---
license: cc-by-4.0
---

# TEMP

Processed standardized expression `.h5ad` files and differential gene expression (DGE) `.h5ad` outputs from TEMP datasets whose upstream terms allow redistribution.

This repository contains:

- processed group-replicate bulk or pseudobulk input files under `<dataset>/`
- DGE outputs under `<dataset>/group_rep/` and `<dataset>/sep_rep/`

The DGE replicate modes indicate whether the DGE analysis was run using all replicates or per replicate (for within-dataset agreement evaluation), shortened to `group_rep` and `sep_rep`.

## License

The collection curation and packaging are released under CC BY 4.0.

CC BY 4.0 for TEMP curation/packaging; preserve each upstream license, notice, and attribution.

Each upstream dataset retains its original license, attribution, and notice requirements. See `upload_manifest.tsv` for processed-file provenance and `dge_upload_manifest.tsv` for per-DGE-file provenance.

## Files

### Processed Input Files

- `l1000_phase1/`: `l1000_phase1_level3_deg_ready_landmark_processed.h5ad` (NCBI/GEO public data; NCBI places no use/distribution restrictions)
- `l1000_phase2/`: `l1000_phase2_level3_deg_ready_landmark_processed.h5ad` (NCBI/GEO public data; NCBI places no use/distribution restrictions)
- `novartis_batch_2500/`: `novartis_standardized_processed.h5ad` (MIT License)
- `op3/`: `op3_standardized_processed.h5ad` (Public GEO data; Open Problems benchmark materials are MIT-licensed)
- `sciplex/`: `srivatsan20_sciplex3_processed.h5ad` (CC BY 4.0)
- `tahoe/`: `tahoe_processed.h5ad` (CC0 1.0)
- `vcpi_0001/`: `vcpi_0001_standardized_processed.h5ad` (CC BY 4.0 for public VCPI releases)
- `vcpi_0002/`: `vcpi_0002_standardized_processed.h5ad` (CC BY 4.0 for public VCPI releases)

### Differential Expression Files

DGE files are organized as `<dataset>/<replicate_mode>/<cell_line>_de.h5ad`. Each file contains treatment-vs-control contrasts for one cell line or context.

| Dataset | `group_rep` files | `sep_rep` files | Total DGE files |
|---|---:|---:|---:|
| `l1000_phase1` | 70 | 70 | 140 |
| `l1000_phase2` | 30 | 30 | 60 |
| `novartis_batch_2500` | 1 | 1 | 2 |
| `op3` | 4 | 4 | 8 |
| `sciplex` | 3 | 3 | 6 |
| `tahoe` | 48 | 48 | 96 |
| `vcpi_0001` | 1 | 1 | 2 |
| `vcpi_0002` | 1 | 1 | 2 |
| **Total** | **158** | **158** | **316** |

## Manifests

- `upload_manifest.tsv`: one row per processed input file, including path, source, upstream license, and required notice.
- `dge_upload_manifest.tsv`: one row per DGE file, including dataset, replicate mode, cell line/context, repository path, source, upstream license, and required notice.

## AnnData Schema

### Processed Input `.h5ad`

Rows in `.obs` represent standardized bulk samples or pseudobulk profiles. Core metadata fields include `plate`, `well`, `cell_type`, `perturbagen`, `pert_type`, `is_control`, `pert_dose_uM`, `pert_time_h`, `suspension_type`, `tissue`, `tissue_type`, `disease`, `library`, `stimulation`, `guide`, `dataset`, `assay`, `development_stage`, `organism`, `sex`, `self_reported_ethnicity`, `pubchem_cid`, `psbulk_cells`, and `psbulk_counts` where available.

Columns in `.var` represent genes and include `symbol`; some files include additional gene annotations such as merged-gene indicators. `.X` stores the standardized expression matrix. For single-cell-derived pseudobulk files, `.X` contains pseudobulk counts and `.layers["psbulk_props"]` may contain pseudobulk proportions. Bulk-derived datasets may represent raw counts, normalized expression, or platform-specific intensity values depending on the upstream assay and preprocessing.

### DGE `.h5ad`

Rows in `.obs` represent treatment-vs-control contrasts for one cell line or context. The row index is the contrast label, and metadata is inherited from the treated condition after DGE preprocessing.

Columns in `.var` represent genes and carry gene annotations from the processed input file.

`.X` is intentionally absent from DGE files; DGE statistics are stored in `.layers`:

- `logFC`
- `stdev.unscaled`
- `stdev.scaled`
- `CI.L`
- `CI.R`
- `AveExpr`
- `t`
- `P.Value`
- `adj.P.Value.within_one_contrast`
- `adj.P.Value.across_all_contrasts`
- `B`

`.uns` includes upstream metadata carried from the processed input plus DGE processing metadata such as `threshold_filter_cells` and `qc_filtering_enabled`.

## Sources And Notices

- `l1000_phase1`: LINCS L1000 Phase I, GEO GSE92742 - https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE92742. Cite LINCS L1000/GSE92742 and preserve upstream attribution.
- `l1000_phase2`: LINCS L1000 Phase II, GEO GSE70138 - https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70138. Cite LINCS L1000/GSE70138 and preserve upstream attribution.
- `novartis_batch_2500`: Novartis DRUG-seq U2OS MoABox Dataset - https://zenodo.org/records/14291446. Retain the Novartis/Zenodo MIT license notice and citation.
- `op3`: OP3 perturbation prediction dataset, GEO GSE279945 - https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE279945. Cite OP3/Open Problems and GSE279945.
- `sciplex`: scPerturb / SrivatsanTrapnell2020_sciplex3 - https://zenodo.org/records/13350497. Cite scPerturb/Sci-Plex and include CC BY 4.0 attribution.
- `tahoe`: Tahoe-100M - https://huggingface.co/datasets/tahoebio/Tahoe-100M. Citation requested by the dataset card; attribution still recommended.
- `vcpi_0001`: Virtual Cell Pharmacology Initiative public release - https://thevirtualcell.com/. Cite VCPI/Ginkgo Datapoints and include CC BY 4.0 attribution.
- `vcpi_0002`: Virtual Cell Pharmacology Initiative public release - https://thevirtualcell.com/. Cite VCPI/Ginkgo Datapoints and include CC BY 4.0 attribution.