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---
configs:
- config_name: ncbi_summary
data_files: "ncbi_summary.parquet"
default: true
- config_name: ncbi_uniprot_summary
data_files: "ncbi_uniprot_summary.parquet"
- config_name: gene_info
data_files: "gene_info.parquet"
- config_name: generated_descriptions_gpt4o_mini_combined
data_files: "generated_descriptions_gpt4o_mini_combined.parquet"
- config_name: generated_descriptions_gpt4o_mini_cell_type_drugs_pathways
data_files: "generated_descriptions_gpt4o_mini_cell_type_drugs_pathways.parquet"
- config_name: generated_descriptions_gpt4o_cell_type
data_files: "generated_descriptions_gpt4o_cell_type.parquet"
- config_name: generated_descriptions_gpt4o_cell_type_tissue_drug_pathway
data_files: "generated_descriptions_gpt4o_cell_type_tissue_drug_pathway.parquet"
---
---
# Gene Description Dataset
This dataset reproduces and expands upon the GenePT project and paper, and makes it easier to reproce and access using standard tools.
The goal is to allow users to compose embeddings across dimensions in order to specialize for specific tasks, and add to the existing
base embeddings by generating new descriptions and embedding them in the same space.
## Dataset Description
This dataset
1. reproduces the data from the GenePT project and paper in a more easy-to-use format. This paper itself aggregates data from multiple sources, so please refer to the paper and repository for detailed source information.
Citation: Chen YT, Zou J. (2023+) GenePT: A Simple But Effective Foundation Model for Genes and Cells Built From ChatGPT. bioRxiv preprint: https://www.biorxiv.org/content/10.1101/2023.10.16.562533v2.
GitHub: https://github.com/yiqunchen/GenePT
2. Adds descriptions of genes extracted from various LLMs, across multiple dimensions, such as regulatory pathways, drug interactions, etc. Currently we use GPT-4o-mini to generate descriptions, and only
have a combined description that includes several factors. We will add composable dimensions soon
## Dataset Structure
The dataset contains six sub-datasets:
1. NCBI Summary - Contains gene descriptions from NCBI
2. NCBI-UniProt Summary - Contains combined gene descriptions from NCBI and UniProt
3. Gene Info Table - Contains contains a mapping between gene_id, ensmble_id and gene functional annotation
4. Generated Descriptions (Aging)
- Contains AI-generated gene descriptions
- Model: GPT-4o-mini
- Factors:
a. Associated genes
b. Aging related information
c. Drug interactions
d. Pathways and biological processes
5. Generated Descriptions (Cell Type and other)
- Contains AI-generated gene descriptions
- Model: GPT-4o-mini
- Factors:
a. Associated genes
b. Cell type
c. Drug interactions
d. Pathways and biological processes
6. Generated Descriptions (Cell Type only, gpt4o)
- Contains AI-generated gene descriptions
- Model: GPT-4o
- Factors:
a. Cell type
6. Generated Descriptions (Cell Type and others, gpt4o)
- Contains AI-generated gene descriptions
- Model: GPT-4o
- Factors:
a. Cell type
b. Tissue type
c. Drugs
d, Pathways and biological processes
## Source Data:
Some of the data was sourced from the following sources upstream of the GenePT project:
- NCBI Gene Database
- UniProt Database
The licenses for these databases continue to apply where applicable.
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