Welcome to the documentation for phenopackets-schema!

The goal of the phenopacket-schema is to define the phenotypic description of a patient/sample in the context of rare disease, common/complex disease, or cancer. The schema as well as source code in Java, C++, and Python is available from the phenopacket-schema GitHub repository.

Contents

• Introduction to Phenopackets
  • Phenopacket basics
  • Requirement Levels
  • Ontologies
  • A short introduction to protobuf
  • FHIR Implementation Guide
• Phenopacket Schema
  • Overview
• Top-Level Elements
  • Phenopacket
  • Family
  • Cohort
  • Interpretation
• Phenopacket building blocks
  • Age
  • AgeRange
  • Biosample
  • Disease
  • Evidence
  • ExternalReference
  • Gene
  • HtsFile
  • Individual
  • KaryotypicSex
  • MetaData
  • OntologyClass
  • Pedigree
  • PhenotypicFeature
  • Procedure
  • Resource
  • Sex
  • Variant
• Working with Phenopackets
  • Example code
  • Security disclaimer
• Phenopacket version 2
  • Version 2.0