pubmed-mcp-server

Pubmed Europepmc Search

pubmed_europepmc_search

Read-only

Search Europe PMC, a broad open-access biomedical corpus. Surfaces preprints (source: PPR), patents (source: PAT), Agricola (source: AGR), plus everything in PubMed (MED) and PMC. Use when additional coverage is needed — preprints and EPMC-only OA records are the typical recovery. Paginate via cursorMark. Defaults to MED, PMC, and PPR; pass sources to include PAT / AGR. Abstracts arrive as a bounded abstractSnippet with abstractTruncated marking the cut ones — pass a hit’s source and epmcId to pubmed_europepmc_fetch for the complete abstract.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`sort`	No	Optional EPMC sort: `<field> asc\|desc`, or several comma-separated keys applied in order (`PUB_YEAR desc, CITED desc`). Documented sortable fields: `P_PDATE_D` (publication date), `CITED` (citation count), `AUTH_FIRST` (first author surname), `PUB_YEAR` (publication year). Examples: `P_PDATE_D desc` (newest first), `CITED desc` (most cited). Omit for relevance ranking. Field and direction match case-insensitively. A field outside the documented set may be honored, silently ignored, or rejected, and a sort using one — or a key without `asc`/`desc` — can fail with `europepmc_invalid_input` naming it, even when Europe PMC honors the field. Note: `P_PDATE_D` is ignored for preprint-only (`sources: ["PPR"]`) result sets — preprints have no populated publication date, so use `PUB_YEAR` to order preprints by date.
`query`	Yes	Europe PMC search query. Supports field tokens like `AUTH:"<name>"`, `JOURNAL:"<title>"`, `TITLE:"<words>"`, `PUB_YEAR:[2020 TO 2024]`, `DOI:"..."`, `EXT_ID:<pmid> AND SRC:MED`, `PMCID:PMC<digits>`. Identifier tokens may be quoted or unquoted — this tool wraps every query with its `sources` filter, and Europe PMC honors a quoted identifier inside that wrapper. A PubMed-indexed article resolves under `SRC:MED`, not `SRC:PMC`, whichever identifier is used. Free text is matched broadly across abstract/title/keywords.
`sources`	No	Filter to specific EPMC sources. Defaults to MED, PMC, PPR when omitted. Pass an explicit array including PAT or AGR to broaden coverage. Allowed values: MED, PMC, PPR, PAT, AGR.
`pageSize`	No	Results per page. Max 100 per EPMC API.
`cursorMark`	No	Pagination cursor. Use `*` (default) for the first page; pass the previous response's `nextCursorMark` for subsequent pages.	*
`resultType`	No	`core` returns abstract, IDs, dates, license; `lite` is a smaller payload with IDs and titles only.	core

Output Schema

TableJSON Schema

Name	Required	Description
`hits`	No	Matching Europe PMC records, in the order EPMC returned them
`error`	No	Present when the call failed. Absent on success.
`query`	No	Effective query string echoed by Europe PMC
`notice`	No	Optional guidance when results are empty or paging overshot
`searchUrl`	No	Europe PMC's website search URL for this query
`cursorMark`	No	Cursor used for this response (echoed from the request)
`totalCount`	No	Total matching records across all pages
`appliedSources`	No	Sources the query was filtered against (defaults applied)
`nextCursorMark`	No	Cursor to pass back as `cursorMark` for the next page. Absent on the final page.

Schema Changelog

Changes observed during successful MCP inspections.

Changed2 schema fields changedSep 23, 2026

changedInput schema / properties / query / description

Previous value: -"Europe PMC search query. Supports field tokens like `AUTH:\"<name>\"`, `JOURNAL:\"<title>\"`, `TITLE:\"<words>\"`, `PUB_YEAR:[2020 TO 2024]`, `DOI:\"...\"`, `EXT_ID:<pmid> AND SRC:MED`, `PMCID:PMC<digits>`. Identifier tokens combined with `AND SRC:` must be unquoted — the quoted form matches nothing. Free text is matched broadly across abstract/title/keywords."New value: +"Europe PMC search query. Supports field tokens like `AUTH:\"<name>\"`, `JOURNAL:\"<title>\"`, `TITLE:\"<words>\"`, `PUB_YEAR:[2020 TO 2024]`, `DOI:\"...\"`, `EXT_ID:<pmid> AND SRC:MED`, `PMCID:PMC<digits>`. Identifier tokens may be quoted or unquoted — this tool wraps every query with its `sources` filter, and Europe PMC honors a quoted identifier inside that wrapper. A PubMed-indexed article resolves under `SRC:MED`, not `SRC:PMC`, whichever identifier is used. Free text is matched broadly across abstract/title/keywords."

