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masa061580
by masa061580

PubMed MCP Server v2.0.0

A local Model Context Protocol (MCP) server that exposes the NCBI PubMed / PubMed Central / iCite APIs to MCP-compatible clients (Claude Desktop, MCP Inspector, etc.) over stdio.

This version (2.0.0) is a complete rewrite of the tool layer to provide feature parity with the remote OAuth-protected sibling project pubmed-mcp-remote-Oauth- — all 10 tools are identical in name, schema, and behavior. The local build simply drops OAuth and runs on stdio so it can be wired into Claude Desktop without authentication.


✨ What's new in v2.0.0

v1.0.2 (legacy)

v2.0.0 (this release)

Tools

8 tools (search_pubmed, get_full_abstract, …)

10 tools with new schema (see below)

Output format

Markdown-formatted strings

Structured JSON for every tool (token-efficient, parser-friendly)

Search

Single sort, no filters

output_mode (minimal/compact/full), pagination, structured filters (date range, publication types, languages, humans-only, has-abstract, free full text)

Full text

Whole-article dump

Section-aware extraction (abstract / introduction / methods / results / discussion / conclusions / references)

Citations

elink only

iCite by default (counts include non-PubMed citations) + elink mode for citing-PMIDs

ID conversion

New convert_ids (PMID ↔ PMCID ↔ DOI)

Bulk fetch

New fetch_batch

Count-only query

New count tool for fast query refinement

HTML entities

Raw

Decoded via he

429 handling

Exponential-backoff retry (1s/2s/4s)

Module structure

Single pubmed-api.ts

Split into pubmed-client.ts (transport) / tools.ts (MCP) / ris-exporter.ts

Breaking change: tool names and response shapes have changed. If you were using v1.x, update your client prompts to the new names.


Related MCP server: Lyra's Expanded Research MCP

🔧 Tools (10)

All tools return JSON in content[0].text.

#

Tool

Purpose

1

search

PubMed search with MeSH support, pagination (retmax/retstart), sort (relevance/pub_date/first_author), output_mode (minimal/compact/full), and structured filters

2

fetch

Single-PMID abstract (OpenAI MCP–compliant document shape)

3

fetch_batch

Multiple-PMID abstracts in one call; optional include_abstract flag

4

get_full_text

PMC full text via JATS XML; section filter [abstract, introduction, methods, results, discussion, conclusions, references, all]; max 20 PMCIDs

5

count

Result count only — fast query refinement

6

find_similar_articles

NCBI elink pubmed_pubmed similarity

7

export_to_ris

Compact RIS for EndNote/Zotero/Mendeley (citation manager auto-fetches full metadata via PMID)

8

get_citation_counts

iCite (default, counts only) or elink (PubMed-internal, with citing PMIDs)

9

convert_ids

PMID ↔ PMCID ↔ DOI via NCBI ID Converter API

10

batch_process

Run any subset of [abstract, citations, similar, ris_export, full_text] against the same PMID set with bounded concurrency

For exact input/output schemas, run tools/list via MCP Inspector or check src/tools.ts.


📋 Prerequisites

  • Node.js ≥ 18 (uses global fetch and AbortSignal.timeout)

  • npm

  • (optional) an NCBI API key — raises the rate limit from 3 req/s to 10 req/s


Without a key, NCBI limits you to 3 requests/sec. With a free personal key, the limit goes up to 10 requests/sec — noticeable when running batch_process or large search paginations.

  1. Create / sign in to an NCBI account: https://account.ncbi.nlm.nih.gov/

  2. Open Account settings (top-right menu → Account settings) → scroll to API Key Management at the bottom of the page.

  3. Click Create an API Key. A 36-character hex string is generated immediately.

  4. Copy that string and put it in the NCBI_API_KEY env var in your claude_desktop_config.json (see the Claude Desktop section below).

