Signor Tools#

Configuration File: signor_tools.json Tool Type: Local Tools Count: 4

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

Available Tools#

SIGNOR_connect_proteins (Type: SIGNORTool)#

Find the curated causal signaling sub-network connecting a set of proteins. Results are recoverab…

SIGNOR_connect_proteins tool specification

Tool Information:

  • Name: SIGNOR_connect_proteins

  • Type: SIGNORTool

  • Description: Find the curated causal signaling sub-network connecting a set of proteins. Results are recoverably paginated with offset and metadata.next_offset. ‘level’ controls how many intermediate steps are allowed.

Parameters:

  • proteins (array) (required) List of two or more UniProt accessions to connect (e.g., [‘P29317’, ‘Q06124’, ‘P04049’, ‘P15056’]). SIGNOR requires UniProt IDs, not gene symbols.

  • level (integer) (optional) Path depth for connecting the proteins: 1 (direct interactions only), 2 (allow one intermediate node), or 3 (allow two intermediate nodes).

  • limit (integer) (optional) Maximum number of interactions to return.

  • offset (integer) (optional) Zero-based interaction offset. Continue with metadata.next_offset.

Example Usage:

query = {
    "name": "SIGNOR_connect_proteins",
    "arguments": {
        "proteins": ["item1", "item2"]
    }
}
result = tu.run(query)

SIGNOR_get_interactions (Type: SIGNORTool)#

Get causal signaling interactions for a protein or entity from SIGNOR. Results are recoverably pa…

SIGNOR_get_interactions tool specification

Tool Information:

  • Name: SIGNOR_get_interactions

  • Type: SIGNORTool

  • Description: Get causal signaling interactions for a protein or entity from SIGNOR. Results are recoverably paginated: start with offset=0 and continue with metadata.next_offset while metadata.has_more is true. Use UniProt IDs (e.g., P04637 for TP53) or SIGNOR entity IDs.

Parameters:

  • entity_id (string) (optional) Entity identifier - typically a UniProt accession (e.g., ‘P04637’ for TP53, ‘Q00987’ for MDM2, ‘P38398’ for BRCA1). Can also be a SIGNOR complex/pathway ID.

  • organism (integer) (optional) NCBI taxonomy ID. 9606 for human, 10090 for mouse.

  • limit (integer) (optional) Maximum number of interactions to return.

  • offset (integer) (optional) Zero-based interaction offset. Continue with metadata.next_offset.

  • protein (string) (optional) Gene symbol or protein name (alias for entity_id; prefer UniProt accession like P04637 for TP53)

Example Usage:

query = {
    "name": "SIGNOR_get_interactions",
    "arguments": {
    }
}
result = tu.run(query)

SIGNOR_get_pathway (Type: SIGNORTool)#

Get signaling interactions in a SIGNOR curated pathway. Results are recoverably paginated: start …

SIGNOR_get_pathway tool specification

Tool Information:

  • Name: SIGNOR_get_pathway

  • Type: SIGNORTool

  • Description: Get signaling interactions in a SIGNOR curated pathway. Results are recoverably paginated: start with offset=0 and continue with metadata.next_offset while metadata.has_more is true. Use pathway IDs from SIGNOR_list_pathways.

Parameters:

  • pathway_id (string) (required) SIGNOR pathway identifier (e.g., ‘SIGNOR-AD’ for Alzheimer, ‘SIGNOR-AML’ for Acute Myeloid Leukemia, ‘SIGNOR-AMPK’ for AMPK signaling). Get IDs from SIGNOR_list_pathways.

  • limit (integer) (optional) Maximum number of interactions to return.

  • offset (integer) (optional) Zero-based pathway-interaction offset. Continue with metadata.next_offset.

Example Usage:

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

SIGNOR_list_pathways (Type: SIGNORTool)#

List curated signaling pathways in the SIGNOR database. Optionally filter by keyword to find path…

SIGNOR_list_pathways tool specification

Tool Information:

  • Name: SIGNOR_list_pathways

  • Type: SIGNORTool

  • Description: List curated signaling pathways in the SIGNOR database. Optionally filter by keyword to find pathways related to diseases (Alzheimer, AML), biological processes (apoptosis, autophagy), or signaling (MAPK, PI3K). Returns pathway IDs that can be used with SIGNOR_get_pathway.

Parameters:

  • query (string) (optional) Optional keyword to filter pathways by name or description (e.g., ‘cancer’, ‘apoptosis’, ‘AML’). Leave empty to list all pathways.

Example Usage:

query = {
    "name": "SIGNOR_list_pathways",
    "arguments": {
    }
}
result = tu.run(query)