Draft Pedigree schema v1: updated model, examples, and proto schema

[tripb]

Summary

Proposes the v1 Pedigree schema, updating the conceptual model from v0.1 and adding a formal proto3 schema modeled on phenopacket-schema conventions.

Individual changes

• sex → sex_assigned_at_birth (now optional; categorical values added)
• gender → gender_identity (categorical values added)
• dateOfBirth → date_of_birth, populationDescriptors → population_descriptors (snake_case)
• karyotypicSex removed (to be represented in linked genotypic data)
• affected removed (to be represented in linked phenotypic data)
• egg_parent and sperm_parent added as shorthand for gamete-provider parent links

ExternalIdentifier (new)

• New concept linking an Individual to identifiers in external systems (EHR, Phenopackets, etc.) via external_id, external_id_system, external_system_endpoint

Relationship changes

• Single relation field replaced by biological_relationship (0..) and social_relationship (0..) for independent multi-valued representation
• twin_group added (monozygotic / dizygotic)
• consanguinity (bool) and consanguinity_note (free text) added

Pedigree changes

• indexPatients → index_patients (snake_case)

Proto schema (new)

• src/main/proto/ga4gh/pedigree/v1/ — four proto3 files:
  • base.proto — OntologyClass, TimeElement, Age, AgeRange, GestationalAge
  • individual.proto — Individual, ExternalIdentifier, SexAssignedAtBirth enum, GenderIdentity enum
  • relationship.proto — Relationship, TwinType enum
  • pedigree.proto — Pedigree, PedigreeStatus enum
• Package namespace: org.ga4gh.pedigree.v1, mirroring phenopacket-schema conventions

Docs

• pedigree-model.rst — updated field tables with all v1 changes
• examples.rst — all YAML examples updated to v1 field names; added consanguinity example
• using-the-pedigree-model.rst — updated relationship direction section; new Biological vs. Social and Consanguinity subsections
• schema.rst — new page documenting the proto schema and how to compile it
• README.md — updated with v1 change summary and proto schema link

Test plan

• Review all field names and descriptions in pedigree-model.rst against the v1 spec CSV
• Verify YAML examples are consistent with updated model (especially relationship structure)
• Compile proto files with protoc to confirm no syntax errors
• Review proto field numbers and optional vs repeated choices
• Verify egg_parent_id / sperm_parent_id consistency note is accurate
• Confirm ExternalIdentifier embedding approach (embedded in Individual vs. separate collection)

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