changedOutput schema / anyOf

Previous value: -[
-  {
-    "not": {
-      "required": [
-        "error"
-      ]
-    },
-    "required": [
-      "hits",
-      "cursorMark",
-      "searchUrl",
-      "query",
-      "totalCount",
-      "appliedSources"
-    ]
-  },
-  {
-    "required": [
-      "error"
-    ]
-  }
-]New value: +[
+  {
+    "not": {
+      "required": [
+        "error"
+      ]
+    },
+    "required": [
+      "hits",
+      "cursorMark",
+      "searchUrl",
+      "totalCount",
+      "query",
+      "appliedSources"
+    ]
+  },
+  {
+    "required": [
+      "error"
+    ]
+  }
+]

Changed2 schema fields changedSep 23, 2026

changedInput schema / properties / sort / description

Previous value: -"Optional EPMC sort: `<field> asc|desc`. Documented sortable fields: `P_PDATE_D` (publication date), `CITED` (citation count), `AUTH_FIRST` (first author surname), `PUB_YEAR` (publication year). Examples: `P_PDATE_D desc` (newest first), `CITED desc` (most cited). Omit for relevance ranking. Fields outside the documented set are rejected by EPMC. Note: `P_PDATE_D` is ignored for preprint-only (`sources: [\"PPR\"]`) result sets — preprints have no populated publication date, so use `PUB_YEAR` to order preprints by date."New value: +"Optional EPMC sort: `<field> asc|desc`, or several comma-separated keys applied in order (`PUB_YEAR desc, CITED desc`). Documented sortable fields: `P_PDATE_D` (publication date), `CITED` (citation count), `AUTH_FIRST` (first author surname), `PUB_YEAR` (publication year). Examples: `P_PDATE_D desc` (newest first), `CITED desc` (most cited). Omit for relevance ranking. Field and direction match case-insensitively. A field outside the documented set may be honored, silently ignored, or rejected, and a sort using one — or a key without `asc`/`desc` — can fail with `europepmc_invalid_input` naming it, even when Europe PMC honors the field. Note: `P_PDATE_D` is ignored for preprint-only (`sources: [\"PPR\"]`) result sets — preprints have no populated publication date, so use `PUB_YEAR` to order preprints by date."

changedOutput schema / properties / error / properties / data / properties / reason / description

Previous value: -"Machine-readable failure mode. Declared by this tool: `europepmc_unreachable`: Europe PMC was unreachable after all retry attempts. `europepmc_invalid_response`: Europe PMC returned a body that could not be parsed (invalid JSON or XML). `europepmc_invalid_input`: Europe PMC rejected the request input (empty query, unknown sort field, malformed parameter). `europepmc_disabled`: Europe PMC service is disabled via EUROPEPMC_ENABLED=false. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `europepmc_unreachable`: Europe PMC failed on every retry attempt — unreachable, an HTTP 404 or 5xx other than a 504 timeout from its search endpoint, or an empty response with no results. `europepmc_invalid_response`: Europe PMC returned a body that could not be parsed (invalid JSON or XML). `europepmc_invalid_input`: Europe PMC rejected the request input — an error message such as an empty query, an empty response to a sort with an undocumented field or no asc/desc direction, or an empty response to a pagination cursor on every attempt. `europepmc_disabled`: Europe PMC service is disabled via EUROPEPMC_ENABLED=false. Other values are possible when a failure originates below the handler."

Changed3 schema fields changedSep 9, 2026

changedOutput schema / properties / hits / items / properties / authors / description

Previous value: -"Formatted author string"New value: +"Formatted author string as display-ready plain text — JATS/HTML markup stripped and HTML entities decoded."

changedOutput schema / properties / hits / items / properties / journal / description

Previous value: -"Journal title"New value: +"Journal title as display-ready plain text — JATS/HTML markup stripped and HTML entities decoded."

changedOutput schema / properties / hits / items / properties / title / description

Previous value: -"Article title"New value: +"Article title as display-ready plain text — JATS/HTML markup stripped and HTML entities decoded."

Changed6 schema fields changedAug 21, 2026

changedInput schema / $schema

Previous value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"

addedInput schema / additionalProperties
```
Added value: +false
```

changedOutput schema / $schema

Previous value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"

addedOutput schema / anyOf

Added value: +[
+  {
+    "not": {
+      "required": [
+        "error"
+      ]
+    },
+    "required": [
+      "hits",
+      "cursorMark",
+      "searchUrl",
+      "query",
+      "totalCount",
+      "appliedSources"
+    ]
+  },
+  {
+    "required": [
+      "error"
+    ]
+  }
+]

