points detected, the following stage adopted standards and interoperability design. In this phase, we worked with FHIR Release 4 [
FHIR is the evolution of interoperability standards from HL7 [
The platform’s methodology considered professionals’ participation from a wide spectrum of areas in the interoperability design level (
In this stage, we matched the defined minimum data set with FHIR. An FHIR-based system’s capabilities were selected by considering which resource was the most adequate from a clinical perspective. These resources can be easily assembled into working systems that solve real-world clinical and administrative problems [
The requirements from the laboratories’ providers and the Chilean government were divided into functional and nonfunctional. This phase is a critical aspect because it lays the foundation for all the software, affecting the development later in the project [
The software was built separating the layer from the data model and the business logic.
Layers of an interoperability architecture. The architecture for sharing the polymerase chain reaction SARS-CoV-2 tests from laboratories to the Chilean government. API: application programming interface; FHIR: Fast Healthcare Interoperability Resources; JWT: JavaScript Object Notation Web Token.
The persistence (storage) was designed with two balanced mirror servers (
The security infrastructure was managed by the Ministry of Health’s private network, which was outsourced to a telecommunication company. The company assumed the management and maintenance of the communications network, which includes more than 1500 health establishments throughout the country, including 120,000 voice points (telephones); 30,000 email boxes; and 200 videoconference rooms. The laboratory that participated in this platform was connected on this secure network [
Moreover, FHIR is suitable for use in the application layer for a broad context: mobile apps, cloud communications, electronic health care record–based data sharing, and server communication in large laboratory providers [
Software testing was focused on functional and nonfunctional requirements. The functional requirements were obtaining the data and sharing the laboratories’ tests using FHIR, tracking PCR SARS-CoV-2 tests, and storing tests with the Chilean Ministry of Health.
The nonfunctional requirements such as performance and security are essential in health care information systems [
Nonfunctional requirements types for interoperable development. Catalog of nonfunctional requirements obtained from Wiegers (2005) and adapted for the interoperable platform to report polymerase chain reaction SARS-CoV-2 tests. FHIR: Fast Healthcare Interoperability Resources; HL7: Health Level 7.
We have implemented the platform with the UC Christus laboratory. This is primarily because they process the PCR SARS-CoV-2 tests for the “Esperanza” Project [
It is critical to build a comprehensive implementation guide [
The interoperable FHIR platform to report PCR SARS-CoV-2 tests from laboratories to the Chilean government was designed and developed following the interoperable methodology previously described. This platform could be used to report PCR SARS-CoV-2 tests from laboratories in any country with minimal changes since the interoperable methodology used is highly structured, reusable, and standardized.
The minimum data set was created from the stakeholder analysis and could extend its use beyond the COVID-19 pandemic.
Data set of laboratory polymerase chain reaction results. The minimum data set to build the polymerase chain reaction SARS-CoV-2 report.
Field | Cardinality | Data type | Length | Description |
Identification type code | 1.. * | Varchar | 10 | Type of code that the patient used to identify themselves |
Identification number | 1.. * | Varchar | 20 | Code that identifies the patient as unique |
Name | 1… * | Varchar | 30 | Patient name |
Last name | 1..1 | Varchar | 30 | Patient’s last name |
Mother’s last name | 1..1 | Varchar | 30 | Patient’s mother’s name |
Birth date | 1..1 | Date | 8 | Patient’s birth date in the format YYYY-MM-DD |
Gender | 1..1 | Varchar | 2 | Patient’s gender |
Test type | 1..1 | Integer | N/Aa | Code of sample type |
Test collection date | 1..1 | Datetime | N/A | Date and time when test collection occurred |
Test reception date | 1..1 | Datetime | N/A | Date and time when the test was received |
Laboratory code | 0..1 | Integer | N/A | Unique code that identifies the laboratory |
Another laboratory | 0..1 | Text | 30 | When “Laboratory Code” is empty, write the laboratory’s name in this field |
Test code | 1..1 | Varchar | 10 | LOINCb Code identifies the test with the international terminology system [ |
Test Result | 1..1 | Varchar | 30 | LOINC identifies the result with the international terminology system [ |
Validation date | 1..1 | Datetime | N/A | This is when the medical technologist accepts the test result |
Petition number | 1..1 | Integer | N/A | Value composed of 2 codes with the following format: Laboratory Code + LISc internal request code (3 + 12) |
aN/A: not applicable.
bLOINC: Logical Observation Identifiers Names and Codes.
cLIS: Laboratory Information Systems.
