Pinnacle Tools

Configuration File: remote_tools/pinnacle_tools.json Tool Type: Remote Tools Count: 1

This page contains all tools defined in the pinnacle_tools.json configuration file.

Available Tools

run_pinnacle_ppi_retrieval (Type: RemoteTool)

Retrieves cell-type-specific protein-protein interaction embeddings from PINNACLE. This tool prov…

run_pinnacle_ppi_retrieval tool specification

Tool Information:

  • Name: run_pinnacle_ppi_retrieval

  • Type: RemoteTool

  • Description: Retrieves cell-type-specific protein-protein interaction embeddings from PINNACLE. This tool provides access to pre-computed PINNACLE (Protein Interaction Network Contextualized Learning) embeddings that represent protein-protein interactions in specific cellular contexts. These embeddings encode functional relationships between proteins as dense vector representations, capturing both direct physical interactions and functional associations.

Parameters:

  • cell_type (string) (required) Target cell type for embedding retrieval. Supports flexible naming: Standard formats: ‘b_cell’, ‘hepatocyte’, ‘cardiomyocyte’; Alternative formats: ‘B-cell’, ‘T cell’, ‘NK cells’; Tissue types: ‘liver’, ‘heart’, ‘brain’, ‘immune’. The tool performs intelligent matching to find the best available match.

  • embed_path (string) (optional) Path to the PINNACLE embeddings file (.pth format). If None, uses PINNACLE_DATA_PATH/pinnacle_embeds/ppi_embed_dict.pth.

Example Usage:

query = {
    "name": "run_pinnacle_ppi_retrieval",
    "arguments": {
        "cell_type": "example_value"
    }
}
result = tu.run(query)