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Provenance of the jump-cp schema

jump-cp is a compatibility preset shipped by cp-anndata-validator. It is not an official schema endorsed by, or produced in cooperation with, the JUMP Cell Painting Consortium. It exists so that AnnData files converted from JUMP-style CellProfiler/CytoTable outputs resolve their columns out of the box, without requiring every user to hand-write a custom schema YAML file.

Sources

  • Column-naming conventions (Metadata_Plate, Metadata_Well, Metadata_Site, Metadata_Source, Metadata_JCP2022, Metadata_Batch, Metadata_pert_type, Metadata_perturbation_modality, Metadata_ObjectNumber) are taken from the public metadata README of the jump-cellpainting/datasets repository: https://github.com/jump-cellpainting/datasets/blob/main/metadata/README.md
  • Feature compartment prefixes (Cells_, Cytoplasm_, Nuclei_, Image_) follow the naming convention documented by pycytominer, the feature-aggregation library used throughout the JUMP pipeline and widely adopted across Cell Painting analyses more generally.

What was and wasn't carried over

The schema (src/cp_anndata_validator/schema/resources/jump-cp.yaml) maps each JUMP metadata column to the same canonical fields used by generic-cell-painting, so that the rest of the package (checks, profile detection, reports) treats a JUMP-style dataset identically to any other:

Canonical field JUMP alias Notes
plate Metadata_Plate
well Metadata_Well
site Metadata_Site single-cell only
cell_id Metadata_ObjectNumber single-cell only
perturbation_id Metadata_JCP2022, then Metadata_broad_sample, then Metadata_pert_iname First match wins; generic aliases follow
control_type Metadata_pert_type JUMP's poscon/negcon/trt convention (plus poscon_/negcon_ prefixes at check time). In LINCS exports this column is control/treatment status — not modality.
perturbation_modality Metadata_perturbation_modality compound/orf/crispr/unknown. Do not use Metadata_pert_type here.
batch Metadata_Batch, then batch_id, then Metadata_Batch_Number Metadata_Batch_Number added in schema v0.2.1 (LINCS-style)
source Metadata_Source JUMP's multi-site data-generation identifier

Every field also keeps its generic-cell-painting-style alias (for example plate_id, well_id) so a dataset that mixes conventions, or that has already been partially renamed, still resolves.

Schema version 0.2.0 also extends measurement_families with the evidenced CellProfiler families ObjectSkeleton, Math, Overlap, SizeShape, AreaOccupied and ImageQuality (shared with generic-cell-painting). Schema version 0.2.1 appends Metadata_Batch_Number to the batch alias list on both built-in schemas.

Explicitly not claimed

  • This preset does not imply JUMP has reviewed, endorsed, or published this package.
  • It does not attempt to encode every JUMP metadata column (see the two README/pycytominer sources above for the complete, authoritative list) — only the subset relevant to this package's validation categories.
  • "Compatibility" refers to column-name aliasing convenience only; it makes no claim about compatibility with any specific JUMP data release version.