Intact Tools

Configuration File: intact_tools.json Tool Type: Local Tools Count: 8

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

Available Tools

intact_get_complex_details (Type: IntActRESTTool)

Get detailed information about a specific protein complex by its complex AC (Complex Accession, e…

intact_get_complex_details tool specification

Tool Information:

• Name: intact_get_complex_details

• Type: IntActRESTTool

• Description: Get detailed information about a specific protein complex by its complex AC (Complex Accession, e.g., ‘CPX-915’). Returns comprehensive complex information including: complex AC, name, synonyms, systematic name, functions, properties, species, ligands, complex assemblies, participants (with interactor details), and associated diseases. To find complex ACs, use intact_get_interactions_by_complex to search for complexes first.

Parameters:

• complex_ac (string) (required) Complex AC (Complex Accession) in format ‘CPX-XXXXX’ (e.g., ‘CPX-915’, ‘CPX-10081’). Get complex ACs from intact_get_interactions_by_complex search results.

• format (string) (optional) No description

Example Usage:

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

intact_get_interaction_details (Type: IntActRESTTool)

Get detailed information about a specific interaction by its IntAct interaction ID. Requires an I…

intact_get_interaction_details tool specification

Tool Information:

• Name: intact_get_interaction_details

• Type: IntActRESTTool

• Description: Get detailed information about a specific interaction by its IntAct interaction ID. Requires an IntAct interaction ID in format ‘EBI-XXXXXX-EBI-YYYYYY’ (e.g., ‘EBI-366083-EBI-366083’). To get interaction IDs: 1) Use intact_get_interactions with a protein/gene identifier - it returns ‘interaction_ids’ field, or 2) Use intact_search_interactions - it also returns ‘interaction_ids’ field. Then use one of those IDs with this tool to get detailed interaction information. Returns complete interaction data including participants, interaction type, detection methods, and publications.

Parameters:

• interaction_id (string) (required) IntAct interaction ID in format ‘EBI-XXXXXX-EBI-YYYYYY’ (e.g., ‘EBI-366083-EBI-366083’). Get these IDs from intact_get_interactions or intact_search_interactions results (see ‘interaction_ids’ field)

• format (string) (optional) No description

Example Usage:

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

intact_get_interaction_network (Type: IntActRESTTool)

Get interaction network centered on a specific interactor. Returns network of interactions with c…

intact_get_interaction_network tool specification

Tool Information:

• Name: intact_get_interaction_network

• Type: IntActRESTTool

• Description: Get interaction network centered on a specific interactor. Returns network of interactions with configurable depth (direct interactions or extended network). Accepts IntAct identifiers (e.g., ‘EBI-1004115’), UniProt IDs (e.g., ‘P04637’), or gene names. Note: For interaction-specific networks, use interaction IDs from intact_get_interactions or intact_search_interactions results.

Parameters:

• identifier (string) (required) IntAct identifier, UniProt ID, or gene name

• depth (integer) (optional) Network depth: 1 for direct interactions only, 2 for 2-hop network, etc. (default: 1)

• format (string) (optional) No description

Example Usage:

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

intact_get_interactions (Type: IntActRESTTool)

Get all interactions involving a specific interactor (protein or gene) by identifier. Uses EBI Se…

intact_get_interactions tool specification

Tool Information:

• Name: intact_get_interactions

• Type: IntActRESTTool

• Description: Get all interactions involving a specific interactor (protein or gene) by identifier. Uses EBI Search API (IntAct domain) for reliable access. Returns list of interactions with interaction IDs (e.g., ‘EBI-366083-EBI-366083’) in the ‘interaction_ids’ field. These IDs can be used with intact_get_interaction_details or intact_get_interaction_network to get detailed information. Accepts UniProt IDs, gene names, or IntAct identifiers.

