Duplicate from tahoebio/Tahoe-100M

Co-authored-by: Shreshth Gandhi <[email protected]>

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README.md

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+---
+license: cc0-1.0
+tags:
+- biology
+- single-cell
+- RNA
+- chemistry
+size_categories:
+- 100M<n<1B
+configs:
+- config_name: expression_data
+  data_files: data/train-*
+  default: true
+- config_name: sample_metadata
+  data_files: metadata/sample_metadata.parquet
+- config_name: gene_metadata
+  data_files: metadata/gene_metadata.parquet
+- config_name: drug_metadata
+  data_files: metadata/drug_metadata.parquet
+- config_name: cell_line_metadata
+  data_files: metadata/cell_line_metadata.parquet
+- config_name: obs_metadata
+  data_files: metadata/obs_metadata.parquet
+- config_name: pseudobulk_differential_expression
+  data_files: metadata/pseudobulk_differential_expression/train-*
+dataset_info:
+  features:
+  - name: genes
+    sequence: int64
+  - name: expressions
+    sequence: float32
+  - name: drug
+    dtype: string
+  - name: sample
+    dtype: string
+  - name: BARCODE_SUB_LIB_ID
+    dtype: string
+  - name: cell_line_id
+    dtype: string
+  - name: moa-fine
+    dtype: string
+  - name: canonical_smiles
+    dtype: string
+  - name: pubchem_cid
+    dtype: string
+  - name: plate
+    dtype: string
+  splits:
+  - name: train
+    num_bytes: 1693653078843
+    num_examples: 95624334
+  download_size: 337644770670
+  dataset_size: 1693653078843
+---
+
+# Tahoe-100M
+Tahoe-100M is a giga-scale single-cell perturbation atlas consisting of over 100 million transcriptomic profiles from 
+50 cancer cell lines exposed to 1,100 small-molecule perturbations. Generated using Vevo Therapeutics' 
+Mosaic high-throughput platform, Tahoe-100M enables deep, context-aware exploration of gene function, cellular states, and drug responses at unprecedented scale and resolution.
+This dataset is designed to power the development of next-generation AI models of cell biology, 
+offering broad applications across systems biology, drug discovery, and precision medicine.
+
+**Preprint**: [Tahoe-100M: A Giga-Scale Single-Cell Perturbation Atlas for Context-Dependent Gene Function and Cellular Modeling](https://www.biorxiv.org/content/10.1101/2025.02.20.639398v1)
+
+<img src="https://pbs.twimg.com/media/Gkpp8RObkAM-fxe?format=jpg&name=4096x4096" width="1024" height="1024">
+
+## Quickstart
+```python
+from datasets import load_dataset
+# Load dataset in streaming mode
+ds = load_dataset("tahoebio/Tahoe-100m", streaming=True, split="train")
+# View the first record
+next(ds.iter(1))
+```
+### Tutorials
+Please refer to our tutorials for examples on using the data, accessing metadata tables and converting to/from the anndata format.
+
+Please see the [Data Loading Tutorial](tutorials/loading_data.ipynb) for a walkthrough on using the data.
+
+<table>
+  <thead>
+    <tr>
+      <th>Notebook</th>
+      <th>URL</th>
+      <th>Colab</th>
+    </tr>
+  </thead>
+  <tbody>
+    <tr>
+      <td>Loading the dataset from huggingface, accessing metadata, mapping to anndata</td>
+      <td>
+        <a href="https://huggingface.co/datasets/tahoebio/Tahoe-100M/blob/main/tutorials/loading_data.ipynb" target="_blank">
+          Link
+        </a>
+      </td>
+      <td>
+        <a href="https://colab.research.google.com/#fileId=https://huggingface.co/datasets/tahoebio/Tahoe-100M/blob/main/tutorials/loading_data.ipynb" target="_blank">
+          <img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open in Colab"/>
+        </a>
+      </td>
+    </tr>
+  </tbody>
+</table>
+
+### Community Resources
+
+Here are a links to few resources created by the community. We would love to feature additional tutorials from the community, if you have built something on top of 
+Tahoe-100M, please let us know and we would love to feature your work.
+
+<table>
+  <thead>
+    <tr>
+      <th>Resource</th>
+      <th>Contributor</th>
+      <th>URL</th>
+    </tr>
+  </thead>
+  <tbody>
+    <tr>
+      <td>Analysis guide for Tahoe-100M using rapids-single-cell, scanpy and dask</td>
+      <td><a href="https://github.com/scverse" target="_blank">SCVERSE</a></td>
+      <td><a href="https://github.com/theislab/vevo_Tahoe_100m_analysis/tree/tahoe-DGX-fix" target="_blank">Link</a></td>
+    </tr>
+    <tr>
+      <td>Tutorial for accessing Tahoe-100M h5ad files hosted by the Arc Institute</td>
+      <td><a href="https://github.com/ArcInstitute" target="_blank">Arc Institute</a></td>
+      <td><a href="https://github.com/ArcInstitute/arc-virtual-cell-atlas/blob/main/tahoe-100M/tutorial-py.ipynb" target="_blank">Link</a></td>
+    </tr>
+  </tbody>
+</table>
+
+
+## Dataset Features
+We provide multiple tables with the dataset including the main data (raw counts) in the `expression_data` table as well as 
+various metadata in the `gene_metadata`,`sample_metadata`,`drug_metadata`,`cell_line_metadata`,`obs_metadata` tables.
