pubmed-mcp-server

Pubmed Europepmc Fetch

pubmed_europepmc_fetch

Read-only

Fetch complete Europe PMC records — including the full, untruncated abstract — addressed as records: [{ source, epmcId }], an array even for one record. Pairs with pubmed_europepmc_search, which returns bounded abstractSnippet values and flags cut ones with abstractTruncated: true; copy each hit's source and epmcId into records here to read the whole abstract. This is the retrieval path for preprint (PPR), patent (PAT), and Agricola (AGR) records, which frequently carry no PMID and no DOI, so pubmed_fetch_articles and pubmed_fetch_fulltext cannot address them. Up to 25 records per call. Set maxResponseCharacters to bound the whole response: records past the ceiling are deferred whole and listed in deferred.records for a follow-up call.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`records`	Yes	Records to retrieve, each addressed by the `source` and `epmcId` of a `pubmed_europepmc_search` hit. The whole batch resolves in one Europe PMC request.
`maxResponseCharacters`	No	Opt-in ceiling for the whole response, in characters. Each record is measured as the JSON record it is returned as — title, authors, journal, abstract, identifiers, every field it carries. Records are kept in the order Europe PMC returned them until the next one would cross the ceiling; that record and the rest are deferred whole (never partially populated) and listed in `deferred.records`. Response envelope fields — `notFound`, `deferred` itself — are not counted. Omit to return every resolved record.

Output Schema

TableJSON Schema

Name	Required	Description
`error`	No	Present when the call failed. Absent on success.
`notice`	No	Guidance when one or more requested records could not be resolved, or when `maxResponseCharacters` deferred records — naming how to retrieve them. Absent when every requested record came back.
`records`	No	Resolved records, in the order Europe PMC returned them. Under a `maxResponseCharacters` budget, only the leading records that fit; `deferred.records` lists the rest.
`deferred`	No	Continuation state for records the whole-response budget withheld. Present only when `maxResponseCharacters` deferred at least one record.
`notFound`	No	Requested `source` + `epmcId` pairs Europe PMC returned no record for. Reported in full regardless of where a `maxResponseCharacters` cut lands — these are misses, not deferrals.
`truncated`	No	True when `maxResponseCharacters` withheld at least one resolved record. Absent when the response carries every record that resolved. The continuation state is in `deferred`.

Schema Changelog

Changes observed during successful MCP inspections.

Changed2 schema fields changedOct 12, 2026

changedOutput schema / properties / deferred / properties / nextDeferredCharacters / description

Previous value: -"Serialized size of the next deferred record — the first entry in `records`, where the response stopped. Raise `maxResponseCharacters` to at least this to make progress; a smaller record further down `records` cannot be reached until this one fits."New value: +"Serialized size of the next deferred record — the first entry in `records`, where the response stopped — and the continuation ceiling: re-calling with the deferred pairs needs `maxResponseCharacters` ≥ this to return anything, and a smaller record further down `records` cannot be reached until this one fits. Repeating this same call needs `maxResponseCharacters` ≥ `returnedCharacters` + this to return this record as well."

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

Previous 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 in place of results, an empty response to a sort with an undocumented field or no asc/desc direction, or a pagination cursor it cannot read (an empty response on the last attempt the retry budget allows, or a second HTTP 503 when the first page of the same query is served). `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 in place of results; a sort it cannot use (one whose keys are not each a field plus asc/desc, rejected before any request; an empty response to a sort with an undocumented field; or a second HTTP 503 to a sorted search when the same query without the sort is served); or a pagination cursor it cannot read (an empty response on the last attempt the retry budget allows, or a second HTTP 503 when the first page of the same query is served). `europepmc_disabled`: Europe PMC service is disabled via EUROPEPMC_ENABLED=false. Other values are possible when a failure originates below the handler."

Changed1 schema field changedOct 9, 2026
- changedInput schema / properties / maxResponseCharacters / maximum
```
Previous value: -1000000New value: +9007199254740991
```

Changed6 schema fields changedOct 4, 2026

addedInput schema / properties / maxResponseCharacters

Added value: +{
+  "description": "Opt-in ceiling for the whole response, in characters. Each record is measured as the JSON record it is returned as — title, authors, journal, abstract, identifiers, every field it carries. Records are kept in the order Europe PMC returned them until the next one would cross the ceiling; that record and the rest are deferred whole (never partially populated) and listed in `deferred.records`. Response envelope fields — `notFound`, `deferred` itself — are not counted. Omit to return every resolved record.",
+  "maximum": 1000000,
+  "minimum": 1,
+  "type": "integer"
+}

addedOutput schema / properties / deferred

Added value: +{
+  "additionalProperties": false,
+  "description": "Continuation state for records the whole-response budget withheld. Present only when `maxResponseCharacters` deferred at least one record.",
+  "properties": {
+    "deferredCount": {
+      "description": "Records that resolved but were withheld to stay under the ceiling",
+      "type": "number"
+    },
+    "maxResponseCharacters": {
+      "description": "The `maxResponseCharacters` ceiling this response was budgeted against",
+      "type": "number"
+    },
+    "nextDeferredCharacters": {
+      "description": "Serialized size of the next deferred record — the first entry in `records`, where the response stopped. Raise `maxResponseCharacters` to at least this to make progress; a smaller record further down `records` cannot be reached until this one fits.",
+      "type": "number"
+    },
+    "records": {
+      "description": "The deferred records, in response order, each as the resolved record's own `source` + `epmcId` — a `PMC` request answered by its `MED` record is listed as that `MED` pair. Pass them back as `records` to retrieve them. Never contains a pair from `notFound`.",
+      "items": {
+        "additionalProperties": false,
+        "description": "One deferred record, addressed by its own `source` + `epmcId`",
+        "properties": {
+          "epmcId": {
+            "description": "Europe PMC's internal record id",
+            "type": "string"
+          },
+          "source": {
+            "description": "Europe PMC source the record was resolved from",
+            "enum": [
+              "MED",
+              "PMC",
+              "PPR",
+              "PAT",
+              "AGR"
+            ],
+            "type": "string"
+          }
+        },
+        "required": [
+          "source",
+          "epmcId"
+        ],
+        "type": "object"
+      },
+      "type": "array"
+    },
+    "returnedCharacters": {
+      "description": "Serialized characters the returned records account for",
+      "type": "number"
+    }
+  },
+  "required": [
+    "maxResponseCharacters",
+    "returnedCharacters",
+    "deferredCount",
+    "records",
+    "nextDeferredCharacters"
+  ],
+  "type": "object"
+}

