pubmed-mcp-server

Pubmed Format Citations

pubmed_format_citations

Read-only

Generate formatted citations for PubMed articles in APA, MLA, BibTeX, RIS, or Vancouver styles, with support for requesting one or multiple formats at once.

Instructions

Get formatted citations for PubMed articles in one or more formats (apa, mla, bibtex, ris, vancouver). Pass a single format as a string or multiple as an array. Retractions, errata, and expressions of concern NCBI links to an article come back in notices; Vancouver and APA also cite a retraction in the reference itself.

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "pmids": "<pmids>"
    },
    "name": "pubmed_format_citations"
  }
}

Input Schema

Name	Required	Description	Default
`pmids`	Yes	PubMed IDs to cite
`format`	No	Citation format(s) to generate — single style as a string or multiple as an array. Allowed values: apa, mla, bibtex, ris, vancouver.	apa

Output Schema

Name	Required	Description
`error`	No	Present when the call failed. Absent on success.
`notice`	No	Optional guidance when no citations were produced — points to discovery tools. Absent when at least one citation was produced.
`citations`	No	Citations per article
`totalFormatted`	No	Number of PMIDs successfully formatted
`totalSubmitted`	No	Number of PMIDs submitted for citation formatting
`unavailablePmids`	No	PMIDs PubMed returned no record for, so nothing could be cited for them. That is all this reports: PubMed omits a PMID it does not recognize silently, with no error and no reason, so the absence says nothing about whether the PMID exists. Use `pubmed_search_articles` to find PMIDs that do resolve.

Schema Changelog

Changes observed during successful MCP inspections.

Changed1 schema field changedv2.12.1Nov 11, 2026

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

Previous value: -"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities failed on every attempt the retry budget allowed — retries ran out, or the next backoff would overrun the total deadline. `ncbi_rate_limited`: NCBI answered HTTP 429 (too many requests) and the call stopped on it — retries ran out, the next backoff would overrun the total deadline, or the Retry-After NCBI named outlasts the time left or the 30-second backoff cap. `ncbi_deadline_exceeded`: The total NCBI request deadline expired before NCBI answered successfully — mid-request, while queued, or during a retry backoff. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities failed on every attempt the retry budget allowed — retries ran out, the next backoff would overrun the total deadline, or the call made one attempt without retrying because the previous call to the same E-utility had failed on every attempt. `ncbi_rate_limited`: NCBI answered HTTP 429 (too many requests) and the call stopped on it — retries ran out, the next backoff would overrun the total deadline, or the Retry-After NCBI named outlasts the time left or the 30-second backoff cap. `ncbi_deadline_exceeded`: The total NCBI request deadline expired before NCBI answered successfully — mid-request, while queued, or during a retry backoff. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). Other values are possible when a failure originates below the handler."

Changed1 schema field changedv2.11.1Oct 28, 2026

changedOutput schema / properties / citations / items / properties / citations / description

Previous value: -"Citations keyed by style"New value: +"Citations keyed by style. APA and MLA are Markdown — the journal, volume and book title in *italics*, every other character of the record escaped so it renders as written; BibTeX, RIS and Vancouver are plain text."

Changed1 schema field changedv2.10.22Oct 14, 2026

addedOutput schema / properties / citations / items / properties / notices

Added value: +{
+  "description": "Retraction, erratum, and expression-of-concern notices NCBI links to this article, in NCBI's order. Vancouver notes each `RetractionIn` and `ErratumIn` after the reference and APA each `RetractionIn`; the other types, and MLA, BibTeX, and RIS, carry none, so check this before citing. Absent when NCBI links none.",
+  "items": {
+    "additionalProperties": false,
+    "description": "A linked notice that qualifies the cited article",
+    "properties": {
+      "note": {
+        "description": "NCBI's note on the link, e.g. the correction an erratum makes. Absent when NCBI gives none.",
+        "type": "string"
+      },
+      "pmid": {
+        "description": "PMID of the notice — pass it to `pubmed_fetch_articles` to read it. Absent when the notice has no PMID, as with many errata.",
+        "type": "string"
+      },
+      "refSource": {
+        "description": "Citation of the notice as NCBI writes it (e.g. \"Lancet. 2010 Feb 6;375(9713):445. doi: 10.1016/S0140-6736(10)60175-4.\").",
+        "type": "string"
+      },
+      "refType": {
+        "description": "NCBI's `RefType` for the link: RetractionIn, RetractedandRepublishedIn, ExpressionOfConcernIn, ErratumIn, or CorrectedandRepublishedIn.",
+        "enum": [
+          "RetractionIn",
+          "RetractedandRepublishedIn",
+          "ExpressionOfConcernIn",
+          "ErratumIn",
+          "CorrectedandRepublishedIn"
+        ],
+        "type": "string"
+      }
+    },
+    "required": [
+      "refType",
+      "refSource"
+    ],
+    "type": "object"
+  },
+  "type": "array"
+}

Changed2 schema fields changedv2.10.19Sep 30, 2026

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

Previous value: -"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities failed on every attempt the retry budget allowed — retries ran out, or the next backoff would overrun the total deadline. `ncbi_rate_limited`: NCBI answered HTTP 429 (too many requests) and the call stopped on it — retries ran out, the next backoff would overrun the total deadline, or the Retry-After NCBI named outlasts the time left or the 30-second backoff cap. `ncbi_deadline_exceeded`: The total NCBI request deadline expired before NCBI answered successfully — mid-request, while queued, or during a retry backoff. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). Other values are possible when a failure originates below the handler."

