Forge Tools pride_proteomics

pride_proteomics read

scidex.forge.pride_proteomics

Query the EMBL-EBI PRIDE database for proteomics experiments matching one or more gene symbols. Returns mass-spectrometry project accessions, titles, organisms, instruments, peptide/protein counts, and PubMed IDs. Complements expression-atlas adapters (GTEx, GEO, EBI Atlas) with direct proteomics evidence. Free REST API — no authentication required.

HTTP: POST /api/scidex/forge/pride_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.pride_proteomics``.",
  "properties": {
    "gene_symbols": {
      "description": "HGNC gene symbols to query (e.g. ``['TP53', 'BRCA1']``). One PRIDE API call is issued per gene; results are deduplicated by project accession.",
      "items": {
        "type": "string"
      },
      "maxItems": 10,
      "minItems": 1,
      "title": "Gene Symbols",
      "type": "array"
    },
    "organisms": {
      "description": "Organism name filter applied client-side after the API response. Defaults to ``['Homo sapiens']``. Empty list disables filtering (returns all organisms).",
      "items": {
        "type": "string"
      },
      "title": "Organisms",
      "type": "array"
    },
    "instrument_filter": {
      "description": "Optional instrument name filter (case-insensitive substring match). Examples: ``['Orbitrap', 'Q Exactive', 'Fusion']``. Empty list disables filtering.",
      "items": {
        "type": "string"
      },
      "title": "Instrument Filter",
      "type": "array"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of experiments to return (1–100, default 20).",
      "maximum": 100,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "gene_symbols"
  ],
  "title": "ForgePRIDEIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "PRIDEExperiment": {
      "description": "One PRIDE proteomics project in the response.",
      "properties": {
        "project_accession": {
          "description": "PRIDE project accession (e.g. ``PXD000001``).",
          "title": "Project Accession",
          "type": "string"
        },
        "title": {
          "default": "",
          "description": "Human-readable project title.",
          "title": "Title",
          "type": "string"
        },
        "description": {
          "default": "",
          "description": "Project description / abstract.",
          "title": "Description",
          "type": "string"
        },
        "organism": {
          "default": "",
          "description": "Primary organism (e.g. ``Homo sapiens``).",
          "title": "Organism",
          "type": "string"
        },
        "instrument": {
          "default": "",
          "description": "Mass spectrometry instrument used (e.g. ``Q Exactive``).",
          "title": "Instrument",
          "type": "string"
        },
        "publication_date": {
          "default": "",
          "description": "Submission date (ISO 8601, e.g. ``2023-05-12``).",
          "title": "Publication Date",
          "type": "string"
        },
        "matched_proteins": {
          "description": "Protein accessions matched by the search query, when available.",
          "items": {
            "type": "string"
          },
          "title": "Matched Proteins",
          "type": "array"
        },
        "peptide_count": {
          "default": 0,
          "description": "Number of identified peptides (FDR-filtered when reported).",
          "minimum": 0,
          "title": "Peptide Count",
          "type": "integer"
        },
        "protein_count": {
          "default": 0,
          "description": "Number of identified proteins (FDR-filtered when reported).",
          "minimum": 0,
          "title": "Protein Count",
          "type": "integer"
        },
        "pubmed_id": {
          "default": "",
          "description": "PubMed identifier of the associated publication, if any.",
          "title": "Pubmed Id",
          "type": "string"
        }
      },
      "required": [
        "project_accession"
      ],
      "title": "PRIDEExperiment",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.pride_proteomics``.",
  "properties": {
    "experiments": {
      "description": "PRIDE proteomics projects matching the query, capped at ``limit``. Empty when no projects are found.",
      "items": {
        "$ref": "#/$defs/PRIDEExperiment"
      },
      "title": "Experiments",
      "type": "array"
    }
  },
  "title": "ForgePRIDEOut",
  "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/pride_proteomics' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene_symbols": []
}'

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