Skip to main content
Glama

pubmed-mcp-server

by io.github.cyanheads
OverviewDiscussionsAdmin

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
NameRequiredDescriptionDefault
queryYesMeSH descriptor name or free-text term to look up. Must carry a term: a value of only whitespace or invisible characters, such as a zero-width space, is rejected rather than searched.
offsetNoResult 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.
maxResultsNoMaximum results
includeDetailsNoFetch full MeSH records (scope notes, tree numbers, entry terms)

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
errorNoPresent when the call failed. Absent on success.
queryNoOriginal search query
noticeNoOptional 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.
offsetNoResult offset this page was read from
resultsNoMatching MeSH records
nextOffsetNoOffset to request for the next page. Omitted when this is the last page, so its absence is the end-of-results signal.
totalCountNoTotal MeSH descriptors matching the query upstream, before the maxResults cap

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed3 schema fields changed
    • changedOutput schema / properties / results / items / properties / meshId / description
      Previous 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."New value: +"Canonical MeSH unique identifier (e.g. \"D003924\", \"C000626284\", \"Q000009\") — resolves at the MeSH Browser and NLM linked data. A pharmacological-action record carries its descriptor's UI. Omitted only when eSummary returned no record for this UID."
    • changedOutput schema / properties / results / items / properties / treeNumbers / description
      Previous 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."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, and for pharmacological-action records, whose descriptor carries the tree positions."
    • changedOutput schema / properties / results / items / required
      Previous value: -[
-  "meshId",
-  "entrezUid",
-  "name"
-]New value: +[
+  "entrezUid",
+  "name"
+]
  2. Changed3 schema fields changed
    • changedInput schema / properties / query / description
      Previous 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."New value: +"MeSH descriptor name or free-text term to look up. Must carry a term: a value of only whitespace or invisible characters, such as a zero-width space, 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`: 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."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). `blank_query`: The query contains no search term: nothing is left once whitespace and invisible characters such as a zero-width space are disregarded. pubmed_search_articles and pubmed_europepmc_search first decode HTML entities and also disregard markup and parentheses, so `()`, `<b></b>`, and `&nbsp;` hold no term there; pubmed_search_articles also disregards bracketed field tags such as `[pdat]`. 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",
-  "blank_query"
-]New value: +[
+  "queue_full",
+  "ncbi_unreachable",
+  "ncbi_rate_limited",
+  "ncbi_deadline_exceeded",
+  "ncbi_invalid_response",
+  "ncbi_resource_not_found",
+  "blank_query"
+]
  3. Changed1 schema field changed
    • 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."
  4. Changed1 schema field changed
    • 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."
  5. Changed3 schema fields changed
    • 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"
+]
  6. Changed6 schema fields changed
    • 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"
-]
  7. Changed6 schema fields changed
    • 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"
+]
  8. Changed1 schema field changed
    • 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."
  9. Changed3 schema fields changed
    • 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"
+]
  10. Changed2 schema fields changed
    • 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"
+]
  11. Changed7 schema fields changed
    • 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"
+]
  12. Changed1 schema field changed
    • addedOutput schema / properties / results / items / description
      Added value: +"Matching MeSH descriptor record"
  13. First observed

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 genuine behavioral context beyond that: the shape of the returned descriptor records (tree numbers, scope notes, entry terms) and the pagination model for paging past the maxResults cap.

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 sentences, zero filler, with the purpose front-loaded ahead of the return/pagination detail. Nothing is repeated or padding, though the second sentence is a dense clause stack rather than cleanly separated points.

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 read-only lookup tool with a fully documented schema and an output schema covering return values, the description supplies enough to call it correctly. It needn't explain the record fields in detail since the output schema exists, though it does so anyway.

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 the schema already documents all four parameters, including offset's nextOffset chaining and the whitespace-rejection rule for query. The description only adds a brief mention of offset-based paging, which is already in the schema, so 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?

The description gives a specific verb pair (search/explore) and a precise resource (the MeSH controlled vocabulary), which is inherently distinguishable from the article-oriented siblings like pubmed_search_articles and pubmed_find_related. It does not explicitly name an alternative, but the resource itself separates it cleanly from every sibling.

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 implied rather than stated: an agent can infer it should call this when it needs MeSH descriptor data, but the description never says when to prefer it over pubmed_search_articles or pubmed_spell_check, nor any prerequisite for looking up a descriptor. Adequate but with a clear gap.

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 toolsInspect
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.

Resources