pubmed-mcp-server

Pubmed Format Citations

pubmed_format_citations

Read-only

Generate formatted citations for PubMed articles in APA, MLA, BibTeX, RIS, or Vancouver by passing PMIDs and one or more citation styles.

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.

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.

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

B3.1/5.0

Behavior2/5

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

Annotations already declare readOnlyHint and openWorldHint, so the safety profile is covered. The description adds no behavioral context of its own, such as whether unknown PMIDs are skipped, batching limits (max 50), or error handling, so beyond the safety hints it contributes little.

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?

Two short sentences, front-loaded with the core action and ending with the parameter usage hint. Efficient, though the second sentence largely duplicates the schema's format description.

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 and parameters are fully documented, so the description need not explain return values. It is sufficient for correct invocation, with only routing guidance against siblings missing.

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% and both parameters carry their own descriptions, including the enum values and the string-vs-array duality. The description merely restates the format semantics already present in the schema, so the baseline 3 applies.

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') and enumerates supported styles, which is clear. It does not differentiate itself from the closest sibling pubmed_lookup_citation, so an agent must infer the boundary.

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?

No when-to-use guidance, no conditions, and no named alternatives. The reader gets no help deciding between this and pubmed_lookup_citation or pubmed_fetch_articles.

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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