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.

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 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

B3.4/5.0

Behavior3/5

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

Annotations already declare readOnlyHint=true and openWorldHint=true, so the description does not need to re-state that this is a safe read operation. The description adds the format flexibility (string or array), but that is also present in the schema. No additional behavioral details like authentication or rate limits are given, matching the baseline for annotation-covered tools.

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?

Two sentences with no filler. The first sentence front-loads the core action and supported formats; the second explains the parameter usage pattern. Every word earns its place, and the description is appropriately sized for a simple, two-parameter tool.

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?

For a 2-parameter read-only tool with an output schema, the description adequately covers the core purpose and how to specify formats. It does not mention that format defaults to 'apa' or that it is optional, but the schema already carries that information. Overall it provides enough context for correct invocation, with only minor redundancy.

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%, with both pmids and format having descriptive text and full enum explanations in the schema. The description's phrase 'Pass a single format as a string or multiple as an array' merely restates the schema's anyOf structure, adding no new semantic value beyond the schema.

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 names a specific verb ('Get'), a clear resource ('formatted citations for PubMed articles'), and lists the exact supported formats (apa, mla, bibtex, ris, vancouver). This clearly distinguishes it from article fetching or searching, but it does not explicitly contrast with sibling tools like pubmed_lookup_citation, so it falls short of full sibling differentiation.

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

Usage Guidelines2/5

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

The description provides no guidance on when to choose this tool over alternatives such as pubmed_lookup_citation or pubmed_fetch_articles. It only explains how to pass formats, not when this tool is appropriate or when another should be used. No exclusions or alternative routing are mentioned.

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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