Phenopacket & Ontologies

LIVE

Phenopacket Export (GA4GH v2)

• HPO-coded phenotypic features with structured negation (excluded: true)
• MONDO-coded diseases
• Medications as Treatment blocks (PRESCRIPTION by default)
• Variant interpretations when gene and variant are both present
• HPO autocomplete in-modal for adding symptoms before export
• Append-only audit log of every export

Honesty rails locked. Every exported Phenopacket carries acmgPathogenicityClassification: NOT_PROVIDED and interpretationStatus: CANDIDATE. ARIA does not assert pathogenicity claims.

Ontology Manager

Explainer popover defines HPO and MONDO in plain language. Full modal for managing imports: Bundled subset / Downloading / Parsing / Validating / Writing / Imported / Failed. Optional full HPO (~21 MB) and MONDO (~98 MB) downloads from official GitHub releases. CC-BY attribution on every download.

SSSOM round-trip

Simple Standard for Sharing Ontology Mappings, v0.11. Export TSV for collaborators (canonical YAML header, 12 columns, curie_map). Import TSV without impersonating the curated seed set — imported rows are clamped to a user:* author namespace.

ConceptReviewQueue

Safety gate for mappings imported from external Phenopackets. Before / after diff on every conflict. "I understand" checkbox required before any overwrite. Compare-and-swap semantics.

Why it exists

GA4GH standards are the export format and the import format here. Supporting Phenopacket v2 natively means ARIA's data can be consumed by CHOP, Cornell, BCM, and every biopharma company already in the standard, without custom adapters.