Indra Tools

Configuration File: indra_tools.json Tool Type: Local Tools Count: 3

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

Available Tools

INDRA_get_evidence_count (Type: INDRADBTool)

Get the total number of literature evidence items in INDRA DB for a gene, protein, or chemical wi…

INDRA_get_evidence_count tool specification

Tool Information:

  • Name: INDRA_get_evidence_count

  • Type: INDRADBTool

  • Description: Get the total number of literature evidence items in INDRA DB for a gene, protein, or chemical without fetching full statements. Useful for quickly assessing how much is known about an entity in the literature. Optionally filter by statement type.

Parameters:

  • operation (string) (optional) Operation type (fixed: get_evidence_count)

  • agent (string) (required) Gene symbol, protein name, or chemical name (e.g., ‘TP53’, ‘EGFR’)

  • type (string) (optional) Optional: filter by statement type (e.g., ‘Activation’, ‘Inhibition’, ‘Phosphorylation’)

Example Usage:

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

INDRA_get_statement_by_hash (Type: INDRADBTool)

Get a specific INDRA statement by its hash with full evidence details. Use statement hashes retur…

INDRA_get_statement_by_hash tool specification

Tool Information:

  • Name: INDRA_get_statement_by_hash

  • Type: INDRADBTool

  • Description: Get a specific INDRA statement by its hash with full evidence details. Use statement hashes returned by INDRA_get_statements to retrieve comprehensive evidence for a specific biological relationship.

Parameters:

  • operation (string) (optional) Operation type (fixed: get_statement_by_hash)

  • hash (string) (required) Statement hash from INDRA_get_statements results

  • ev_limit (integer) (optional) Maximum evidence items to return (default: 10)

Example Usage:

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

INDRA_get_statements (Type: INDRADBTool)

Get literature-mined biological statements for a gene, protein, or chemical from INDRA DB. Return…

INDRA_get_statements tool specification

Tool Information:

  • Name: INDRA_get_statements

  • Type: INDRADBTool

  • Description: Get literature-mined biological statements for a gene, protein, or chemical from INDRA DB. Returns mechanistic relationships (Activation, Inhibition, Phosphorylation, Complex, etc.) with supporting evidence from PubMed articles. INDRA aggregates knowledge from 30+ NLP readers across millions of publications. Use ‘agent’ for the entity name (e.g., ‘TP53’, ‘EGFR’, ‘gefitinib’). Optionally filter by statement ‘type’ (Activation, Inhibition, Phosphorylation, etc.) or specify ‘agent2’ for pairwise interactions.

Parameters:

  • operation (string) (optional) Operation type (fixed: get_statements)

  • agent (string) (required) Gene symbol, protein name, or chemical name (e.g., ‘TP53’, ‘EGFR’, ‘gefitinib’, ‘BRAF’)

  • type (string) (optional) Filter by statement type: Activation, Inhibition, Phosphorylation, Dephosphorylation, Ubiquitination, Complex, IncreaseAmount, DecreaseAmount, Translocation, Autophosphorylation

  • agent2 (string) (optional) Second agent for pairwise queries (e.g., agent=’BRAF’ agent2=’MAP2K1’)

  • limit (integer) (optional) Maximum statements to return (default: 10)

  • ev_limit (integer) (optional) Maximum evidence items per statement (default: 2)

Example Usage:

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