addedOutput schema / properties / error

Added value: +{
+  "additionalProperties": {},
+  "description": "Present when the call failed. Absent on success.",
+  "properties": {
+    "code": {
+      "description": "JSON-RPC error code for this failure.",
+      "maximum": 9007199254740991,
+      "minimum": -9007199254740991,
+      "type": "integer"
+    },
+    "data": {
+      "additionalProperties": {},
+      "properties": {
+        "reason": {
+          "description": "Machine-readable failure mode. Declared by this tool: `europepmc_unreachable`: Europe PMC was unreachable after all retry attempts. `europepmc_invalid_response`: Europe PMC returned a body that could not be parsed (invalid JSON or XML). `europepmc_invalid_input`: Europe PMC rejected the request input (empty query, unknown sort field, malformed parameter). `europepmc_disabled`: Europe PMC service is disabled via EUROPEPMC_ENABLED=false. Other values are possible when a failure originates below the handler.",
+          "examples": [
+            "europepmc_unreachable",
+            "europepmc_invalid_response",
+            "europepmc_invalid_input",
+            "europepmc_disabled"
+          ],
+          "type": "string"
+        },
+        "recovery": {
+          "additionalProperties": {},
+          "description": "Actionable next step for the caller.",
+          "properties": {
+            "hint": {
+              "type": "string"
+            }
+          },
+          "required": [
+            "hint"
+          ],
+          "type": "object"
+        },
+        "retryable": {
+          "description": "Whether retrying may succeed.",
+          "type": "boolean"
+        }
+      },
+      "type": "object"
+    },
+    "message": {
+      "description": "Human-readable description of what went wrong.",
+      "type": "string"
+    }
+  },
+  "required": [
+    "code",
+    "message"
+  ],
+  "type": "object"
+}

removedOutput schema / required

Removed value: -[
-  "hits",
-  "cursorMark",
-  "searchUrl",
-  "query",
-  "totalCount",
-  "appliedSources"
-]

Changed1 schema field changedJul 26, 2026

changedOutput schema / properties / hits / items / properties / doi / description

Previous value: -"DOI when present"New value: +"DOI when present, cased as Europe PMC reports it. DOIs are case-insensitive by spec and no case normalization is applied here, so the same DOI can arrive in a different case from `pubmed_fetch_articles` (Europe PMC `10.1056/nejmoa2212948`, NCBI `10.1056/NEJMoa2212948`) — a byte-for-byte comparison across the two reports a false mismatch."

Changed3 schema fields changedJul 26, 2026

changedOutput schema / properties / hits / items / properties / abstractSnippet / description

Previous value: -"First few hundred characters of the abstract as display-ready plain text — JATS/HTML markup stripped and HTML entities decoded — when `resultType: \"core\"` is requested"New value: +"First 400 characters of the abstract as display-ready plain text — JATS/HTML markup stripped and HTML entities decoded — when `resultType: \"core\"` is requested, with a trailing … appended when the abstract was cut. Check `abstractTruncated` before treating it as the whole abstract."

addedOutput schema / properties / hits / items / properties / abstractTruncated

Added value: +{
+  "description": "Whether `abstractSnippet` was cut short of the full abstract. Retrieve the complete text with `pubmed_europepmc_fetch` using this record’s `source` and `epmcId`. Present whenever `abstractSnippet` is; omitted when Europe PMC carries no abstract.",
+  "type": "boolean"
+}

changedOutput schema / properties / hits / items / properties / epmcId / description

Previous value: -"Europe PMC's internal record id; key for `fullTextXML` lookup"New value: +"Europe PMC's internal record id. Pass it with this hit's `source` to `pubmed_europepmc_fetch` for the complete record. Europe PMC's `fullTextXML` is keyed on `pmcId`, not on this id, so records without a PMC counterpart have no full text to fetch."

Changed1 schema field changedJul 26, 2026

changedInput schema / properties / query / description

Previous value: -"Europe PMC search query. Supports field tokens like `AUTH:\"<name>\"`, `JOURNAL:\"<title>\"`, `TITLE:\"<words>\"`, `PUB_YEAR:[2020 TO 2024]`, `DOI:\"...\"`, `EXT_ID:\"<pmid>\" AND SRC:MED`. Free text is matched broadly across abstract/title/keywords."New value: +"Europe PMC search query. Supports field tokens like `AUTH:\"<name>\"`, `JOURNAL:\"<title>\"`, `TITLE:\"<words>\"`, `PUB_YEAR:[2020 TO 2024]`, `DOI:\"...\"`, `EXT_ID:<pmid> AND SRC:MED`, `PMCID:PMC<digits>`. Identifier tokens combined with `AND SRC:` must be unquoted — the quoted form matches nothing. Free text is matched broadly across abstract/title/keywords."

