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