phenopackets

Repository for the GA4GH phenopacket schema

Collections of GA4GH phenopackets that represent individuals with Mendelian diseases.

An app and library for building, conversion, and validation of GA4GH Phenopackets.

A Python library for discovery of genotype-phenotype associations

EXPERIMENTAL rendering of phenopackets in linkml

Analysis of LLMs for Clinical Observations

GA4GH Phenopacket to LLM prompt

Reference java implementation for phenopackets

The web UI for Convert-Pheno, a software toolkit for the interconversion of standard data models for phenotypic data

Phenopackets-based metadata service for the Bento platform. Docs: https://metadata-service.readthedocs.io

A command line utility for operating over Phenotype eXchange Format (PXF) files.

Export Phenopackets from OMOP

Validation of phenopackets in C++

Phenotype2Phenopacket is a command-line tool that converts a phenotype annotation into GA4GH Phenopackets, facilitating standardised phenotypic data representation.

A Python library to map from any bespoke tabular data format to the GA4GH Phenopacket schema.

Structured rare-disease case data mined from the literature, with per-field provenance and a reproducible benchmark against 4,147 expert-curated phenopackets

Importing and exporting Phenopackets from and to the SAMS application. Resources used in my BSc Thesis @ FU Berlin.

A QC and explainability toolkit for phenotype cohorts: HPO/Phenopacket quality control, annotation-bias checks, outliers, ontology-aware group comparison and robust cohort structure.