changedOutput schema / properties / notFound / description

Previous value: -"Requested `source` + `epmcId` pairs Europe PMC returned no record for"New value: +"Requested `source` + `epmcId` pairs Europe PMC returned no record for. Reported in full regardless of where a `maxResponseCharacters` cut lands — these are misses, not deferrals."

changedOutput schema / properties / notice / description

Previous value: -"Guidance when one or more requested records could not be resolved. Absent when every record came back."New value: +"Guidance when one or more requested records could not be resolved, or when `maxResponseCharacters` deferred records — naming how to retrieve them. Absent when every requested record came back."

changedOutput schema / properties / records / description

Previous value: -"Resolved records, in the order Europe PMC returned them"New value: +"Resolved records, in the order Europe PMC returned them. Under a `maxResponseCharacters` budget, only the leading records that fit; `deferred.records` lists the rest."

addedOutput schema / properties / truncated

Added value: +{
+  "description": "True when `maxResponseCharacters` withheld at least one resolved record. Absent when the response carries every record that resolved. The continuation state is in `deferred`.",
+  "type": "boolean"
+}

Changed1 schema field changedSep 28, 2026

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

Previous 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."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 in place of results, an empty response to a sort with an undocumented field or no asc/desc direction, or a pagination cursor it cannot read (an empty response on the last attempt the retry budget allows, or a second HTTP 503 when the first page of the same query is served). `europepmc_disabled`: Europe PMC service is disabled via EUROPEPMC_ENABLED=false. Other values are possible when a failure originates below the handler."

Changed1 schema field changedSep 23, 2026

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 / records / 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 / records / 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 / records / items / properties / title / description

Previous value: -"Record title"New value: +"Record 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": [
+      "records"
+    ]
+  },
+  {
+    "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: -[
-  "records"
-]
```

Changed3 schema fields changedJul 26, 2026

changedInput schema / properties / records / items / properties / source / description

Previous value: -"Europe PMC source corpus — `MED` (PubMed), `PMC` (PubMed Central), `PPR` (preprint), `PAT` (patent), `AGR` (Agricola). Copy it from the search hit's `source`."New value: +"Europe PMC source corpus — `MED` (PubMed), `PMC` (PubMed Central), `PPR` (preprint), `PAT` (patent), `AGR` (Agricola). Copy it from the search hit's `source`. `PMC` paired with a PMCID resolves whether or not the article is also indexed in PubMed, and a PubMed-indexed one comes back as its canonical `MED` record carrying that PMCID in `pmcId`."

changedOutput schema / properties / notFound / items / properties / source / description

Previous value: -"Europe PMC source corpus — `MED` (PubMed), `PMC` (PubMed Central), `PPR` (preprint), `PAT` (patent), `AGR` (Agricola). Copy it from the search hit's `source`."New value: +"Europe PMC source corpus — `MED` (PubMed), `PMC` (PubMed Central), `PPR` (preprint), `PAT` (patent), `AGR` (Agricola). Copy it from the search hit's `source`. `PMC` paired with a PMCID resolves whether or not the article is also indexed in PubMed, and a PubMed-indexed one comes back as its canonical `MED` record carrying that PMCID in `pmcId`."

changedOutput schema / properties / records / 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."

AddedJul 26, 2026

TDQS

A4.8/5.0

Behavior5/5

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

Annotations only declare readOnly and openWorld; the description adds substantial behavior beyond that: a 25-record batch ceiling, single-request resolution, and precise truncation semantics (records deferred whole, never partially populated, listed in deferred.records, envelope fields uncounted). This is exactly the extra context annotations do not carry.

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?

Front-loaded with the core action and the full-abstract payoff, then the pairing workflow, then the batch limit and ceiling behavior. Some parenthetical detail is dense, but every sentence carries distinct information and nothing is padding.

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?

With an output schema present, the description need not explain return fields, yet it still clarifies the deferred.records envelope behavior. Batch limits, addressing format, and sibling routing are all covered for a two-parameter retrieval tool.

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% and the schema already documents source/epmcId and maxResponseCharacters thoroughly, so the baseline is 3. The description adds value by stressing the array-form requirement even for a single record and by restating the deferral behavior of maxResponseCharacters in workflow terms.

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?

States a specific verb and resource ('Fetch complete Europe PMC records — including the full, untruncated abstract') and immediately distinguishes itself from pubmed_europepmc_search, pubmed_fetch_articles, and pubmed_fetch_fulltext. An agent can tell exactly what this retrieves and what it does not.

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?

Names the sibling to pair with, explains the workflow (copy source and epmcId from search hits), and gives the exclusion case explicitly: PPR/PAT/AGR records have no PMID/DOI so the other fetch tools cannot address them. When-to-use and when-not-to-use are both covered.

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 Fetch

Input Schema

Output Schema

Schema Changelog

TDQS

Glama MCP Gateway

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