pubmed-mcp-server

Pubmed Spell Check

pubmed_spell_check

Read-only

Correct misspelled PubMed search terms via NCBI ESpell and return a fixed query, helping recover zero-hit or thin article results and resolve drug, gene, disease, or author name typos.

Instructions

Spell-check a PubMed search query against NCBI ESpell and get the corrected query back. Use after a zero-hit or thin pubmed_search_articles result, or when a drug, gene, disease, or author name may be misspelled — every misspelled token is corrected in one call (alzhiemer diseese treatmnt outcomse → alzheimer disease treatment outcomes), and hasSuggestion is false when NCBI has no change to offer. Re-run the search with corrected.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`query`	Yes	PubMed search query to spell-check. Must carry a term: a value of only whitespace or invisible characters, such as a zero-width space, is rejected rather than sent to ESpell.

Output Schema

TableJSON Schema

Name	Required	Description
`error`	No	Present when the call failed. Absent on success.
`original`	No	Original query
`corrected`	No	Corrected query (same as original if no suggestion)
`hasSuggestion`	No	Whether NCBI suggested a correction

Schema Changelog

Changes observed during successful MCP inspections.

Changed3 schema fields changedv2.10.19Sep 30, 2026

changedInput schema / properties / query / description

Previous value: -"PubMed search query to spell-check. Must carry a term: a blank or whitespace-only value is rejected rather than sent to ESpell."New value: +"PubMed search query to spell-check. Must carry a term: a value of only whitespace or invisible characters, such as a zero-width space, is rejected rather than sent to ESpell."

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"
+]

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). `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."

Changed3 schema fields changedv2.10.12Sep 11, 2026

changedInput schema / properties / query / description

Previous value: -"PubMed search query to spell-check"New value: +"PubMed search query to spell-check. Must carry a term: a blank or whitespace-only value is rejected rather than sent to ESpell."

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 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": [
+      "original",
+      "corrected",
+      "hasSuggestion"
+    ]
+  },
+  {
+    "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: -[
-  "original",
-  "corrected",
-  "hasSuggestion"
-]

Addedv2.7.6May 29, 2026
Removedv2.7.4May 24, 2026
Addedv2.3.2Apr 4, 2026

TDQS

A4.5/5.0

Behavior4/5

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

Annotations already declare readOnlyHint and openWorldHint, so safety is covered. The description adds real behavior beyond that: all misspelled tokens are fixed in a single call, and hasSuggestion is false when NCBI offers no change — a non-obvious edge case. It omits any mention of external-service latency or rate limits, keeping it short of a 5.

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?

Front-loaded with purpose, then trigger conditions, then a compact example, then the follow-up action. Dense but every clause carries information; no filler.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

An output schema exists, and the description still names the key return fields (corrected, hasSuggestion) and their meaning, so the agent knows exactly how to branch on the result. With one fully documented parameter and annotations covering safety, nothing needed for correct invocation is 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 description coverage is 100% and the single parameter already documents minLength and the whitespace/zero-width-space rejection rule. The description's concrete example ('alzhiemer diseese treatmnt outcomse' → 'alzheimer disease treatment outcomes') illustrates effect but adds no syntax or constraint detail the schema lacks, so baseline 3 applies.

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?

States a specific verb+resource ('Spell-check a PubMed search query') plus the upstream service (NCBI ESpell) and the return ('get the corrected query back'). It is immediately distinguishable from siblings like pubmed_search_articles, which are referenced by name as the tool it complements.

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

Usage Guidelines5/5

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

Gives explicit triggers: 'after a zero-hit or thin pubmed_search_articles result, or when a drug, gene, disease, or author name may be misspelled.' It also closes the loop by telling the agent to 'Re-run the search with corrected,' so the workflow around the sibling is fully specified.

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

Deploy Server

Pubmed Spell Check

Instructions

Input Schema

Output Schema

Schema Changelog

TDQS

Other Tools