API – Application Programming Interface – a protocol for communicating with a software application
FHIR - Fast Healthcare Interoperability Resources – a standard for exchanging healthcare information electronically
EHR – Electronic Health Record (e.g., Epic) - an IT system that stores data and captures the patient’s health records in real-time.
EDW – Enterprise Data Warehouse – a database often used by EHRs to store clinical notes, billing information, patient satisfaction, etc.
Health Institutions and the PHC¶
Health Institutions can either send their data to an EDW where data is stored and converted to FHIR before being sent to the PHC, or they use an API to skip the EDW and directly convert the data to FHIR and send the data to the PHC.
Data in the EDW is often structured differently than in the EHR. How it's structured depends on the EDW team and their vendors as there is no standard.
Conduits from an EDW or an EHR can have many paths into the PHC. Most health ecosystems require data expertise on their side to help map the non-genomic health data into FHIR in preparation for the PHC environment. This mapping is diverse and non-standardized between the EHR vendors and can be a complicated process. However, our Customer Engagement team will work with you and your team to make a successful conduit.
Many times the process of converting data into FHIR and importing it into the PHC will show opportunities for health institutions to improve their own data collection procedures.
Options for getting data into the PHC:
The Health Institution IT can convert the data to FHIR and push it into the PHC via the PHC FHIR API.
The Health Institution IT can convert the data into files containing FHIR resources and use the PHC Task Service to push the data into the PHC.
If the health information is in a CSV file, the PHC Task Service can be used to convert data into FHIR and push it into the PHC.
If you use Cerbo EHR, LifeOmic's EHR integration can handle the conversion.
Genomics Labs and the PHC¶
The PHC can store genomic data and aid you in interacting and visualizing results. Here are the steps needed to get genomic data into the PHC:
The Health Institution sends samples to the sequencing lab.
The Health Institution creates a FHIR Patient resource for each subject that provided a sample for sequencing. The FHIR Patient resource is created using the PHC FHIR API, CLI, or UI.
The sequencing lab provides the results of the sequencing to the Health Institution in the form of files. The type and format of the files vary by sequencing lab.
The Health Institution uploads the files to the PHC using the PHC Files API, CLI, or UI.
Now both the genomic files and subject data are in the PHC, but the PHC needs to be told to index the genomic files and associate it with a subject. The Health Institution can initiate the indexing of the genomic data by using the PHC API, CLI, or UI (coming soon). The Health Institution will need to know which files belong to which PHC subjects. This could be done by mapping a lab provided identifier with a PHC subject. PHC subjects are typically referenced by the ID of the FHIR Patient resource. The FHIR Patient resource can also be extended to contain other identifier information like MRN or Lab Identifier to make the mapping easier.