Unite attributes librarygeneration 20251212

[puja-trivedi]

This PR contains changes to the LibraryGeneration Model that were made to unify the information between the MOWG metadata spreadsheet and the NIMP terminology list. Specifically focusing on if every attribute has a BICAN UUID and if that matches what is in the NIMP database.

[gemini-code-assist]

Summary of Changes

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This pull request implements a significant standardization and expansion of the data schema related to library generation processes. It involves a comprehensive refactoring of attribute and slot definitions across multiple TSV files, aiming to unify common fields, improve consistency, and enrich the permissible values for various experimental techniques and biological metadata. These changes are crucial for enhancing the clarity and interoperability of the data model.

Highlights

• Schema Standardization: The headers and column order in Attributes.tsv and Slots.tsv have been significantly refactored and standardized, consolidating related fields and introducing new ones like 'Local Variable Name'.
• Attribute and Slot Unification: Attributes and slots previously tied to specific process classes (e.g., CdnaAmplification, CellBarcoding) have been merged into their respective sample classes (e.g., AmplifiedCdna, BarcodedCellSample), streamlining the data model. The cell_label_barcode was unified across dissociated and enriched cell samples.
• Expanded Value Sets: The ValueSets.tsv file has been updated to include a broader range of permissible values for barcoded_cell_sample_technique and library_technique, reflecting new experimental methods. A comprehensive list of species with NCBI Taxonomy IDs was also added.
• Terminology Refinement: Age unit terminology in ValueSets.tsv was standardized to singular forms (e.g., 'day' instead of 'days'), and Donor's identifier slot was updated to subject_id with a new UUID and definition.
• Cross-Reference Introduction: New xref slots have been introduced across various biological entities in Slots.tsv, standardizing how cross-references are handled within the schema.

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[gemini-code-assist]

Code Review

This pull request introduces a significant refactoring of the schema attributes, primarily within the TSV files that define the LinkML model. The changes focus on unifying attributes under more appropriate classes and standardizing slot names, such as using preparation_date across different process classes. This greatly improves the consistency and maintainability of the schema. Additionally, new enum values have been added, and xref slots are introduced for better data integration. Overall, these are excellent improvements. I've found one minor typo in a slot definition that should be addressed.