The key is tied to your NCBI account; revoke or rotate it any time from the same page. Don't commit it to git or share it — it's effectively your identity on the E-utilities API.

📚 Official policy: https://support.nlm.nih.gov/kbArticle/?pn=KA-05317


🚀 Installation

The server is published on npm as pubmed_mcp_server2. For Claude Desktop you don't need to install anything manually — npx -y pubmed_mcp_server2 will fetch and run it.

If you'd rather build from source (development):

git clone https://github.com/masa061580/pubmed_mcp_server2.git
cd pubmed_mcp_server2
npm install
npm run build      # produces dist/index.js

Smoke test (optional)

# From a clone:
( echo '{"jsonrpc":"2.0","id":0,"method":"initialize","params":{"protocolVersion":"2024-11-05","capabilities":{},"clientInfo":{"name":"test","version":"1.0"}}}'
  echo '{"jsonrpc":"2.0","method":"notifications/initialized"}'
  echo '{"jsonrpc":"2.0","id":1,"method":"tools/list"}'
  sleep 1
) | node dist/index.js

# Or directly from npm:
npx -y pubmed_mcp_server2

The server should list all 10 tools.


🖥️ Claude Desktop configuration

Edit (create if missing):

  • macOS~/Library/Application Support/Claude/claude_desktop_config.json

  • Windows%APPDATA%\Claude\claude_desktop_config.json

{
  "mcpServers": {
    "pubmed": {
      "command": "npx",
      "args": ["-y", "pubmed_mcp_server2"],
      "env": {
        "NCBI_API_KEY": ""
      }
    }
  }
}

Alternative (from a local clone)

{
  "mcpServers": {
    "pubmed": {
      "command": "node",
      "args": [
        "/ABSOLUTE/PATH/TO/pubmed_mcp_server2/dist/index.js"
      ],
      "env": {
        "NCBI_API_KEY": ""
      }
    }
  }
}

Notes:

  • Set NCBI_API_KEY to your key, or remove the env block entirely if you don't have one. With a key the rate limit goes from 3 req/s → 10 req/s.

  • Windows users: if npx is not on PATH inside Claude Desktop, use the full path to npx.cmd (e.g. C:\\Program Files\\nodejs\\npx.cmd).

  • macOS + nvm: if Claude Desktop can't find npx, replace "command": "npx" with the absolute path (e.g. /Users/you/.nvm/versions/node/v20.x.x/bin/npx). Claude Desktop's PATH may not include nvm shims.

  • For the local-clone variant, use the absolute path to dist/index.js and run npm run build first.

  • Fully quit and relaunch Claude Desktop after editing (Cmd+Q on macOS).

Logs

tail -f "$HOME/Library/Logs/Claude/mcp-server-pubmed.log"

🛠️ MCP Inspector

# Run the published package directly:
npx @modelcontextprotocol/inspector npx -y pubmed_mcp_server2

# Or inspect a local build:
npx @modelcontextprotocol/inspector node /ABSOLUTE/PATH/TO/dist/index.js

📦 Project structure

src/
├── index.ts          # stdio entry point — registers tools, connects transport
├── tools.ts          # 10 MCP tool definitions (zod schemas + handlers)
├── pubmed-client.ts  # NCBI E-utilities / iCite / ID-Converter client (XML parsing, 429 retry, timeouts)
└── ris-exporter.ts   # Minimal RIS format generator

The server is stateless — every request creates fresh state. Safe for concurrent invocations.


🤝 Sibling project

A remote, OAuth-protected variant deployed on Cloudflare Workers lives at: 👉 masa061580/pubmed-mcp-remote-Oauth-

Both servers expose the same 10 tools with identical schemas, so client prompts/workflows are portable between them.