The diagram created represents the complete process for obtaining the data and sharing the laboratories’ tests with FHIR, tracking PCR SARS-CoV-2 tests, and storing tests by the Chilean government. Moreover, the process identified the end point where the institutions share information (
Business Process Model and Notation diagram for the interoperable platform. The process modeled defines the workflow of the information and the end points where the institutions can interchange data. DB: database; FHIR: Fast Healthcare Interoperability Resources.
The match between the minimum data set and FHIR is shown in
With the clinFHIR modeler, we created a graph view (
Data set of laboratory results: the minimum data set matches each element with the FHIR.
Field | FHIRa | Resource and element |
Identification type code | Patient | Patient.identifier.type |
Identification number | Patient | Patient.identifier.value |
Name | Patient | Patient.name.given |
Last name | Patient | Patient.name.extension |
Mother’s last name | Patient | Patient.name.extension |
Birth date | Patient | Patient.birthDate |
Gender | Patient | Patient.gender |
Test type | Specimen | Specimen.type |
Test collection date | Specimen | Specimen.collection.collected |
Test reception date | Specimen | Specimen.receivedTime |
Laboratory code | DiagnosticReport | DiagnosticReport.performer.organization.identifier |
Another laboratory | DiagnosticReport | DiagnosticReport.performer.organization.identifier |
Test code | Observation | DiagnosticReport.result.code |
Test result | Observation | DiagnosticReport.result.valueCodeableConcept |
Validation date | Observation | DiagnosticReport.result.effectiveDateTime |
Petition number | DiagnosticReport | DiagnosticReport.identifier |
aFHIR: Fast Healthcare Interoperability Resources.
clinFHIR diagram with the resources and references. This graph shows the resources and element in the source resource that represents the reference.
The agile methodology is characterized by having light and evolutionary documentation. The design documentation (BPMN process, list of requirements, match standards, database model, and sequence diagrams) is necessary to document and follow the platform’s development.
The development of the proposed architecture began with the configuration of the security layer (
At the end of this stage, we generated the message container (
JWT authentication server. The security layer was configured with JWT to obtain valid credentials and access the HAPI FHIR server. API: application programming interface; FHIR: Fast Healthcare Interoperability Resources; JWT: JavaScript Object Notation Web Token.
Fast Healthcare Interoperability Resources Bundle (part of the complete Bundle) that contains the resources selected for polymerase chain reaction SARS-CoV-2 tests.
Software testing was focused on testing both functional and nonfunctional requirements. The functional requirements were tested with the critical features that an interoperable web platform should have. In this sense, three functionalities were measured: (1) obtaining the data and sharing the laboratories’ tests with FHIR, (2) tracking PCR SARS-CoV-2 tests, and (3) storing tests with the Chilean government (
Nonfunctional requirements were tested considering the classification previously described (
Results from testing the functional requirements. Each functional requirement was tested.
Test | Data | Result expected | Result |
Obtaining the data and sharing the laboratories’ tests with FHIRa | FHIR in JSONb format with the full data set | Success | Bundle with links to resources created; success |
Obtaining the data and sharing the laboratories’ tests with standard FHIR | FHIR in JSON format |
Failure | Bundle with errors; failure |
Tracking PCRc SARS-CoV-2 tests | Request sent to FHIR server | Success | Bundle with resources; success |
Storing tests with the Chilean government | Request sent with laboratory code | Success | Bundle with resources only for laboratory code; success |
aFHIR: Fast Healthcare Interoperability Resources.
bJSON: JavaScript Object Notation.
cPCR: polymerase chain reaction.
The result of testing the nonfunctional requirements. Each nonfunctional requirement was tested.
Nonfunctional requirements | Results | Description | |
|
|||
HL7a interfaces | FHIRb R4 | Interfaces with HL7 FHIR specification | |
Format | JSONc, UMLd, XML, and TURTLE | Several formats facilitate the use of the HL7 FHIR interfaces | |
Documentation | Implementation guide based on HL7 FHIR specification | Documentation standard | |
Usability | Technical and nontechnical people understand FHIR resources. | The quality attribute that assesses how easy user interfaces are to use | |
|
|||
Response time | 240 milliseconds | The time they were spent waiting for a response from service: |
|
Throughput | 28.3 requests/second | Messages are processed successfully per unit of time: |
|
Process management time | 131 milliseconds | The time spent per task: |
|
Main memory storage | 4 GB+ | Main memory to store data temporarily | |
Secondary storage | 5.7 MB with 11,827 resources | Persistent memory to store data permanently |
aHL7: Health Level 7.
bFHIR: Fast Healthcare Interoperability Resources.
cJSON: JavaScript Object Notation.
dUML: Unified Modeling Language.
