Forge Tools proteomexchange

proteomexchange read

scidex.forge.proteomexchange

Search ProteomeXchange consortium for proteomics datasets across PRIDE, MassIVE, PeptideAtlas, and iProX repositories. Supports keyword search (query_type='search') and direct accession lookup (query_type='accession'). Returns dataset accession, title, species, instrument, submission date, repository, and PubMed IDs. Covers 35K+ public proteomics datasets. Broader multi-repository coverage than forge.pride_proteomics. Free REST API — no authentication required.

HTTP: POST /api/scidex/forge/proteomexchange

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.proteomexchange``.",
  "properties": {
    "query": {
      "description": "Keyword query (``query_type='search'``) or accession (``query_type='accession'``). Examples: ``'cancer proteome'``, ``'PXD000001'``, ``'MSV000079843'``.",
      "title": "Query",
      "type": "string"
    },
    "query_type": {
      "default": "search",
      "description": "One of ``'search'`` (keyword search across all repositories) or ``'accession'`` (direct accession lookup). Defaults to ``'search'``.",
      "title": "Query Type",
      "type": "string"
    },
    "limit": {
      "default": 10,
      "description": "Maximum number of datasets to return (1–50, default 10). Ignored in ``'accession'`` mode (always returns ≤1 dataset).",
      "maximum": 50,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeProteomexchangeIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "PxDataset": {
      "description": "One ProteomeXchange dataset entry in the response.",
      "properties": {
        "accession": {
          "description": "ProteomeXchange accession (e.g. ``PXD000001``, ``MSV000079843``).",
          "title": "Accession",
          "type": "string"
        },
        "title": {
          "default": "",
          "description": "Human-readable dataset title.",
          "title": "Title",
          "type": "string"
        },
        "species": {
          "default": "",
          "description": "Primary species (e.g. ``Homo sapiens``).",
          "title": "Species",
          "type": "string"
        },
        "instrument": {
          "default": "",
          "description": "Mass spectrometry instrument used (e.g. ``Q Exactive``).",
          "title": "Instrument",
          "type": "string"
        },
        "submission_date": {
          "default": "",
          "description": "Submission/publication date (ISO 8601, e.g. ``2023-05-12``).",
          "title": "Submission Date",
          "type": "string"
        },
        "repository": {
          "default": "",
          "description": "Source repository name (``PRIDE``, ``MassIVE``, ``PeptideAtlas``, ``iProX``). Derived from the accession prefix when not explicit in the API response.",
          "title": "Repository",
          "type": "string"
        },
        "pubmed_ids": {
          "description": "PubMed identifiers of publications associated with this dataset.",
          "items": {
            "type": "string"
          },
          "title": "Pubmed Ids",
          "type": "array"
        }
      },
      "required": [
        "accession"
      ],
      "title": "PxDataset",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.proteomexchange``.",
  "properties": {
    "query": {
      "description": "The original query string.",
      "title": "Query",
      "type": "string"
    },
    "query_type": {
      "description": "The query mode used (``'search'`` or ``'accession'``).",
      "title": "Query Type",
      "type": "string"
    },
    "datasets": {
      "description": "ProteomeXchange datasets matching the query. Empty when no results are found.",
      "items": {
        "$ref": "#/$defs/PxDataset"
      },
      "title": "Datasets",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "``True`` when the query returned no results (accession not in any repository, or keyword matched nothing).",
      "title": "Not Found",
      "type": "boolean"
    }
  },
  "required": [
    "query",
    "query_type"
  ],
  "title": "ForgeProteomexchangeOut",
  "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/proteomexchange' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "query": ""
}'

Discussion

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