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  • Add CellMatch schema for matching cells between datasets
  • Add CellSimilarity schema for scoring similarity between two cells
  • Add CellMatchReference schema (reference annotation version)
  • Add CellTypeReferenceUser schema extending CellTypeReference with user_id
  • Register all new schemas in type_mapping for system availability

- Add CellMatch schema for matching cells between datasets
- Add CellSimilarity schema for scoring similarity between two cells
- Add CellMatchReference schema (reference annotation version)
- Add CellTypeReferenceUser schema extending CellTypeReference with user_id
- Register all new schemas in type_mapping for system availability
@sdorkenw sdorkenw requested review from Copilot and fcollman August 29, 2025 00:17
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Pull Request Overview

This PR adds new annotation schemas for cell matching functionality between datasets and extends the existing cell type reference schema with user tracking. The changes introduce cell similarity scoring capabilities and provide a reference annotation version for cell matching workflows.

  • Added three new schemas for cell matching: CellMatch, CellSimilarity, and CellMatchReference
  • Extended CellTypeReference with CellTypeReferenceUser schema that includes user_id tracking
  • Registered all new schemas in the type_mapping for system-wide availability

Reviewed Changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 2 comments.

File Description
emannotationschemas/schemas/matching.py New file containing CellMatch, CellSimilarity, and CellMatchReference schemas for cell matching functionality
emannotationschemas/schemas/cell_type_local.py Added CellTypeReferenceUser schema extending CellTypeReference with user_id field
emannotationschemas/init.py Updated imports and type_mapping to register new schemas

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sdorkenw and others added 2 commits August 28, 2025 17:20
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
- Set index=True for match_id in CellMatch schema
- Set index=True for match_id in CellMatchReference schema
- Improves query performance for cell matching lookups
@fcollman fcollman merged commit 459f32a into master Aug 29, 2025
2 checks passed
@sdorkenw sdorkenw deleted the add-cell-matching-schemas branch September 2, 2025 17:41
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3 participants