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pubmed-mcp-server

by io.github.cyanheads
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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

NameRequiredDescriptionDefault
recordsYesRecords to retrieve, each addressed by the `source` and `epmcId` of a `pubmed_europepmc_search` hit. The whole batch resolves in one Europe PMC request.
maxResponseCharactersNoOpt-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

NameRequiredDescriptionDefault
errorNoPresent when the call failed. Absent on success.
noticeNoGuidance 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.
recordsNoResolved records, in the order Europe PMC returned them. Under a `maxResponseCharacters` budget, only the leading records that fit; `deferred.records` lists the rest.
deferredNoContinuation state for records the whole-response budget withheld. Present only when `maxResponseCharacters` deferred at least one record.
notFoundNoRequested `source` + `epmcId` pairs Europe PMC returned no record for. Reported in full regardless of where a `maxResponseCharacters` cut lands — these are misses, not deferrals.
truncatedNoTrue 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.

  1. Changed3 schema fields changed
    • changedOutput schema / properties / records / items / properties / hasFullTextXml / description
      Previous value: -"Whether Europe PMC publishes a fullTextXML for this record. Derived from `inPMC` — only records with a PMC counterpart have JATS via Europe PMC."New value: +"Whether Europe PMC publishes a fullTextXML for this record: true when Europe PMC marks it open access and lists a full-text id for it, open-access preprints (`PPR`) included; false otherwise. Absent when Europe PMC reports no open-access status."
    • changedOutput schema / properties / records / items / properties / journal / description
      Previous value: -"Journal title as display-ready plain text — JATS/HTML markup stripped and HTML entities decoded."New value: +"Journal name as Europe PMC reports it — its MEDLINE abbreviation where it records one (e.g. `Otolaryngol Pol`), else the full journal title — the same name `pubmed_europepmc_search` returns for the record. Display-ready plain text — JATS/HTML markup stripped and HTML entities decoded. Absent when Europe PMC carries no journal, as for preprints."
    • addedOutput schema / properties / records / items / properties / license
      Added value: +{
+  "description": "License Europe PMC records for this record, verbatim (e.g. `cc by`, `cc by-nc-nd`, `cc0`). Relayed as Europe PMC states it, never interpreted. Absent when Europe PMC supplies none.",
+  "type": "string"
+}
  2. Changed2 schema fields changed
    • 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."
  3. Changed1 schema field changed
    • changedInput schema / properties / maxResponseCharacters / maximum
      Previous value: -1000000New value: +9007199254740991
  4. Changed6 schema fields changed
    • 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"
+}
  5. Changed1 schema field changed
    • 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."
  6. Changed1 schema field changed
    • 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."
  7. Changed3 schema fields changed
    • 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."
  8. Changed6 schema fields changed
    • 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"
-]
  9. Changed3 schema fields changed
    • 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."
  10. Added

TDQS

A4.4/5.0
Behavior4/5

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

With readOnlyHint and openWorldHint already declared, the description adds valuable behavioral context: a 25-record per-call limit and detailed deferral semantics via maxResponseCharacters ('records past the ceiling are deferred whole and listed in deferred.records'). It does not cover error handling or rate limiting, but the added context goes well beyond 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 front-loaded with purpose and usage, and each sentence contributes useful information. It is slightly longer than strictly necessary, but every clause (search pairing, source coverage, limits, deferral) earns its place.

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?

Given a simple two-parameter schema, rich annotations, and an existing output schema, the description covers everything an agent needs: purpose, alternatives, special source handling, call limits, and response-bounding behavior. No critical gaps remain.

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

Parameters3/5

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

Schema coverage is 100%, so the schema already fully documents both records and maxResponseCharacters. The description reinforces the array syntax ('an array even for one record') and copying from search hits, but adds no new parameter semantics beyond what the schema provides.

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 states a specific verb and resource: 'Fetch complete Europe PMC records — including the full, untruncated abstract'. It explicitly differentiates from siblings by naming pubmed_europepmc_search and explaining the retrieval gap for preprint/patent/Agricola records that pubmed_fetch_articles and pubmed_fetch_fulltext cannot address.

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 clearly instructs to pair with pubmed_europepmc_search, copy each hit's source and epmcId into records, and use this tool specifically for records lacking PMIDs/DOIs. It explicitly names alternatives that cannot handle them, giving strong when-to-use and when-not-to-use guidance.

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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