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Glama

pubmed-mcp-server

by io.github.cyanheads

Pubmed Spell Check

pubmed_spell_check
Read-only

Spell-check a query and get NCBI's suggested correction. Useful for refining search queries.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
queryYesPubMed search query to spell-check

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
errorNoPresent when the call failed. Absent on success.
originalNoOriginal query
correctedNoCorrected query (same as original if no suggestion)
hasSuggestionNoWhether NCBI suggested a correction

Schema Changelog

Changes observed during successful MCP inspections. Dates show when Glama detected each change.

  1. 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": [
+      "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"
-]
  2. First observed

TDQS

B3.4/5.0
Behavior3/5

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

The readOnlyHint annotation covers the readonly nature, so the description doesn't need to repeat that. However, the description is thin on what the

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, no redundancy, and the second sentence adds the use case. Efficient and clear without wasted words.

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

Completeness3/5

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

For a single-parameter tool with a readOnlyHint, it is reasonably complete. However, it omits the output format (e.g., does it return a single suggested query or a list of alternatives?) and any mention of error behavior for invalid queries. The description is adequate for a simple tool but lacks depth expected from a tool targeting refined usage.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

The only parameter, 'query', is fully described in the schema with a clear description (

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 clearly states the tool's function: 'Spell-check a query and get NCBI's suggested correction.' It also adds a use case ('useful for refining search queries') that gives context. The one-parameter tool is well-defined enough to understand its primary purpose without ambiguity.

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?

Only a vague hint about refining search queries. No guidance on when to invoke it, what types of queries benefit, or how to interpret the result in the context of sibling search tools. An agent would need to infer typical usage from the title and description.

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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TDQS

A4.2/5.0
Disambiguation4/5

The tools constitute a well-designed set targeting distinct workflow steps: searching (pubmed_search_articles, pubmed_europepmc_search), fetching (pubmed_fetch_articles, pubmed_fetch_fulltext, pubmed_europepmc_fetch), ID conversion (pubmed_convert_ids), related articles (pubmed_find_related), citations (pubmed_format_citations, pubmed_lookup_citation), MeSH lookup (pubmed_lookup_mesh), and spelling (pubmed_spell_check). While search and fetch tools in PubMed vs Europe PMC overlap somewhat, the descriptions explicitly differentiate them (local PubMed vs broader Europe PMC with preprints/patents), so ambiguity is minor.

Naming Consistency5/5

All tools follow a consistent `pubmed_` prefix followed by verb_noun pattern: `search_articles`, `fetch_articles`, `lookup_citation`, `format_citations`, `convert_ids`, `find_related`, etc. The verbs are all lowercase snake_case, and the pattern is uniform across the entire set, even for the Europe PMC variants (`pubmed_europepmc_search`, `pubmed_europepmc_fetch`).

Tool Count5/5

11 tools makes for a well-scoped server. Each tool serves a clearly distinct purpose within the biomedical literature retrieval domain: searching, fetching metadata/full-text, ID conversion, citation formatting/lookup, MeSH exploration, related-articles, and spell-check. No tool feels redundant or trivial; the count is appropriate for the domain's complexity.

Completeness5/5

The tool set provides comprehensive coverage of the core PubMed/PMC workflow: search with full query syntax, fetch metadata and full text, convert identifiers across DOI/PMID/PMCID, find related articles, format citations, and explore MeSH vocabulary. Notable gaps like more advanced search history management or batch operations exist but are not essential to the domain's core purpose. The fallback logic (e.g., europepmc_fetch for non-PMC records, fulltext fallback chain) fills potential dead ends.

Resources