+
+The main data can be downloaded as follows:
+```python
+from datasets import load_dataset
+tahoe_100m_ds = load_dataset("tahoebio/Tahoe-100M", streaming=True, split="train")
+```
+Setting `stream=True` instantiates an `IterableDataset` and prevents needing to 
+download the full dataset first. See [tutorial](tutorials/loading_data.ipynb) for an end-to-end example.
+
+The expression_data table has the following fields:
+
+| **Field Name**         | **Type**          | **Description**                                                                                                                                                                                                                                                                                                                                                                         |
+|------------------------|-------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| `genes`                | `sequence<int64>` | Gene identifiers (integer token IDs) corresponding to each gene with non-zero expression in the cell. This sequence aligns with the `expressions` field. The gene_metadata table can be used to map the token_IDs to gene_symbols or ensembl_IDs. The first entry for each row is just a marker token and should be ignored (See [data-loading tutorial](tutorials/loading_data.ipynb)) |
+| `expressions`          | `sequence<float32>` | Raw count values for each gene, aligned with the `genes` field. The first entry just marks a CLS token and should be ignored when parsing.                                                                                                                                                                                                                                              |
+| `drug`               | `string`    | Name of the treatment. DMSO_TF marks vehicle controls, use DMSO_TF along with plate to get plate matched controls.                                                                                                                                                                                                                                                                      |
+| `sample`             | `string`     | Unique identifier for the sample from which the cell was derived. Can be used to merge information from the `sample_metadata` table. Distinguishes replicate treatments.                                                                                                                                                                                                                |
+| `BARCODE_SUB_LIB_ID`| `string`     | Combination of barcode and sublibary identifiers. Unique for each cell in the dataset. Can be used as an index key when referencing to the `obs_metadata` table.                                                                                                                                                                                                                        |
+| `cell_line_id`       | `string`     | Unique identifier for the cancer cell line from which the cell originated. We use Cellosaurus IDs were, but additional identifiers such as DepMap IDs are provided in the `cell_line_metadata` table.                                                                                                                                                                                   |
+| `moa-fine`           | `string`     | Fine-grained mechanism of action (MOA) annotation for the drug, specifying the biological process or molecular target affected. Derived from MedChemExpress and curated with GPT-based annotations.                                                                                                                                                                                     |
+| `canonical_smiles`   | `string`     | Canonical SMILES (Simplified Molecular Input Line Entry System) string representing the molecular structure of the perturbing compound.                                                                                                                                                                                                                                                 |
+| `pubchem_cid`        | `string`     | PubChem Compound Identifier for the drug, allowing cross-referencing with public chemical databases. An empty string is used for DMSO controls. Please cast to int before querrying pubchem.                                                                                                                                                                                            |
+| `plate`              | `string`     | Identifier for the 96-well plate (1–14) in which the mixed-cell spheroid was seeded and treated.                                                                                                                                                                                                                                                                                        |
+
+
+## Additional metadata
+
+### Gene Metadata
+```python
+gene_metadata = load_dataset("taheobio/Tahoe-100M","gene_metadata", split="train")
+```
+
+| Column Name   | Description                                                                                                 |
+|---------------|-------------------------------------------------------------------------------------------------------------|
+| `gene_symbol` | The HGNC-approved gene symbol corresponding to each gene (e.g., *TP53*, *BRCA1*).                           |
+| `ensembl_id`  | The Ensembl gene identifier (e.g., *ENSG00000000003*) based on Ensembl release 109 and genome build 38.     |
+| `token_id`    | An integer token ID used to represent each gene. This is the ID used in the `genes` field in the main data. |
+
+
+
+### Sample Metadata
+
+```python
+sample_metadata = load_dataset("tahoebio/Tahoe-100M","sample_metadata", split="train")
+```
+The sample_metadata has additional information for aggregate quality metrics for the sample as well as the concentration.
