Add cell matching schemas and CellTypeReferenceUser#98
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sdorkenw
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Aug 29, 2025
- 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
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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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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
approved these changes
Aug 29, 2025
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