| --- |
| 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. |
|
|
