Applying Fast Healthcare Interoperability Resources (FHIR) for Pathogen Genomics at the Point of Care

Modern-day microbial diagnostics and genomics have the potential to revolutionize individual and population-level infectious disease prevention, patient care, and treatment. To realize the potential, we need new approaches to standardizing testing and genomic data so that complex data and knowledge can be integrated at the point of care reliably and without ambiguity. We provide a series of approaches to pathogen genomic information standardization and guides to improve data interoperability which is key to harnessing the power of modern testing and genomics data. We develop generalizable knowledge and guidance to integrate the systems of terminology management, data modeling and inference that can provide flexibility for collaborative development across multiple domains (i.e. public health, clinical, academic research and open source communities) in order to significantly speed up the applications of pathogen genomic knowledge. We observed numerous advantages to using healthcare-specific standards such as Fast Healthcare Interoperability Resources (FHIR) and Clinical Quality Language (CQL). Advantages include convenient information models, mechanisms for verification, and the availability of tools, documentation and expertise to provide assistance during development. We also found the critical role of community-driven domain-specific ontologies which provide a source of terminologies thereby addressing content coverage gaps in the common clinical terminologies. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work has been supported by grant to Dr. William Hsiao from the Canadian Institutes of Health Research (Project Grant Number: PJT-159456) and the Genome BC and Genome Canada (Grant Number: 286GET) ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present work are contained in the manuscript