📚 NCBI Compliance

This server respects NCBI E-utilities guidelines:

  • Sends tool and email parameters on every request

  • Honors rate limits (3 req/s without key, 10 req/s with key)

  • Uses POST for large ID lists (efetch)

  • Retries 429 with exponential backoff (max 3 attempts)

  • 30s AbortSignal.timeout on every fetch

Please supply your own NCBI_API_KEY for production use and update email/tool in src/pubmed-client.ts to identify your deployment.


📝 License

MIT — see LICENSE.

Available Tools

10 tools
batch_processA

Run multiple operations against the same set of PMIDs in one call. Helpful for systematic-review style workflows. operations is an array drawn from: 'abstract', 'citations', 'similar', 'ris_export', 'full_text'. Respects NCBI rate limits via max_concurrency (default 3).

ParametersJSON Schema
NameRequiredDescriptionDefault
pmidsYesPMIDs to operate on
operationsYesWhich operations to run
max_concurrencyNo

TDQS

A3.9/5.0
Behavior3/5

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

With no annotations provided, the description carries the full burden of behavioral disclosure. It adds value by mentioning rate-limit respect via max_concurrency, a meaningful behavioral trait. Yet it lacks a safety profile (read-only vs. mutation), return format, or error/partial-failure behavior, so it is not comprehensive.

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 long, with the primary purpose front-loaded in the first sentence. Every clause contributes useful information (purpose, use case, operation types, rate-limit behavior) without extraneous fluff.

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?

The description covers the tool's purpose, operations, and rate limiting, but the absence of an output schema means the agent is left unaware of return values, error handling, or partial-failure behavior. For a batch tool with moderate complexity, this is a notable gap.

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?

The schema already describes pmids and operations, and the description largely repeats the operations enum and max_concurrency default. It adds slight semantic value by explaining max_concurrency in relation to rate limits, but does not deepen understanding of pmids or operations beyond what the schema provides.

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: 'Run multiple operations against the same set of PMIDs in one call.' It specifies the resource (PMIDs) and differentiates from siblings by emphasizing the combination of multiple operations in a single batch call, which is unique among the listed siblings.

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

Usage Guidelines4/5

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

The phrase 'Helpful for systematic-review style workflows' gives clear context for when to use the tool. However, it does not explicitly name alternative tools or state when not to use it, so it falls short of full exclusion guidance.

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

convert_idsA

Convert between PMID, PMCID, and DOI identifiers using NCBI ID Converter API.

ParametersJSON Schema
NameRequiredDescriptionDefault
idsYesList of identifiers to convert
to_typeYesDesired output identifier type
from_typeYesType of input identifiers

TDQS

A4/5.0
Behavior3/5

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

The description mentions the NCBI ID Converter API, offering a bit of external context, but it does not disclose response format, error behavior, or rate limits. With no annotations, the description carries the full burden, yet it only covers the basic conversion functionality.

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 a single sentence that is direct and front-loaded, with no wasted words. It efficiently conveys the tool's core purpose.

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's simplicity and well-specified schema, the description is adequate for an agent to understand its function. It does not explain return format, but the purpose is unambiguous and the schema covers operational details like batch limits.

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?

The input schema fully describes each parameter with enums and descriptions, covering 100% of parameters. The description adds no additional meaning beyond naming the supported identifier types, which the schema already enumerates.

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 converts between PMID, PMCID, and DOI identifiers, specifying the verb 'Convert' and the resource. It distinguishes itself from sibling tools that fetch or search articles rather than convert ID types.

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

Usage Guidelines4/5

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

The description makes the tool's purpose evident and gives context for when to use it, but it does not explicitly state when not to use it or name alternative tools. The differentiation from siblings is implicit rather than explicit.

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

countA

Get only the count of search results for query adjustment and optimization. Fast — retrieves no actual data. Useful for refining search strategies.

