Forge Tools cptac_proteomics

cptac_proteomics read

scidex.forge.cptac_proteomics

Query CPTAC (Clinical Proteomics Tumor Analysis Consortium) Data Portal for protein and phosphoproteomics expression across tumour types. CPTAC provides deep mass-spec proteomics and phosphoproteomics linked to TCGA tumour samples, enabling multi-omic integration. Distinct from proteomexchange (repository search), prIDE (experiment lookup), and proteomicsdb (expression atlas). Input: gene_symbol (HGNC, e.g. 'TP53'), cancer_type (cohort code like 'LUAD'/'UCEC'/'GBM' or free-text like 'lung adenocarcinoma'), include_phospho (default True), limit (default 20, max 50). Output: protein_expression_zscore, phosphosite-level z-scores, sample_count, cohort_study. API: https://cptac-data-portal.georgetown.edu — free, no auth required.

HTTP: POST /api/scidex/forge/cptac_proteomics

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.cptac_proteomics``.",
  "properties": {
    "gene_symbol": {
      "description": "HGNC gene symbol to query (e.g. ``'TP53'``, ``'EGFR'``, ``'BRCA1'``). Case-insensitive; normalised to upper-case before the API call.",
      "maxLength": 64,
      "title": "Gene Symbol",
      "type": "string"
    },
    "cancer_type": {
      "description": "CPTAC cancer-type identifier.  Accepts either the cohort code (e.g. ``'LUAD'``, ``'UCEC'``, ``'GBM'``) or a free-text name (e.g. ``'lung adenocarcinoma'`` → ``'LUAD'``). Valid cohort codes: ['BRCA', 'CCRCC', 'COAD', 'GBM', 'HNSCC', 'LSCC', 'LUAD', 'OV', 'PDAC', 'UCEC'].",
      "maxLength": 128,
      "title": "Cancer Type",
      "type": "string"
    },
    "include_phospho": {
      "default": true,
      "description": "Whether to include phosphoproteomics site-level data (default True). Set to False to skip the phospho query for faster results.",
      "title": "Include Phospho",
      "type": "boolean"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of phosphosite records to return (most significant by absolute z-score). Default 20, max 50.",
      "maximum": 50,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "gene_symbol",
    "cancer_type"
  ],
  "title": "ForgeCptacIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "CptacPhosphoSite": {
      "description": "One phosphosite-level expression measurement from CPTAC.",
      "properties": {
        "phosphosite": {
          "description": "Phosphosite identifier (e.g. 'S15', 'T37', 'Y42'). Format: single-letter amino-acid code + 1-based integer position.",
          "title": "Phosphosite",
          "type": "string"
        },
        "phospho_expression_zscore": {
          "anyOf": [
            {
              "type": "number"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Site-level phospho-expression z-score from CPTAC phosphoproteomics. Positive = hyper-phosphorylated in tumour vs. normal. None when site is not quantified in the cohort.",
          "title": "Phospho Expression Zscore"
        },
        "peptide_sequence": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Peptide sequence surrounding the phosphosite (if available).",
          "title": "Peptide Sequence"
        }
      },
      "required": [
        "phosphosite"
      ],
      "title": "CptacPhosphoSite",
      "type": "object"
    },
    "CptacProteinExpression": {
      "description": "Protein-level expression result from CPTAC.",
      "properties": {
        "gene_symbol": {
          "description": "HGNC gene symbol queried.",
          "title": "Gene Symbol",
          "type": "string"
        },
        "cancer_type": {
          "description": "CPTAC cohort code (e.g. 'LUAD', 'UCEC').",
          "title": "Cancer Type",
          "type": "string"
        },
        "cohort_study": {
          "description": "Full CPTAC study identifier (e.g. 'CPTAC-LUAD', 'CPTAC-UCEC').",
          "title": "Cohort Study",
          "type": "string"
        },
        "protein_expression_zscore": {
          "anyOf": [
            {
              "type": "number"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Mass-spec protein expression z-score. Positive = over-expressed in tumour vs. adjacent normal. None when quantification is not available for this gene/cohort.",
          "title": "Protein Expression Zscore"
        },
        "sample_count": {
          "description": "Number of tumour samples with quantified expression.",
          "title": "Sample Count",
          "type": "integer"
        },
        "phosphosites": {
          "description": "Phosphosite-level expression records, sorted by |z-score| descending.",
          "items": {
            "$ref": "#/$defs/CptacPhosphoSite"
          },
          "title": "Phosphosites",
          "type": "array"
        }
      },
      "required": [
        "gene_symbol",
        "cancer_type",
        "cohort_study",
        "sample_count"
      ],
      "title": "CptacProteinExpression",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.cptac_proteomics``.",
  "properties": {
    "results": {
      "description": "Protein expression records for the queried gene/cancer combination. Normally a single record; multiple records appear when the gene has multiple protein entries in the CPTAC dataset.",
      "items": {
        "$ref": "#/$defs/CptacProteinExpression"
      },
      "title": "Results",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when CPTAC returned no data for the gene/cancer pair.",
      "title": "Not Found",
      "type": "boolean"
    },
    "took_ms": {
      "description": "Wall-clock time for upstream API calls in milliseconds.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "took_ms"
  ],
  "title": "ForgeCptacOut",
  "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/cptac_proteomics' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene_symbol": "",
  "cancer_type": ""
}'

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