Schema Valid Is Not Exchange Ready
Clinical phenotype data can satisfy JSON syntax while omitting ontology resources, repeating assertions, or marking the same term both observed and excluded.
phenopacketlint checks packet identity and metadata, resource references, ontology identifier shape, labels, duplicates, and observed-versus-excluded contradictions, then produces field-level errors, warnings, and a quality score.
Make Every Finding Actionable
The validator preserves paths into the packet and runs identically through the CLI, API, responsive workbench, Docker image, and test suite. No patient payload leaves the local process.
The Demo
The committed rare-disease fixture contains three phenotype features: two observed and one excluded. It passes every semantic check with a quality score of 100.
This is an exchange-readiness layer, not a replacement for the official protobuf validator, terminology services, consent review, or clinical interpretation.
Standards Basis
The checks target the GA4GH Phenopacket Schema v2 exchange model for computable phenotype and disease information.
Read the GA4GH Phenopackets v2.