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README.md

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----
-license: mit
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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"
+---
+
+---
+
+# 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 four main components:
+
+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 (Combined)
+  - 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
+
+## Dataset Creation
+
+Source Data:
+- NCBI Gene Database
+- UniProt Database
+