studio2ga4gh 0.3.0

Convert Pedigree Studio sessions to GA4GH Pedigree Standard and Phenopackets

studio2ga4gh

Convert Pedigree Studio session JSON files to GA4GH interoperability formats:

• GA4GH Pedigree Standard — relationship-graph model using the Kinship Ontology (KIN)
• Phenopackets Family — PED-compatible pedigree with disease information

Installation

pip install studio2ga4gh

Usage

Command line

studio2ga4gh session.json
studio2ga4gh session.json -o my_family -d ./output/

This produces two files per pedigree:

• {name}_ga4gh.json — GA4GH Pedigree (relationship graph with KIN ontology codes)
• {name}_phenopackets.json — Phenopackets Family (PED-compatible pedigree + diseases)

Python API

import studio2ga4gh, json

with open("session.json") as f:
    session = json.load(f)

result = studio2ga4gh.convert(session)
print(result.summary)
for filename, content in result.files:
    print(f"--- {filename} ---")
    print(content[:200])

What Each Output Contains

GA4GH Pedigree (_ga4gh.json)

The rich graph-based format from the GA4GH Pedigree Standard. It represents each parent-child and twin relationship as an explicit edge with a KIN ontology code:

Relationship	KIN Code	Label
Biological mother	KIN:027	isBiologicalMotherOf
Biological father	KIN:028	isBiologicalFatherOf
Adoptive parent	KIN:022	isAdoptiveParentOf
Identical twin	KIN:010	isMonozygoticMultipleBirthSiblingOf
Non-identical twin	KIN:011	isDizygoticMultipleBirthSiblingOf

Dashed child lines in Pedigree Studio (adoption) are exported as isAdoptiveParentOf rather than biological parent relationships.

Phenopackets Family (_phenopackets.json)

The GA4GH Phenopackets schema Family element, containing:

• A PED-compatible pedigree with Person records (familyId, individualId, parents, sex, affectedStatus)
• A proband Phenopacket with disease terms extracted from the legend
• relatives Phenopackets for affected family members with their diseases
• consanguinousParents flag if any consanguineous partnerships exist

Phenotype Mapping

Disease/condition names are taken from the Pedigree Studio legend labels. The converter maps visual markers to affected status using the same logic as studio2ped.

Multiple Pedigrees

If the session contains disconnected pedigrees, numbered file pairs are produced:

pedigree_1_ga4gh.json
pedigree_1_phenopackets.json
pedigree_2_ga4gh.json
pedigree_2_phenopackets.json

License

MIT