Pharos Tools

Configuration File: pharos_tools.json Tool Type: Local Tools Count: 7

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

Available Tools

Pharos_get_disease_targets (Type: PharosTool)

Get drug targets associated with a disease from Pharos. Returns targets with TDL classification t…

Pharos_get_disease_targets tool specification

Tool Information:

  • Name: Pharos_get_disease_targets

  • Type: PharosTool

  • Description: Get drug targets associated with a disease from Pharos. Returns targets with TDL classification to identify druggable vs understudied proteins for the disease. Supports TDL filtering to find Tdark opportunities.

Parameters:

  • disease (string) (required) Disease name (e.g., ‘breast cancer’, ‘Alzheimer disease’, ‘diabetes mellitus’)

  • tdl (string) (optional) Optional filter by Target Development Level

  • top (integer) (optional) Maximum number of results (1-100)

Example Usage:

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

Pharos_get_ligand_targets (Type: PharosTool)

Get all protein targets for a drug or ligand from Pharos/TCRD (reverse polypharmacology). Given o…

Pharos_get_ligand_targets tool specification

Tool Information:

  • Name: Pharos_get_ligand_targets

  • Type: PharosTool

  • Description: Get all protein targets for a drug or ligand from Pharos/TCRD (reverse polypharmacology). Given one drug/ligand (by name or Pharos ligand ID), returns its SMILES, total targetCount, and every recorded bioactivity with the target (gene symbol, Target Development Level Tclin/Tchem/Tbio/Tdark, protein family), activity type, value, and mechanism of action. Use to map a drug’s full target landscape and off-targets.

Parameters:

  • ligid (string) (required) Ligand name or Pharos ligand ID (e.g., ‘Haloperidol’, ‘Imatinib’).

Example Usage:

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

Pharos_get_target (Type: PharosTool)

Get detailed drug target information from Pharos/TCRD by gene symbol or UniProt ID. Returns Targe…

Pharos_get_target tool specification

Tool Information:

  • Name: Pharos_get_target

  • Type: PharosTool

  • Description: Get detailed drug target information from Pharos/TCRD by gene symbol or UniProt ID. Returns Target Development Level (Tdark/Tbio/Tchem/Tclin), protein family, diseases, ligands, and druggability data. Essential for identifying understudied proteins.

Parameters:

  • gene (string) (optional) Gene symbol (e.g., ‘EGFR’, ‘TP53’, ‘BRCA1’). Use either gene or uniprot.

  • uniprot (string) (optional) UniProt accession (e.g., ‘P00533’). Use either gene or uniprot.

Example Usage:

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

Pharos_get_target_expression (Type: PharosTool)

Get GTEx baseline tissue RNA expression (per-tissue TPM) for a drug target from Pharos/TCRD (by g…

Pharos_get_target_expression tool specification

Tool Information:

  • Name: Pharos_get_target_expression

  • Type: PharosTool

  • Description: Get GTEx baseline tissue RNA expression (per-tissue TPM) for a drug target from Pharos/TCRD (by gene symbol or UniProt ID). Returns one record per GTEx tissue with tissue name, TPM value, and gender stratification when available. Use to assess where a target is naturally expressed (e.g., for on-target tissue-toxicity reasoning).

Parameters:

  • gene (string) (optional) Gene symbol (e.g., ‘DRD2’, ‘EGFR’). Use either gene or uniprot.

  • uniprot (string) (optional) UniProt accession (e.g., ‘P14416’). Use either gene or uniprot.

Example Usage:

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

Pharos_get_target_ligands (Type: PharosTool)

Get per-target ligand and drug bioactivities from Pharos/TCRD for a drug target (by gene symbol o…

Pharos_get_target_ligands tool specification

Tool Information:

  • Name: Pharos_get_target_ligands

  • Type: PharosTool

  • Description: Get per-target ligand and drug bioactivities from Pharos/TCRD for a drug target (by gene symbol or UniProt ID). Returns ligandCounts (total ligand and approved-drug counts) plus the top ligands with synonyms (ChEMBL etc.) and measured bioactivities: activity type (IC50/Ki/EC50/Kd), value (typically -log10 molar / pActivity), and mechanism of action. Use to assess chemical tractability and known chemistry of a target.

Parameters:

  • gene (string) (optional) Gene symbol (e.g., ‘DRD2’, ‘EGFR’). Use either gene or uniprot.

  • uniprot (string) (optional) UniProt accession (e.g., ‘P14416’). Use either gene or uniprot.

  • top (integer) (optional) Maximum number of ligands to return (1-50).

Example Usage:

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

Pharos_get_tdl_summary (Type: PharosTool)

Get Target Development Level statistics from Pharos. Returns counts of human proteome targets at …

Pharos_get_tdl_summary tool specification

Tool Information:

  • Name: Pharos_get_tdl_summary

  • Type: PharosTool

  • Description: Get Target Development Level statistics from Pharos. Returns counts of human proteome targets at each TDL: Tclin (approved drugs), Tchem (chemical probes), Tbio (biological annotations), Tdark (understudied). Use to understand druggable genome coverage.

Parameters:

No parameters required.

Example Usage:

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

Pharos_search_targets (Type: PharosTool)

Search drug targets in Pharos database by keyword. Supports filtering by Target Development Level…

Pharos_search_targets tool specification

Tool Information:

  • Name: Pharos_search_targets

  • Type: PharosTool

  • Description: Search drug targets in Pharos database by keyword. Supports filtering by Target Development Level (Tdark for understudied, Tchem for chemically tractable, Tclin for approved drugs). Returns TDL, protein family, and novelty scores.

Parameters:

  • query (string) (required) Search query (gene name, protein name, or keyword)

  • tdl (string) (optional) Filter by Target Development Level. Tdark=understudied, Tbio=biological annotations, Tchem=chemical probes, Tclin=approved drugs.

  • top (integer) (optional) Maximum number of results (1-100)

Example Usage:

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