ParametersJSON Schema
NameRequiredDescriptionDefault
queryYesSearch query string with MeSH/PubMed syntax support

TDQS

A4/5.0
Behavior3/5

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

The description discloses key behavioral traits: it is fast and retrieves no actual data. Without annotations, it carries the burden, but it doesn't mention potential rate limits, exact return format, or whether the count respects all query filters. It adds some value but not exhaustive 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 short sentences, highly efficient, and front-loaded with the main purpose. Every sentence adds value without unnecessary fluff.

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 simple count tool with one parameter and no output schema, the description covers the essential purpose and usage. It could mention what the count represents (e.g., total matching entities across all pages) but is otherwise sufficient for a tool of this complexity.

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?

The input schema already provides 100% coverage for the single 'query' parameter with a helpful description including syntax support. The tool description adds no additional parameter semantics beyond what the schema states, so it stays at baseline.

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 purpose: 'Get only the count of search results'. It explicitly differentiates from the sibling 'search' tool by emphasizing it retrieves no actual data, only the count.

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

Usage Guidelines4/5

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

The description mentions it is 'Useful for refining search strategies' and notes it is 'Fast', implying it should be used when only the count is needed. However, it does not explicitly state when not to use it or name alternatives beyond this context.

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

export_to_risA

Export PubMed articles to RIS format for citation managers (EndNote/Zotero/Mendeley). Returns compact RIS with minimal metadata — citation managers auto-fetch the rest via PMID.

ParametersJSON Schema
NameRequiredDescriptionDefault
pmidsYesList of PubMed IDs (PMIDs)

TDQS

A4.2/5.0
Behavior4/5

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

With no annotations provided, the description must carry the behavioral burden. It discloses the key behavioral trait: returns compact RIS with minimal metadata, and explains the rationale (auto-fetch via PMID). It does not mention error handling or rate limits, but for a read-only export tool, this is adequate.

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 long, front-loaded with the main purpose, and the second sentence adds necessary context about the minimal metadata. There is no redundancy or waste.

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 simple tool with one parameter and no output schema, the description explains the return format (compact RIS) and the reason for it. It lacks explicit error behavior, but that is not critical for the tool's function.

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?

The schema already provides a description for the only parameter ('List of PubMed IDs (PMIDs)') with 100% coverage. The description adds no additional detail about parameter semantics, so it relies on the schema.

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 action ('Export PubMed articles to RIS format') and specifically targets citation managers (EndNote/Zotero/Mendeley). This distinguishes it from siblings like 'fetch' or 'fetch_batch' which retrieve data rather than export to a specific format.

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

Usage Guidelines4/5

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

It provides context for when to use the tool (for citation manager exports) and explains that the compact output is sufficient because citation managers auto-fetch via PMID. However, it does not explicitly describe when not to use it or mention alternative tools for full metadata retrieval.

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

fetchA

Retrieve abstract for a single PMID (OpenAI MCP compliant). Accepts exactly one PMID. For multiple PMIDs, use fetch_batch.

ParametersJSON Schema
NameRequiredDescriptionDefault
idYesSingle PubMed ID (PMID) — NO arrays or comma-separated values

TDQS

A4.2/5.0
Behavior3/5

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

No annotations are provided, so the description must carry the transparency burden. It notes that the tool is 'OpenAI MCP compliant' and reinforces the single-PMID constraint, but does not disclose behavior for invalid PMIDs, rate limits, or the return format beyond 'abstract'. This leaves some ambiguity for unexpected inputs.

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, front-loads the core purpose, and includes a pointer to the batch alternative. No wasted words.

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 one-parameter, no-output-schema tool, the description covers purpose and constraint well. It lacks explicit return structure and error handling, but the output is implicitly the abstract. Given the simplicity, it is mostly complete.

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% with a detailed description: 'Single PubMed ID (PMID) — NO arrays or comma-separated values.' The description adds the 'exactly one' constraint and batch usage, but the parameter meaning is already fully covered by the schema, so baseline 3 is appropriate.

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 uses a specific verb ('Retrieve') and resource ('abstract for a single PMID'), clearly stating the scope. It distinguishes from siblings by explicitly stating 'Accepts exactly one PMID' and directing multi-PMID requests to fetch_batch.

