Pathways Logic

Question

[sciwiseg]

Might a logic circuit be derived from pathway data, from locations like Reactome . A netlist from pathway data is being considered.

Upon querying colab, it suggests something like this:

import xml.etree.ElementTree as ET

def pathway_to_logic(input_file, output_file): """ Convert Reactome pathway data into a logic circuit description. """ try:

    # Parse XML pathway data
    tree = ET.parse(input_file)
    root = tree.getroot()

    # Initialize a logic circuit description
    logic_circuit = []

    for interaction in root.findall(".//interaction"):
        source = interaction.find("source").text
        target = interaction.find("target").text
        interaction_type = interaction.get("type")

        # Map interaction to logic gate
        if interaction_type == "activation":
            logic_gate = f"{target} = {source} AND {target}"
        elif interaction_type == "inhibition":
            logic_gate = f"{target} = NOT {source}"
        else:
            logic_gate = f"{target} = {source} (UNKNOWN INTERACTION)"

        logic_circuit.append(logic_gate)

    # Write the logic circuit to a file
    with open(output_file, "w") as out_file:
        for gate in logic_circuit:
            out_file.write(f"{gate}\n")

    print(f"Logic circuit saved to {output_file}")

except Exception as e:
    print(f"Error processing pathway data: {e}")

Example usage

input_file = "example_reactome.xml" # Replace with Reactome data file output_file = "logic_circuit.txt" # Output file for logic description pathway_to_logic(input_file, output_file)