changedOutput schema / properties / error / properties / data / properties / reason / examples

Previous value: -[
-  "queue_full",
-  "ncbi_unreachable",
-  "ncbi_deadline_exceeded",
-  "ncbi_invalid_response",
-  "ncbi_resource_not_found"
-]New value: +[
+  "queue_full",
+  "ncbi_unreachable",
+  "ncbi_rate_limited",
+  "ncbi_deadline_exceeded",
+  "ncbi_invalid_response",
+  "ncbi_resource_not_found"
+]

Changed1 schema field changedv2.10.18Sep 23, 2026

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

Previous value: -"Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). Other values are possible when a failure originates below the handler."

Changed1 schema field changedv2.10.12Sep 11, 2026

changedOutput schema / properties / unavailablePmids / description

Previous value: -"Requested PMIDs that did not return article metadata"New value: +"PMIDs PubMed returned no record for, so nothing could be cited for them. That is all this reports: PubMed omits a PMID it does not recognize silently, with no error and no reason, so the absence says nothing about whether the PMID exists. Use `pubmed_search_articles` to find PMIDs that do resolve."

Changed6 schema fields changedv2.10.4Aug 28, 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": [
+      "citations",
+      "totalSubmitted",
+      "totalFormatted"
+    ]
+  },
+  {
+    "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: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). Other values are possible when a failure originates below the handler.",
+          "examples": [
+            "queue_full",
+            "ncbi_unreachable",
+            "ncbi_deadline_exceeded",
+            "ncbi_invalid_response",
+            "ncbi_resource_not_found"
+          ],
+          "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: -[
-  "citations",
-  "totalSubmitted",
-  "totalFormatted"
-]

Changed3 schema fields changedv2.9.1Jun 9, 2026

changedInput schema / properties / format / anyOf

Previous value: -[
-  {
-    "description": "Single citation style. One of: apa, mla, bibtex, ris.",
-    "enum": [
-      "apa",
-      "mla",
-      "bibtex",
-      "ris"
-    ],
-    "type": "string"
-  },
-  {
-    "description": "Multiple citation styles to generate. Each entry: apa, mla, bibtex, or ris.",
-    "items": {
-      "enum": [
-        "apa",
-        "mla",
-        "bibtex",
-        "ris"
-      ],
-      "type": "string"
-    },
-    "minItems": 1,
-    "type": "array"
-  }
-]New value: +[
+  {
+    "description": "Single citation style. One of: apa, mla, bibtex, ris, vancouver.",
+    "enum": [
+      "apa",
+      "mla",
+      "bibtex",
+      "ris",
+      "vancouver"
+    ],
+    "type": "string"
+  },
+  {
+    "description": "Multiple citation styles to generate. Each entry: apa, mla, bibtex, ris, or vancouver.",
+    "items": {
+      "enum": [
+        "apa",
+        "mla",
+        "bibtex",
+        "ris",
+        "vancouver"
+      ],
+      "type": "string"
+    },
+    "minItems": 1,
+    "type": "array"
+  }
+]

changedInput schema / properties / format / description

Previous value: -"Citation format(s) to generate — single style as a string or multiple as an array. Allowed values: apa, mla, bibtex, ris."New value: +"Citation format(s) to generate — single style as a string or multiple as an array. Allowed values: apa, mla, bibtex, ris, vancouver."

addedOutput schema / properties / notice

Added value: +{
+  "description": "Optional guidance when no citations were produced — points to discovery tools. Absent when at least one citation was produced.",
+  "type": "string"
+}

Addedv2.7.6May 29, 2026
Removedv2.7.4May 24, 2026
Addedv2.3.2Apr 4, 2026

TDQS

A3.8/5.0

Behavior4/5

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

Annotations already cover the safety profile (readOnlyHint, openWorldHint), and the description goes beyond them by disclosing that retraction, erratum, and expression-of-concern links surface in `notices`, and that Vancouver/APA embed retraction notices in the reference. That is genuinely useful output behavior not implied by the annotations.

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

Conciseness5/5

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

Three tightly packed sentences: purpose first, accepted input shape second, edge-case output behavior last. No filler and no repetition of the tool name or title.

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

Completeness4/5

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

An output schema exists so return values need not be enumerated, and the description still flags the `notices` field where it matters most. The one gap is that it never situates the tool relative to siblings, which for a small two-parameter tool is the main remaining question an agent might have.

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 description coverage is 100%, so both `pmids` and `format` are fully documented with allowed values and the string-or-array polymorphism. The description's format sentence largely restates the schema rather than adding syntax, limits, or caveats.

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

Purpose4/5

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

States a specific verb and resource ('Get formatted citations for PubMed articles') plus the scope of supported styles, which immediately separates it from fetch/search siblings. It stops short of naming a sibling it is not, so an agent must infer that other tools handle retrieval rather than formatting.

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

Usage Guidelines3/5

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

Usage is only implied by the purpose statement; there is no explicit when-to-use versus alternatives such as fetching raw article data or converting IDs. The guidance about passing one style as a string or many as an array is input mechanics, not tool selection guidance.

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

Deploy Server

Pubmed Format Citations

Instructions

Tool call template

Input Schema

Output Schema

Schema Changelog

TDQS

Other Tools