Clue Tools

Configuration File: clue_tools.json Tool Type: Local Tools Count: 5

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

Available Tools

CLUE_get_cell_lines (Type: ClueTool)

Get cell line information used in L1000 Connectivity Map experiments. Returns cell line metadata …

CLUE_get_cell_lines tool specification

Tool Information:

  • Name: CLUE_get_cell_lines

  • Type: ClueTool

  • Description: Get cell line information used in L1000 Connectivity Map experiments. Returns cell line metadata including tissue of origin, growth properties, and available data types. Use cell_id for specific cell line lookup. Example: Get information about MCF7 breast cancer cell line.

Parameters:

  • operation (string) (required) Operation type

  • cell_id ([‘string’, ‘null’]) (optional) Cell line identifier (e.g., ‘MCF7’, ‘A375’, ‘PC3’)

  • limit (integer) (optional) Maximum number of results

Example Usage:

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

CLUE_get_gene_expression (Type: ClueTool)

Get gene information from L1000 Connectivity Map landmark and inferred gene set. Returns gene met…

CLUE_get_gene_expression tool specification

Tool Information:

  • Name: CLUE_get_gene_expression

  • Type: ClueTool

  • Description: Get gene information from L1000 Connectivity Map landmark and inferred gene set. Returns gene metadata including gene symbol, Entrez ID, L1000 gene type (landmark vs inferred). Use gene_symbol to search for specific genes. Example: Look up TP53 or BRCA1 in the L1000 gene space.

Parameters:

  • operation (string) (required) Operation type

  • gene_symbol (string) (optional) Gene symbol to search (e.g., ‘TP53’, ‘BRCA1’)

  • limit (integer) (optional) Maximum number of results

Example Usage:

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

CLUE_get_perturbation (Type: ClueTool)

Get detailed information about a specific L1000 perturbagen from CLUE.io by ID or name. Returns f…

CLUE_get_perturbation tool specification

Tool Information:

  • Name: CLUE_get_perturbation

  • Type: ClueTool

  • Description: Get detailed information about a specific L1000 perturbagen from CLUE.io by ID or name. Returns full metadata including mechanism of action, target, SMILES, dose, time points. Use pert_id for exact ID lookup or pert_iname for name search. Example: Get full details for imatinib compound.

Parameters:

  • operation (string) (required) Operation type

  • pert_id ([‘string’, ‘null’]) (optional) Perturbagen ID (e.g., ‘BRD-K12345678’). Mutually exclusive with pert_iname.

  • pert_iname ([‘string’, ‘null’]) (optional) Perturbagen name (e.g., ‘imatinib’). Mutually exclusive with pert_id.

Example Usage:

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

CLUE_search_compounds (Type: ClueTool)

Search chemical compounds (small molecule drugs) in the L1000 Connectivity Map. Filters to trt_cp…

CLUE_search_compounds tool specification

Tool Information:

  • Name: CLUE_search_compounds

  • Type: ClueTool

  • Description: Search chemical compounds (small molecule drugs) in the L1000 Connectivity Map. Filters to trt_cp perturbation type. Search by drug name or mechanism of action (MOA). Returns compound metadata including targets, pathways, and clinical status. Example: Find all kinase inhibitors or HDAC inhibitors.

Parameters:

  • operation (string) (required) Operation type

  • pert_iname (string) (optional) Compound name search (partial match). E.g., ‘imatinib’, ‘vorinostat’

  • moa (string) (optional) Mechanism of action search. E.g., ‘HDAC inhibitor’, ‘kinase inhibitor’

  • limit (integer) (optional) Maximum number of results

Example Usage:

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

CLUE_search_signatures (Type: ClueTool)

Search L1000 Connectivity Map perturbation signatures from CLUE.io. Returns perturbation records …

CLUE_search_signatures tool specification

Tool Information:

  • Name: CLUE_search_signatures

  • Type: ClueTool

  • Description: Search L1000 Connectivity Map perturbation signatures from CLUE.io. Returns perturbation records including genetic and chemical perturbagens with metadata. Use pert_type to filter by type (trt_cp=compounds, trt_oe=overexpression, trt_sh=knockdown). Use pert_iname for fuzzy name search. Example: Find all imatinib signatures or all compound perturbagens.

Parameters:

  • operation (string) (required) Operation type

  • pert_type (string) (optional) Perturbation type filter: ‘trt_cp’ (compounds), ‘trt_oe’ (overexpression), ‘trt_sh’ (shRNA knockdown), ‘trt_xpr’ (CRISPR)

  • pert_iname (string) (optional) Perturbagen name to search (partial match). E.g., ‘imatinib’, ‘TP53’

  • limit (integer) (optional) Maximum number of results to return

Example Usage:

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