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--- |
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configs: |
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- config_name: ncbi_summary |
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data_files: "ncbi_summary.parquet" |
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default: true |
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- config_name: ncbi_uniprot_summary |
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data_files: "ncbi_uniprot_summary.parquet" |
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- config_name: gene_info |
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data_files: "gene_info.parquet" |
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- config_name: generated_descriptions_gpt4o_mini_combined |
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data_files: "generated_descriptions_gpt4o_mini_combined.parquet" |
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--- |
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--- |
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# Gene Description Dataset |
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This dataset reproduces and expands upon the GenePT project and paper, and makes it easier to reproce and access using standard tools. |
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The goal is to allow users to compose embeddings across dimensions in order to specialize for specific tasks, and add to the existing |
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base embeddings by generating new descriptions and embedding them in the same space. |
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## Dataset Description |
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This dataset |
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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. |
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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. |
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GitHub: https://github.com/yiqunchen/GenePT |
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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 |
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have a combined description that includes several factors. We will add composable dimensions soon |
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## Dataset Structure |
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The dataset contains four main components: |
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1. NCBI Summary - Contains gene descriptions from NCBI |
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2. NCBI-UniProt Summary - Contains combined gene descriptions from NCBI and UniProt |
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3. Gene Info Table - Contains contains a mapping between gene_id, ensmble_id and gene functional annotation |
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4. Generated Descriptions (Combined) |
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- Contains AI-generated gene descriptions |
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- Model: GPT-4o-mini |
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- Factors: |
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a. Associated genes |
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b. Aging related information |
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c. Drug interactions |
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d. Pathways and biological processes |
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## Source Data: |
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Some of the data was sourced from the following sources upstream of the GenePT project: |
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- NCBI Gene Database |
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- UniProt Database |
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The licenses for these databases continue to apply where applicable. |
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