Fig. 3: RareLink command-line interface and data flow for the Kabuki Type 1 evaluation cohort. | npj Genomic Medicine

Fig. 3: RareLink command-line interface and data flow for the Kabuki Type 1 evaluation cohort.

From: RareLink: scalable REDCap-based framework for rare disease interoperability linking international registries to FHIR and Phenopackets

Fig. 3: RareLink command-line interface and data flow for the Kabuki Type 1 evaluation cohort.

a The RareLink CLI is organised into five primary command groups—framework (global configuration), setup (local installation), redcap (interaction with a REDCap project), fhir (FHIR export via the RareLink-FHIR module) and phenopackets (Phenopacket generation via the RareLink-Phenopackets module)—with further subcommands under each. Future releases will extend functionality as requirements evolve. b Key data-flow steps (download-records, phenopackets export, fhir export) are invoked after setup (setup keys, fhir setup, and, if necessary, fhir hapi-server and redcap validate-hgvs) on the CLI to fetch, validate, and transform REDCap data into the LinkML representation of the RareLink-CDM, Phenopackets, and FHIR instances (Supplementary Fig. 1 for full console output). The LinkML data can be imported back into REDCap using the redcap upload-records command. If the evaluation cohort had been imported from another retrospective database, LinkML-Map could also have been used. CDM common data model. FHIR Fast Healthcare Interoperability Resources. LinkML unified data modeling language. REDCap Research Electronic Data Capture.

Back to article page