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CL_Markers_Mappings

A repository for mapping gene markers in CL to various external databases such as UniProt.

Status

STATUS: DRAFT

Prerequisites

  1. Ensure Python is installed: If you don't have Python 3 installed, you can download it from python.org.

  2. Install the required packages:

    pip install requests

Setup and Usage

  1. Clone the repository:

    git clone https://github.com/Cellular-Semantics/CL_Markers_Mappings
cd CL_Markers_Mappings

  2. Run the UniProt Mapping Script:

    python3 uniprot_mapping.py
    • This script will map gene markers to UniProt IDs for human and mouse, and outputs the information into a CSV file.
    • The CSV file generated is named uniprot_mapping.csv in the CL_Markers_Mappings directory. The file contains the UniProt IDs and additional information for the specified gene markers.

Customization

Modify the Script: Update the uniprot_mapping.py script to include or exclude fields according to your requirements.

# Example
params = {
    "query": query,
    "format": "json",
    "fields": "accession,id,reviewed,protein_name,gene_names,organism_id"  # Customize these fields as needed
}

For a complete list of available fields, refer to the UniProtKB Return Fields Documentation.

Example Output

The output CSV file uniprot_mapping.csv will contain the following columns:

Marker Organism UniProt ID Entry Name Reviewed Protein Names Genes
CX3CR1 Human P49238 CX3C1_HUMAN Yes CX3C chemokine receptor 1 CX3CR1