Changed1 schema field changedJun 18, 2026

changedOutput schema / properties / hits / items / properties / abstractSnippet / description

Previous value: -"First few hundred characters of the abstract when `resultType: \"core\"` is requested"New value: +"First few hundred characters of the abstract as display-ready plain text — JATS/HTML markup stripped and HTML entities decoded — when `resultType: \"core\"` is requested"

Changed3 schema fields changedJun 11, 2026

removedOutput schema / properties / hitCount

Removed value: -{
-  "description": "Total matching records across all pages",
-  "type": "number"
-}

addedOutput schema / properties / totalCount

Added value: +{
+  "description": "Total matching records across all pages",
+  "type": "number"
+}

changedOutput schema / required

Previous value: -[
-  "hits",
-  "cursorMark",
-  "searchUrl",
-  "query",
-  "hitCount",
-  "appliedSources"
-]New value: +[
+  "hits",
+  "cursorMark",
+  "searchUrl",
+  "query",
+  "totalCount",
+  "appliedSources"
+]

Changed1 schema field changedJun 9, 2026

changedInput schema / properties / sort / description

Previous value: -"Optional EPMC sort: `<field> asc|desc`. Documented sortable fields: `P_PDATE_D` (publication date), `CITED` (citation count), `AUTH_FIRST` (first author surname), `PUB_YEAR` (publication year). Examples: `P_PDATE_D desc` (newest first), `CITED desc` (most cited). Omit for relevance ranking. Fields outside the documented set are rejected by EPMC."New value: +"Optional EPMC sort: `<field> asc|desc`. Documented sortable fields: `P_PDATE_D` (publication date), `CITED` (citation count), `AUTH_FIRST` (first author surname), `PUB_YEAR` (publication year). Examples: `P_PDATE_D desc` (newest first), `CITED desc` (most cited). Omit for relevance ranking. Fields outside the documented set are rejected by EPMC. Note: `P_PDATE_D` is ignored for preprint-only (`sources: [\"PPR\"]`) result sets — preprints have no populated publication date, so use `PUB_YEAR` to order preprints by date."

Changed1 schema field changedMay 30, 2026

changedOutput schema / required

Previous value: -[
-  "query",
-  "hits",
-  "hitCount",
-  "cursorMark",
-  "appliedSources",
-  "searchUrl"
-]New value: +[
+  "hits",
+  "cursorMark",
+  "searchUrl",
+  "query",
+  "hitCount",
+  "appliedSources"
+]

Changed1 schema field changedMay 20, 2026

changedInput schema / properties / sort / description

Previous value: -"Optional EPMC sort spec, e.g. `FIRST_PIDATE desc` (newest first) or `CITED desc` (most cited). Omit for relevance order."New value: +"Optional EPMC sort: `<field> asc|desc`. Documented sortable fields: `P_PDATE_D` (publication date), `CITED` (citation count), `AUTH_FIRST` (first author surname), `PUB_YEAR` (publication year). Examples: `P_PDATE_D desc` (newest first), `CITED desc` (most cited). Omit for relevance ranking. Fields outside the documented set are rejected by EPMC."

AddedMay 19, 2026

TDQS

A4.8/5.0

Behavior5/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

The description discloses multiple non-obvious behaviors: it always wraps queries with its `sources` filter, notes that a PMID resolves under `SRC:MED` rather than `SRC:PMC`, explains how sort fields can be silently ignored or trigger `europepmc_invalid_input`, and details the `abstractSnippet` with `abstractTruncated` flag. This goes well beyond the readOnlyHint and openWorldHint annotations.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is compact yet dense — every sentence contributes a distinct fact (sources, defaults, pagination, abstract truncation, the fetch sibling). It is longer than the terse one-liner ideal but avoids fluff and front-loads the key purpose and usage guidance.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

This is a search tool with an output schema, so return values are already structured. The description covers all operational aspects an agent needs: default source set, pagination mechanics, error behavior, abstract truncation, and the path to full abstracts. Nothing essential is missing for a tool of this complexity.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100%, so a baseline of 3 applies. The description adds value beyond the schema by explaining the preprint-specific exception for `P_PDATE_D`, the risk of undocumented sort fields, and the default source set. These nuances are genuinely helpful for correct invocation, though the schema already covers most parameter intent.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description opens with a specific verb ('Search') and a clear resource ('Europe PMC'), then enumerates the additional source coverage (preprints, patents, Agricola) that distinguishes it from a plain PubMed search. It also names the sibling `pubmed_europepmc_fetch` for retrieving full abstracts, so an agent can readily discriminate between the two.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines5/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

It explicitly states when to use this tool ('Use when additional coverage is needed — preprints and EPMC-only OA records are the typical recovery'), provides pagination guidance via `cursorMark`, and directs the agent to a sibling for complete abstracts. No room for inference about the intended use case.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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Pubmed Europepmc Search

Input Schema

Output Schema

Schema Changelog

TDQS

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