Parameters:

• identifier (string) (required) IntAct identifier, UniProt ID, or gene name

• format (string) (optional) No description

Example Usage:

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

intact_get_interactions_by_complex (Type: IntActRESTTool)

Search for protein complexes in IntAct database using Complex Web Service. Accepts complex names …

intact_get_interactions_by_complex tool specification

Tool Information:

• Name: intact_get_interactions_by_complex

• Type: IntActRESTTool

• Description: Search for protein complexes in IntAct database using Complex Web Service. Accepts complex names (e.g., ‘TP53’, ‘ndc80’), complex ACs (e.g., ‘CPX-915’), or gene names. Returns complex information including complex AC, name, description, organism, and interactors. Use the complex ACs from results to find related interactions. Note: This searches for complexes, not interactions directly. To find interactions involving a complex, use the complex name or AC with intact_search_interactions.

Parameters:

• complex_id (string) (required) Complex name (e.g., ‘TP53’, ‘ndc80’), complex AC (e.g., ‘CPX-915’), or gene name

• size (integer) (optional) Maximum number of results to return (default: 25, max: 100)

• first (integer) (optional) First result index for pagination (default: 0)

• format (string) (optional) No description

Example Usage:

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

intact_get_interactions_by_organism (Type: IntActRESTTool)

Get all interactions for a specific organism by taxonomy ID. Uses EBI Search API (IntAct domain) …

intact_get_interactions_by_organism tool specification

Tool Information:

• Name: intact_get_interactions_by_organism

• Type: IntActRESTTool

• Description: Get all interactions for a specific organism by taxonomy ID. Uses EBI Search API (IntAct domain) to find interactions involving proteins from the specified organism. Returns list of interactions with interaction IDs in the ‘interaction_ids’ field. These IDs can be used with intact_get_interaction_details to get detailed information. Common taxonomy IDs: 9606 (Homo sapiens), 10090 (Mus musculus), 10116 (Rattus norvegicus), 7227 (Drosophila melanogaster), 6239 (Caenorhabditis elegans), 7955 (Danio rerio).

Parameters:

• taxid (string) (required) NCBI taxonomy ID (e.g., ‘9606’ for human, ‘10090’ for mouse). Find taxonomy IDs at https://www.ncbi.nlm.nih.gov/taxonomy

• size (integer) (optional) Maximum number of results to return (default: 25, max: 100)

• format (string) (optional) No description

Example Usage:

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

intact_get_interactor (Type: IntActRESTTool)

Get detailed information about a specific interactor from IntAct database by IntAct identifier (e…

intact_get_interactor tool specification

Tool Information:

• Name: intact_get_interactor

• Type: IntActRESTTool

• Description: Get detailed information about a specific interactor from IntAct database by IntAct identifier (e.g., ‘EBI-1004115’). Note: This requires an IntAct-specific identifier, not UniProt IDs. For UniProt IDs, use intact_get_interactions instead. Returns interactor details including names, aliases, organism, and cross-references.

Parameters:

• identifier (string) (required) IntAct identifier (e.g., ‘EBI-1004115’) or UniProt ID (e.g., ‘P04637’) or gene name

• format (string) (optional) Response format

Example Usage:

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

intact_search_interactions (Type: IntActRESTTool)

Search for interactions in IntAct database using EBI Search API (IntAct domain). Supports searchi…

intact_search_interactions tool specification

Tool Information:

• Name: intact_search_interactions

• Type: IntActRESTTool

• Description: Search for interactions in IntAct database using EBI Search API (IntAct domain). Supports searching by protein names, gene names, interaction types, or other criteria. Use ‘*’ as query to get all interactions (may be slow). Returns interaction entries with interaction IDs (e.g., ‘EBI-366083-EBI-366083’) in the ‘interaction_ids’ field. These IDs can be used with intact_get_interaction_details or intact_get_interaction_network to get detailed information.

Parameters:

• query (string) (required) Search query string (e.g., protein name, gene name, interaction type)

• first (integer) (optional) First result index for pagination (default: 0)

• max (integer) (optional) Maximum number of results to return (default: 25, max: 100)

• format (string) (optional) No description

Example Usage:

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

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