pubmed-mcp-server

Pubmed Lookup Mesh

pubmed_lookup_mesh

Read-only

Search and explore the MeSH (Medical Subject Headings) controlled vocabulary. Returns descriptor records with tree numbers, scope notes, and entry terms, plus pagination via offset for paging past the maxResults cap.

Input Schema

TableJSON Schema

Name	Required	Description
`query`	Yes	MeSH descriptor name or free-text term to look up. Must carry a term: a blank or whitespace-only value is rejected rather than searched.
`offset`	No	Result offset for pagination (0-based). Pass the `nextOffset` from the previous response to get the following page; the exact-descriptor match is pinned to the first page only.
`maxResults`	No	Maximum results
`includeDetails`	No	Fetch full MeSH records (scope notes, tree numbers, entry terms)

Output Schema

TableJSON Schema

Name	Required	Description
`error`	No	Present when the call failed. Absent on success.
`query`	No	Original search query
`notice`	No	Optional guidance when no descriptors matched or the offset overshot the result set — suggests spell-check, free-text search, or resetting the offset. Absent on successful result pages.
`offset`	No	Result offset this page was read from
`results`	No	Matching MeSH records
`nextOffset`	No	Offset to request for the next page. Omitted when this is the last page, so its absence is the end-of-results signal.
`totalCount`	No	Total MeSH descriptors matching the query upstream, before the maxResults cap

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`: 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). `blank_query`: The query holds no search term once whitespace, and any markup the tool strips first, are removed — so NCBI would receive a blank term. 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). `blank_query`: The query holds no search term once whitespace, and anything the tool strips before searching, are removed — so NCBI would receive a blank term. pubmed_search_articles strips markup, bracketed field tags, and parentheses, so a bare field tag such as `[pdat]` or empty parentheses `()` count as blank there. Other values are possible when a failure originates below the handler."

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). `blank_query`: The query holds no search term once whitespace, and any markup the tool strips first, are removed — so NCBI would receive a blank term. 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). `blank_query`: The query holds no search term once whitespace, and any markup the tool strips first, are removed — so NCBI would receive a blank term. Other values are possible when a failure originates below the handler."

Changed3 schema fields changedSep 11, 2026

changedInput schema / properties / query / description

Previous value: -"MeSH descriptor name or free-text term to look up"New value: +"MeSH descriptor name or free-text term to look up. Must carry a term: a blank or whitespace-only value is rejected rather than searched."

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`: 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). `blank_query`: The query holds no search term once whitespace, and any markup the tool strips first, are removed — so NCBI would receive a blank term. 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_deadline_exceeded",
+  "ncbi_invalid_response",
+  "ncbi_resource_not_found",
+  "blank_query"
+]

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": [
+      "query",
+      "offset",
+      "results",
+      "totalCount"
+    ]
+  },
+  {
+    "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: -[
-  "query",
-  "offset",
-  "results",
-  "totalCount"
-]

Changed6 schema fields changedJul 26, 2026

addedInput schema / properties / offset

Added value: +{
+  "default": 0,
+  "description": "Result offset for pagination (0-based). Pass the `nextOffset` from the previous response to get the following page; the exact-descriptor match is pinned to the first page only.",
+  "maximum": 9007199254740991,
+  "minimum": 0,
+  "type": "integer"
+}

addedOutput schema / properties / nextOffset

Added value: +{
+  "description": "Offset to request for the next page. Omitted when this is the last page, so its absence is the end-of-results signal.",
+  "type": "number"
+}

changedOutput schema / properties / notice / description

Previous value: -"Optional guidance when no descriptors matched — suggests spell-check or free-text search. Absent on successful results."New value: +"Optional guidance when no descriptors matched or the offset overshot the result set — suggests spell-check, free-text search, or resetting the offset. Absent on successful result pages."

addedOutput schema / properties / offset

Added value: +{
+  "description": "Result offset this page was read from",
+  "type": "number"
+}

changedOutput schema / properties / totalCount / description

Previous value: -"Total matching MeSH descriptors"New value: +"Total MeSH descriptors matching the query upstream, before the maxResults cap"

changedOutput schema / required

Previous value: -[
-  "query",
-  "results",
-  "totalCount"
-]New value: +[
+  "query",
+  "offset",
+  "results",
+  "totalCount"
+]

Changed1 schema field changedJun 18, 2026

changedOutput schema / properties / results / items / properties / treeNumbers / description

Previous value: -"MeSH tree numbers"New value: +"Navigable MeSH tree numbers (e.g. \"D02.078.370.141.450\"). Omitted for supplementary concept records (SCRs), which map to a heading rather than occupying a tree position."