+
+| Column Name            | Description                                                                                                                                                             |
+|------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| `sample`               | Unique identifier for the sample from which the cell was derived. Unique key for this table.                                                                            |
+| `plate`                | Identifier (1–14) for the 96-well plate for the sample                                                                                                                  |
+| `mean_gene_count`      | Average number of unique genes detected per cell for the given sample.                                                                                                  |
+| `mean_tscp_count`      | Average number of transcripts (UMIs) detected per cell in the sample.                                                                                                   |
+| `mean_mread_count`     | Average number of reads per cell.                                                                                                                                       |
+| `mean_pcnt_mito`       | Mean percentage of total reads that map to mitochondrial genes, across cells in the sample.                                                                             |
+| `drug`                 | Name of the treatment used to perturb the cells in the sample.                                                                                                          |
+| `drugname_drugconc`    | String combining the compound name, concentration and concentration unit (e.g., `[('8-Hydroxyquinoline',0.05,'uM')]`), used to uniquely label each treatment condition. |
+
+### Drug Metadata
+```python
+drug_metadata =  load_dataset("tahoebio/Tahoe-100M","drug_metadata", split="train")
+```
+The drug_metadata has additional information about each treatment.
+
+
+| Column Name            | Description                                                                                                                                                               |
+|------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| `drug`                 | Name of the treatment used to perturb the cells in the sample. Unique key for this table                                                                                  |
+| `targets`             | List of gene symbols representing the known molecular targets of the compound. Targets were proposed by GPT-4o based on compound names and then validated against MedChemExpress information. |
+| `moa-broad`           | Broad classification of the compound’s mechanism of action (MOA), typically categorized as "inhibitor/antagonist," "activator/agonist," or "unclear." GPT-4o inferred this using compound target data and curated descriptions from MedChemExpress. |
+| `moa-fine`            | Specific functional annotation of the compound's MOA (e.g., "Proteasome inhibitor" or "MEK inhibitor"). These fine-grained labels were selected from a curated list of 25 MOA categories and assigned by GPT-4o with validation against compound descriptions. |
+| `human-approved`      | Indicates whether the compound is approved for human use ("yes" or "no"). GPT-4o provided these labels using prior knowledge and validation from public sources such as clinicaltrials.gov. |
+| `clinical-trials`     | Indicates whether the compound has been evaluated in any registered clinical trials ("yes" or "no"). Determined using GPT-4o and corroborated using clinicaltrials.gov searches. |
+| `gpt-notes-approval`  | Contextual notes generated by GPT-4o summarizing the compound’s approval status, common clinical usage, or nuances such as formulation-specific approvals. |
+| `canonical_smiles`    | The compound's SMILES (Simplified Molecular Input Line Entry System) representation, capturing its molecular structure as a text string. |
+| `pubchem_cid`         | The PubChem Compound Identifier (CID), a unique numerical ID linking the compound to its entry in the PubChem database. |
+
+### Cell Line Metadata
+
+```python
+cell_line_metadata = load_dataset("tahoebio/Tahoe-100M","cell_line_metadata", split="train")
+```
+The cell-line metadata table has additional information about the key driver mutations for each cell line.
+
+| Column Name                       | Description                                                                                                                                                                              |
+|----------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| `cell_name`                      | Standard name of the cancer cell line (e.g., *A549*).                                                                                                                                    |
+| `Cell_ID_DepMap`                 | Unique identifier for the cell line in the DepMap project (e.g., *ACH-000681*)                                                                                                           |
+| `Cell_ID_Cellosaur`              | Cellosaurus accession ID (e.g., *CVCL_0023*). This is the ID used in the main dataset.                                                                                                   |
+| `Organ`                          | Tissue or organ of origin for the cell line (e.g., *Lung*), used to interpret lineage-specific responses and biological context.                                                         |
+| `Driver_Gene_Symbol`            | HGNC-approved symbol of a known or putative driver gene with functional alterations in this cell line (e.g., *KRAS*, *CDKN2A*). We report a curated list of driver mutations per cell-line. |
+| `Driver_VarZyg`                  | Zygosity of the driver variant (e.g., *Hom* for homozygous, *Het* for heterozygous)                                              |
+| `Driver_VarType`                | Type of genetic alteration (e.g., *Missense*, *Frameshift*, *Stopgain*, *Deletion*)                                                          |
+| `Driver_ProtEffect_or_CdnaEffect`| Specific protein or cDNA-level annotation of the mutation (e.g., *p.G12S*, *p.Q37*), providing precise information on the variant’s consequence.                                         |
+| `Driver_Mech_InferDM`            | Inferred functional mechanism of the mutation (e.g., *LoF* for loss-of-function, *GoF* for gain-of-function)                     |
+| `Driver_GeneType_DM`            | Classification of the driver gene as an *Oncogene* or *Suppressor*                                                                      |
+
+## Citation
+Please cite:
+```
+@article{zhang2025tahoe,
+  title={Tahoe-100M: A Giga-Scale Single-Cell Perturbation Atlas for Context-Dependent Gene Function and Cellular Modeling},
+  author={Zhang, Jesse and Ubas, Airol A and de Borja, Richard and Svensson, Valentine and Thomas, Nicole and Thakar, Neha and Lai, Ian and Winters, Aidan and Khan, Umair and Jones, Matthew G and others},
+  journal={bioRxiv},
+  pages={2025--02},
+  year={2025},
+  publisher={Cold Spring Harbor Laboratory}
+}
+```

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