# External reference data provenance

Generated: 2026-05-17T21:08:16+00:00

## What this layer is

`data/external_reference/` is the reusable external benchmark surface for Z-Screen experiments. It is intentionally separate from the internal Z-Screen source layers in `data/raw/`, `data/mrna_latents/`, `data/condition_representations/`, `data/gene_effects/`, and `data/image_features/`.

## Curation done for this clean release

- Copied Tahoe metadata Parquets unchanged from the legacy benchmarking bundle.
- Copied LINCS compressed metadata unchanged where already compressed.
- Gzip-compressed two LINCS beta metadata text files so the clean release remains validation-friendly while preserving decompressed content.
- Converted legacy CSV rank-signature and benchmark-output tables to Parquet with zstd compression. No signatures or scores were recomputed during this curation pass.
- Copied scPerturb file manifests and Enrichr GMT gene sets unchanged.
- Copied the legacy build scripts into `data/external_reference/provenance_scripts/` as provenance only. They document how the current processed reference tables were originally produced.

## Main processed reference tables

| Dataset | Primary path | Notes |
|---|---|---|
| Replogle K562 genome-wide CRISPR KO | `data/external_reference/crispr_perturbation_atlases/replogle_2022_k562_gwps/replogle_rank_signatures_top_genes.parquet` | Best promoter per target gene, knockdown-filtered pseudobulk Z-normalized signatures. |
| Norman and Weissman K562 CRISPRa | `data/external_reference/crispr_perturbation_atlases/norman_weissman_2019_k562_crispra/norman_rank_signatures_top_genes.parquet` | Single and combinatorial CRISPRa pseudobulk effects versus control. |
| Selected THP1 scPerturb CRISPR | `data/external_reference/crispr_perturbation_atlases/scperturb_thp1_selected/scperturb_rank_signatures_top_genes.parquet` | Local THP1 CRISPR signatures from selected scPerturb datasets. Raw H5AD files are not bundled. |
| LINCS L1000 overlap signatures | `data/external_reference/compound_atlases/lincs_l1000/processed/lincs_l1000_rank_signatures_top_genes.parquet` | Level-5 LINCS consensus signatures sliced for Z-Screen overlap compounds. |
| Tahoe-100M metadata | `data/external_reference/compound_atlases/tahoe_100m/metadata/` | Metadata-only. Tahoe pseudobulk signatures are not bundled. |

## Important boundary

The CRISPR tables are external genetic-state references. They are useful for gene-rank and phenomimic comparisons, but a high similarity score should be treated as a perturbation-state hypothesis, not as direct target identification.

For exact file hashes and row counts, see:

- `data/external_reference/catalog/external_reference_file_manifest.csv`
- `data/external_reference/catalog/external_reference_dataset_catalog.csv`