pubmed-mcp-server

Pubmed Format Citations

pubmed_format_citations

Read-only

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.

Input Schema

TableJSON 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

TableJSON 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 changedOct 9, 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 changedSep 28, 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 changedSep 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 changedSep 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 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": [
+      "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 changedJun 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"
+}

Changed1 schema field changedApr 30, 2026

changedInput schema / properties / format / anyOf

Previous value: -[
-  {
-    "enum": [
-      "apa",
-      "mla",
-      "bibtex",
-      "ris"
-    ],
-    "type": "string"
-  },
-  {
-    "items": {
-      "enum": [
-        "apa",
-        "mla",
-        "bibtex",
-        "ris"
-      ],
-      "type": "string"
-    },
-    "minItems": 1,
-    "type": "array"
-  }
-]New 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"
+  }
+]

Changed2 schema fields changedApr 29, 2026

addedInput schema / properties / format

Added value: +{
+  "anyOf": [
+    {
+      "enum": [
+        "apa",
+        "mla",
+        "bibtex",
+        "ris"
+      ],
+      "type": "string"
+    },
+    {
+      "items": {
+        "enum": [
+          "apa",
+          "mla",
+          "bibtex",
+          "ris"
+        ],
+        "type": "string"
+      },
+      "minItems": 1,
+      "type": "array"
+    }
+  ],
+  "default": "apa",
+  "description": "Citation format(s) to generate — single style as a string or multiple as an array. Allowed values: apa, mla, bibtex, ris."
+}

removedInput schema / properties / styles

Removed value: -{
-  "default": [
-    "apa"
-  ],
-  "description": "Citation styles to generate",
-  "items": {
-    "enum": [
-      "apa",
-      "mla",
-      "bibtex",
-      "ris"
-    ],
-    "type": "string"
-  },
-  "type": "array"
-}

Changed1 schema field changedApr 24, 2026
- addedOutput schema / properties / citations / items / description
```
Added value: +"Citations for a single article"
```

Changed4 schema fields changedApr 9, 2026

addedOutput schema / properties / totalFormatted

Added value: +{
+  "description": "Number of PMIDs successfully formatted",
+  "type": "number"
+}

addedOutput schema / properties / totalSubmitted

Added value: +{
+  "description": "Number of PMIDs submitted for citation formatting",
+  "type": "number"
+}

addedOutput schema / properties / unavailablePmids

Added value: +{
+  "description": "Requested PMIDs that did not return article metadata",
+  "items": {
+    "type": "string"
+  },
+  "type": "array"
+}

changedOutput schema / required

Previous value: -[
-  "citations"
-]New value: +[
+  "citations",
+  "totalSubmitted",
+  "totalFormatted"
+]

First observedMar 23, 2026

TDQS

A3.7/5.0

Behavior4/5

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

Annotations already declare readOnlyHint=true and openWorldHint=true, so safety is covered. The description adds genuinely useful behavior beyond that: retractions, errata, and expressions of concern come back in `notices`, and Vancouver/APA also cite a retraction inline in the reference itself — a non-obvious output trait the agent would not learn from the schema.

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?

Three sentences, purpose front-loaded, no filler, and the unusual `notices` behavior is placed last where it is easy to skim. The middle sentence largely duplicates the schema's anyOf constraint, which is the only mild waste.

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?

With an output schema present, the description need not explain return values, and it correctly focuses on formats and the retraction-notice behavior. It is complete enough to call correctly, though it omits any note about the 50-PMID cap or failure behavior for invalid IDs.

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% and both parameters are fully documented in the schema, including the allowed style values and the string-or-array anyOf. The description restates the same single-vs-array rule and the same style list without adding syntax, defaults, or ordering semantics, so baseline 3 is appropriate.

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?

The description states a specific verb and resource ('Get formatted citations for PubMed articles') and enumerates the supported styles, so the tool's function is unmistakable. It does not, however, distinguish itself from siblings such as pubmed_lookup_citation or pubmed_fetch_articles, which an agent may confuse it with when choosing a tool.

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: the agent can infer it should call this when it needs citations in a given style, and the string-vs-array note hints at how to request multiple styles. There is no explicit when-to-use versus alternatives guidance, no mention of the sibling pubmed_lookup_citation, and no stated limits or prerequisites.

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

All pubmed-mcp-server tools Inspect

Try in Browser

One endpoint for every MCP toolRayrun runs every MCP server behind one URL and holds the credentials. Each call is decided per client, tool, and argument, then recorded.ray.runAd

Glama MCP Gateway

Add one secure layer between your agents and this server.