A private secure network managed the security infrastructure. The laboratory was connected by a virtual private network (VPN) with the Ministry of Health. For this solution, we used the VPN for sending bundles (with all the resources involved).
For the authentication and authorization, the platform was implemented through the API gateway with valid credentials and the right access control list. This involves a set of rules or a promise usually executed through agreements that limit access or place restrictions on certain types of information. The authentication was implemented with the JWT with an expiration time, verifying the person’s or device’s identity.
The integrity was tested considering accuracy (number of mistakes that a failure detector made in a certain period) and completeness (number of crashed processes suspected by a failure detector in a certain period). We obtained (
At the beginning of the implementation, a load test with 1000 requests was processed in 35 seconds. The response was under 216.7 milliseconds 50% of the time, and 90% of the time, these response times were under 323 milliseconds. The minimum and maximum response times were 118 milliseconds and 2806 milliseconds, respectively. The platform could process 28.3 requests per second. There were zero request errors. Following previous results, the solution would report 10,000 PCR SARS-CoV-2 tests in roughly 6 minutes.
The standard documentation for this solution is open for the FHIR community [
In this paper, we have designed and developed an interoperable and scalable solution that uses FHIR to access and share LIS data for reporting PCR SARS-CoV-2 tests to the Chilean government. This initiative was proposed as a use case to demonstrate the feasibility and efficiency of interoperability between heterogeneous health care information systems. The contribution was focused on supporting efficient communication in the context of the COVID-19 pandemic, collaborating with Chile’s strategy.
The WHO recommends the TTI strategy as actions that are central to containing the COVID-19 pandemic [
To comply with the WHO’s strategy effectively and efficiently, it is essential to incorporate interoperability and information systems in the data processes involved. In this sense, we need to strengthen and make interoperable the data involved in testing and the subsequent notification to the government [
Multiple countries have had problems counting and knowing the exact number of people infected with SARS-CoV-2 [
Interoperability in health care information systems has been a hard and slow process [
The interoperability area at CENS, in collaboration with Chilean laboratories (public and private), has supported a testing and traceability strategy within the “Esperanza” project [
The main result of this collaboration was the development of an interoperable HL7 FHIR platform to report PCR SARS-CoV-2 tests from laboratories to the Chilean government. This contribution was centered on supporting interoperability and communication with international standards (HL7 FHIR). The described interoperable platform aims to support the efficient reporting of PCR tests with FHIR from all the national laboratories to the Chilean government. The international standards for interoperability for reporting PCR SARS-CoV-2 tests applied in our platform could be applicable and scalable in other countries, contributing to interoperability in health care information systems.
This platform was developed for the Esperanza COVID-19 Project [
The testing and implementation phases were applied with the back-end configuration described in the Methods section.
The prior work developed for reporting PCR SARS-CoV-2 tests from laboratories to the Chilean government was built ad hoc without standards. We made a brief comparison with the preceding solution used and found the following: the prior work does not use interoperability standards (web services–based solution), the response time of the preceding work was higher than 681 milliseconds (three times more), and a simple token managed the security without an expiration time.
The FHIR platform for reporting PCR SARS-CoV-2 tests from laboratories to the Chilean government was implemented online and is currently being used with UC Christus Laboratory.
The platform was tested and implemented adequately. On average, 1000 PCR SARS-CoV-2 tests are processed in 35 seconds, with confidentiality, secure authorization and authentication, and message integrity.
This platform simplifies the reporting of PCR SARS-CoV-2 tests and contributes to reducing the time and probability of mistakes from counting positive cases.
The interoperable solution with FHIR is working successfully and is open for the community, laboratories, and any institution that needs to report PCR SARS-CoV-2 tests.
Minimum data set polymerase chain reaction SARS-CoV-2.
Health Level 7 Fast Healthcare Interoperability Resources Bundle polymerase chain reaction SARS-CoV-2.
application programming interface
Business Process Model and Notation
National Center of Health Information Systems
Fast Healthcare Interoperability Resources
Health Level 7
JavaScript Object Notation
JavaScript Object Notation Web Token
Laboratory Information Systems
polymerase chain reaction
representational state transfer
testing, traceability, and isolation
virtual private network
World Health Organization
The authors would like to acknowledge the Esperanza COVID-19 Project (BPH, UC), CENS CORFO 16CTTS-66390, UC Christus Laboratory, and Unidad de Salud Digital Servicio de Salud Metropolitano Sur Oriente.
None declared.