Forge Tools europepmc

europepmc read

scidex.forge.europepmc

Search Europe PMC for biomedical literature. Broader than PubMed: covers MEDLINE, PubMed Central full-text, and preprints (bioRxiv, medRxiv, ChemRxiv). Supports full-text queries and preprint-source filtering not available in NCBI's Entrez API. Free REST API — no auth required.

HTTP: POST /api/scidex/forge/europepmc

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.europepmc``.",
  "properties": {
    "query": {
      "description": "Free-text or structured Europe PMC query. Supports field tags (``AUTH:smith``, ``JOURNAL:Nature``), boolean operators (``AND``, ``OR``, ``NOT``), MeSH terms, and full-text search.",
      "maxLength": 500,
      "minLength": 1,
      "title": "Query",
      "type": "string"
    },
    "source": {
      "default": "ALL",
      "description": "Literature source filter. ``MED`` — MEDLINE/PubMed; ``PMC`` — PubMed Central full-text; ``PPR`` — preprints (bioRxiv, medRxiv, ChemRxiv); ``ALL`` — all sources (default).",
      "title": "Source",
      "type": "string"
    },
    "date_from": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Inclusive lower publication date, ``YYYY-MM-DD``. Appended to query as ``FIRST_PDATE:[date_from TO *]``.",
      "title": "Date From"
    },
    "date_to": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Inclusive upper publication date, ``YYYY-MM-DD``. Appended to query as ``FIRST_PDATE:[date_from TO date_to]``.",
      "title": "Date To"
    },
    "has_full_text": {
      "default": false,
      "description": "When ``True``, restrict to papers with open-access full text available in Europe PMC (adds ``HAS_FULLTEXT:y`` to query).",
      "title": "Has Full Text",
      "type": "boolean"
    },
    "limit": {
      "default": 10,
      "description": "Maximum number of papers to return (default 10, max 100).",
      "maximum": 100,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeEuropePMCIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "EuropePMCPaper": {
      "description": "One paper from Europe PMC search results.",
      "properties": {
        "pmid": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "PubMed ID (None for non-MED sources).",
          "title": "Pmid"
        },
        "pmcid": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "PubMed Central ID (e.g. PMC1234567).",
          "title": "Pmcid"
        },
        "title": {
          "default": "",
          "description": "Paper title.",
          "title": "Title",
          "type": "string"
        },
        "authors": {
          "description": "Author name list parsed from ``authorString``.",
          "items": {
            "type": "string"
          },
          "title": "Authors",
          "type": "array"
        },
        "journal": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Journal or preprint server name.",
          "title": "Journal"
        },
        "year": {
          "anyOf": [
            {
              "type": "integer"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Publication year.",
          "title": "Year"
        },
        "abstract": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Abstract text (None if absent).",
          "title": "Abstract"
        },
        "source": {
          "default": "",
          "description": "Europe PMC source code: MED, PMC, PPR, PAT, etc.",
          "title": "Source",
          "type": "string"
        },
        "doi": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "DOI (None if absent).",
          "title": "Doi"
        },
        "is_open_access": {
          "default": false,
          "description": "True when ``isOpenAccess`` is ``Y`` in the Europe PMC response.",
          "title": "Is Open Access",
          "type": "boolean"
        }
      },
      "title": "EuropePMCPaper",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.europepmc``.",
  "properties": {
    "query": {
      "description": "The expanded query string sent to Europe PMC.",
      "title": "Query",
      "type": "string"
    },
    "total_results": {
      "description": "Total matching papers reported by Europe PMC.",
      "title": "Total Results",
      "type": "integer"
    },
    "papers": {
      "items": {
        "$ref": "#/$defs/EuropePMCPaper"
      },
      "title": "Papers",
      "type": "array"
    }
  },
  "required": [
    "query",
    "total_results"
  ],
  "title": "ForgeEuropePMCOut",
  "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/europepmc' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "query": ""
}'

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