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 Pharos targets associated with a disease, with a real optional TDL facet filter. Pharos curre…

Pharos_get_disease_targets tool specification

Tool Information:

  • Name: Pharos_get_disease_targets

  • Type: PharosTool

  • Description: Get Pharos targets associated with a disease, with a real optional TDL facet filter. Pharos currently ignores targets top/skip and returns the same first 10 ranked records; the wrapper reports the exact filtered count, accessible_results and truncation rather than offering false pagination.

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) Number of records to return from Pharos’ fixed first-10 ranked window (1-10); its API currently returns at most 10 targets per request. data.count gives the total matches and data.note appears when fewer than requested come back.

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 (IC50/Ki/EC50/Kd), value (typically -log10 molar / pActivity), and mechanism of action. Note the value is a pActivity, NOT nanomolar: a Ki of 9.46 means pKi 9.46 = 0.35 nM. 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 – Pharos’ druggability classification), protein family, novelty score, publication count, associated diseases (full per-disease association counts plus the top 10 diseases with MONDO IDs), and ligand/drug counts plus the top 10 ligands. Essential for identifying understudied proteins. For ligand bioactivity values use Pharos_get_target_ligands.

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 by gene symbol or UniProt ID. Retur…

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 by gene symbol or UniProt ID. Returns exact ligand/drug counts and a native skip/top page of ligands with synonyms and measured bioactivities; use metadata.next_skip to continue through all ligands.

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).

  • skip (integer) (optional) Zero-based offset into the target’s ligand list.

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 by keyword with optional Target Development Level filtering. Pharos…

Pharos_search_targets tool specification

Tool Information:

  • Name: Pharos_search_targets

  • Type: PharosTool

  • Description: Search drug targets in Pharos by keyword with optional Target Development Level filtering. Pharos currently ignores targets top/skip and returns the same first 10 ranked records; this wrapper locally honors top up to 10, reports the exact match count and accessible_results, and warns when the upstream ranked window is truncated.

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) Number of records to return from Pharos’ fixed first-10 ranked window (1-10); its API currently returns at most 10 targets per request. data.count gives the total matches and data.note appears when fewer than requested come back.

Example Usage:

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