Changed3 schema fields changedJun 14, 2026

addedOutput schema / properties / results / items / properties / entrezUid

Added value: +{
+  "description": "NCBI Entrez UID for this record — the join key for E-utilities (eSummary/eFetch db=mesh).",
+  "type": "string"
+}

changedOutput schema / properties / results / items / properties / meshId / description

Previous value: -"MeSH descriptor unique identifier"New value: +"Canonical MeSH DescriptorUI (e.g. \"D003924\") — resolves at the MeSH Browser and NLM linked data. Falls back to the raw Entrez UID when a record is not decodable."

changedOutput schema / properties / results / items / required

Previous value: -[
-  "meshId",
-  "name"
-]New value: +[
+  "meshId",
+  "entrezUid",
+  "name"
+]

Changed2 schema fields changedJun 11, 2026

addedOutput schema / properties / totalCount

Added value: +{
+  "description": "Total matching MeSH descriptors",
+  "type": "number"
+}

changedOutput schema / required

Previous value: -[
-  "query",
-  "results"
-]New value: +[
+  "query",
+  "results",
+  "totalCount"
+]

Changed7 schema fields changedApr 29, 2026

addedInput schema / properties / query

Added value: +{
+  "description": "MeSH descriptor name or free-text term to look up",
+  "minLength": 1,
+  "type": "string"
+}

removedInput schema / properties / term

Removed value: -{
-  "description": "MeSH term to look up",
-  "minLength": 1,
-  "type": "string"
-}

changedInput schema / required

Previous value: -[
-  "term"
-]New value: +[
+  "query"
+]

addedOutput schema / properties / notice

Added value: +{
+  "description": "Optional guidance when no descriptors matched — suggests spell-check or free-text search. Absent on successful results.",
+  "type": "string"
+}

addedOutput schema / properties / query

Added value: +{
+  "description": "Original search query",
+  "type": "string"
+}

removedOutput schema / properties / term

Removed value: -{
-  "description": "Original search term",
-  "type": "string"
-}

changedOutput schema / required

Previous value: -[
-  "term",
-  "results"
-]New value: +[
+  "query",
+  "results"
+]

Changed1 schema field changedApr 24, 2026
- addedOutput schema / properties / results / items / description
```
Added value: +"Matching MeSH descriptor record"
```
First observedMar 23, 2026

TDQS

A4/5.0

Behavior4/5

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

Annotations already declare readOnlyHint=true, so the description doesn't need to repeat that. The description adds value by explaining the pagination mechanism (offset for paging past maxResults cap) and the fact that the exact-descriptor match is pinned to the first page. This goes beyond the annotation and gives useful behavioral context.

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?

The description is two sentences with no filler. The main purpose is front-loaded, followed by output details and pagination. Every sentence adds value and it is concise.

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?

Given the tool has an output schema, the description does not need to detail return values. It covers the core purpose, pagination behavior, and the maxResults cap. It is complete for an agent to decide when to invoke it and understand its basic operation, though it could mention any prerequisites or special cases, but none are apparent.

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 all parameters are well-documented in the schema. The description mentions pagination and maxResults cap but adds minimal new meaning beyond the schema's parameter descriptions. Baseline 3 is appropriate since the schema carries the parameter details.

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 clearly states the tool's function: searching and exploring the MeSH controlled vocabulary, and specifies the output (descriptor records with tree numbers, scope notes, entry terms) and pagination. It distinguishes itself from sibling tools like pubmed_search_articles by focusing on MeSH vocabulary rather than article search.

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?

The description implies usage for MeSH lookups but does not explicitly state when to use it versus alternatives, nor does it provide exclusions. It is clear from context that this is for controlled vocabulary exploration, but there is no explicit routing or comparison to siblings.

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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Pubmed Lookup Mesh

Input Schema

Output Schema

Schema Changelog

TDQS

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