Forge Tools pharos_target

pharos_target read

scidex.forge.pharos_target

Look up a human protein target in the Pharos/TCRD database by gene symbol. Returns the Target Development Level (TDL: Tdark/Tbio/Tchem/Tclin), disease associations, and drug activities. Critical for dark kinome hypothesis generation and target illumination workflows. GraphQL API: https://pharos.nih.gov/api — public, no auth required.

HTTP: POST /api/scidex/forge/pharos_target

Invoke

Calls scidex.tool.invoke on the substrate with this tool name. Edit the JSON below — it must match the input schema. The substrate runs the tool, records the call in substrate_tool_calls, and returns a structured envelope.

Sign in to invoke this tool. Schema and curl snippet are visible to anyone.

Schemas

Input schema 
{
  "additionalProperties": false,
  "description": "Input schema for ``scidex.forge.pharos_target``.",
  "properties": {
    "gene_symbol": {
      "description": "HGNC gene symbol (e.g. ``EGFR``, ``BRAF``, ``CDK4``). Looked up directly in Pharos; case-insensitive on the Pharos side.",
      "maxLength": 30,
      "minLength": 1,
      "title": "Gene Symbol",
      "type": "string"
    },
    "include_disease": {
      "default": true,
      "description": "When True (default), include disease associations from Pharos in the response.",
      "title": "Include Disease",
      "type": "boolean"
    },
    "include_drugs": {
      "default": true,
      "description": "When True (default), include drug / ligand activities from Pharos in the response.",
      "title": "Include Drugs",
      "type": "boolean"
    }
  },
  "required": [
    "gene_symbol"
  ],
  "title": "ForgePharosIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "PharosDiseaseLink": {
      "description": "One disease association in the Pharos response.",
      "properties": {
        "disease_name": {
          "description": "Disease name from Pharos.",
          "title": "Disease Name",
          "type": "string"
        },
        "association_count": {
          "default": 0,
          "description": "Number of evidence items supporting the disease–target association in Pharos.",
          "title": "Association Count",
          "type": "integer"
        }
      },
      "required": [
        "disease_name"
      ],
      "title": "PharosDiseaseLink",
      "type": "object"
    },
    "PharosDrugActivity": {
      "description": "One drug/ligand activity entry in the Pharos response.",
      "properties": {
        "drug_name": {
          "description": "Drug or ligand name.",
          "title": "Drug Name",
          "type": "string"
        },
        "activity_type": {
          "default": "",
          "description": "Activity type, e.g. ``Ki``, ``IC50``, ``Kd``.",
          "title": "Activity Type",
          "type": "string"
        },
        "activity_value": {
          "anyOf": [
            {
              "type": "number"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Numeric activity value (units given by ``activity_unit``).",
          "title": "Activity Value"
        },
        "activity_unit": {
          "default": "",
          "description": "Unit of the activity value, e.g. ``nM``.",
          "title": "Activity Unit",
          "type": "string"
        }
      },
      "required": [
        "drug_name"
      ],
      "title": "PharosDrugActivity",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.pharos_target``.",
  "properties": {
    "target_id": {
      "description": "Pharos/TCRD internal target ID (tcrdid).",
      "title": "Target Id",
      "type": "string"
    },
    "gene_symbol": {
      "description": "Canonical gene symbol as returned by Pharos.",
      "title": "Gene Symbol",
      "type": "string"
    },
    "target_name": {
      "default": "",
      "description": "Full protein/target name.",
      "title": "Target Name",
      "type": "string"
    },
    "uniprot_accession": {
      "default": "",
      "description": "UniProt accession.",
      "title": "Uniprot Accession",
      "type": "string"
    },
    "tdl": {
      "description": "Target Development Level from TCRD: one of ``Tdark``, ``Tbio``, ``Tchem``, ``Tclin``.",
      "title": "Tdl",
      "type": "string"
    },
    "illumination_level": {
      "description": "Human-readable illumination label derived from TDL: ``dark``, ``biology``, ``chemistry``, or ``clinical``.",
      "title": "Illumination Level",
      "type": "string"
    },
    "disease_associations": {
      "items": {
        "$ref": "#/$defs/PharosDiseaseLink"
      },
      "title": "Disease Associations",
      "type": "array"
    },
    "drug_activities": {
      "items": {
        "$ref": "#/$defs/PharosDrugActivity"
      },
      "title": "Drug Activities",
      "type": "array"
    },
    "took_ms": {
      "description": "Wall-clock time for the upstream GraphQL call.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "target_id",
    "gene_symbol",
    "tdl",
    "illumination_level",
    "took_ms"
  ],
  "title": "ForgePharosOut",
  "type": "object"
}

curl snippet

Replace $SCIDEX_JWT with a valid bearer token. Read verbs are usually accessible without auth in dev; production requires a JWT.

curl -sS -X POST '/api/scidex/forge/pharos_target' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene_symbol": ""
}'

Discussion

Posting anonymously. Sign in for attribution.

No comments yet — be the first.