Alias resolution and precedence

Schema field aliases are matched case-insensitively after trimming whitespace, in declaration order. The first exact match wins. There is no regex or fuzzy matching, and no inference from column contents.

Because matching is case-insensitive, the same alias (case-insensitively) cannot appear twice within one field's aliases list, nor be reused across two different fields in the same schema — both are rejected at load time with a descriptive SchemaError.

batch alias precedence (schema v0.2.1)

Schema	Order
generic-cell-painting	batch_id → batch → Metadata_Batch → Metadata_Batch_Number
jump-cp	Metadata_Batch → batch_id → Metadata_Batch_Number

Metadata_Batch_Number is the LINCS-style batch field observed on Cell Painting Gallery Level 4b profiles.

perturbation_id alias precedence (schema v0.2.0+)

Schema	Order
jump-cp	Metadata_JCP2022 → Metadata_broad_sample → Metadata_pert_iname → perturbation_id → pert_id → treatment_id
generic-cell-painting	perturbation_id → pert_id → treatment_id → Metadata_broad_sample → Metadata_pert_iname → Metadata_JCP2022

Metadata_pert_type vs perturbation modality

Metadata_pert_type is an alias of control_type only (control vs treatment / poscon / negcon / trt). It is not an alias of perturbation_modality. In LINCS exports that column commonly means control status, not chemical/genetic modality — see Public-data pilots.

Implementation

• Resolution: src/cp_anndata_validator/schema/resolve.py
• Schema load validation: src/cp_anndata_validator/schema/loader.py
• Tests: tests/test_schema_resolution.py, tests/test_batch_alias_lincs.py

See also ADR-0005 and Known limitations.