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?

The description explicitly provides an alternative for a different scenario: 'For multiple PMIDs, use fetch_batch.' This is a clear when-not and alternative. It also implies when to use (when you have a single PMID and need its abstract).

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

fetch_batchA

Retrieve abstracts for multiple PMIDs in a single batch request. Returns structured data per PMID. Set include_abstract=false to omit the abstract field (e.g., when you only need full author lists).

ParametersJSON Schema
NameRequiredDescriptionDefault
pmidsYesList of PubMed IDs (PMIDs)
include_abstractNoWhether to include the abstract field (default true)

TDQS

A4.4/5.0
Behavior4/5

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

With no annotations, the description carries the burden of behavioral disclosure. It states that the tool returns structured data per PMID and explains the effect of include_abstract=false with an example. This covers the core behavior, though it does not mention error handling or rate limits.

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, front-loaded with the main purpose, followed by a relevant parameter tip. No redundant wording or filler.

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's simplicity (2 params, no output schema or annotations), the description is mostly complete: it explains the batch behavior, the return shape, and the optional flag. It could be slightly more explicit about output field details or potential limitations, but overall sufficient for a straightforward fetch tool.

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?

Schema coverage is 100%, so parameters are already documented. The description adds value by clarifying the batch context for 'pmids' and providing a use-case example for 'include_abstract' beyond the schema's default-value explanation.

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 'Retrieve abstracts for multiple PMIDs in a single batch request' with a specific verb, resource, and scope. It distinguishes itself from siblings like 'fetch' (single-PMID) and 'get_full_text' by specifying batch abstract retrieval.

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

Usage Guidelines4/5

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

The description implies the primary use case (multiple PMIDs) and provides a concrete guideline for setting include_abstract=false when only full author lists are needed. However, it does not explicitly contrast with siblings like 'fetch' or 'batch_process'.

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

find_similar_articlesA

Find similar articles for a given PMID using MeSH terms and title-based similarity. Useful for literature review and related research discovery.

ParametersJSON Schema
NameRequiredDescriptionDefault
pmidYesPubMed ID of the reference article
retmaxNoMaximum number of similar articles (1-100, default: 20)

TDQS

A4/5.0
Behavior3/5

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

No annotations are provided, so the description carries the burden. It discloses the matching mechanism (MeSH terms and title-based similarity), but does not mention output format, error handling, or read-only nature. While the method detail adds some transparency, it lacks behavioral depth.

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: the first states the core function and method, the second states the intended use case. No wasted words, and key information is front-loaded.

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?

The tool is simple (2 params, no output schema), and the description covers purpose and method adequately. However, without an output schema, it does not describe the return format or error behavior, which is a minor gap. Overall, it is sufficiently complete for an agent to invoke the tool correctly.

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% with both parameters (pmid and retmax) clearly documented. The description adds no extra meaning beyond what the schema already provides, so baseline 3 is appropriate.

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 function: 'Find similar articles for a given PMID' using a specific method (MeSH terms and title-based similarity). This distinguishes it from siblings like search or fetch, which serve different purposes.

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

Usage Guidelines4/5

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

The description provides context for when to use it: 'Useful for literature review and related research discovery.' It does not explicitly name alternatives or exclusions, but the unique function makes the use case clear.

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

get_citation_countsA

Get citation counts for PMIDs. Default source is iCite (counts only, includes citations from outside PubMed). Set citing_source='pubmed' for elink-based PubMed-internal citations and to retrieve citing PMIDs (useful for backward snowballing).

ParametersJSON Schema
NameRequiredDescriptionDefault
pmidsYesList of PubMed IDs (PMIDs), max 1000
citing_sourceNo'icite' (default, counts only) or 'pubmed' (elink, includes citing PMIDs)icite
include_citing_pmidsNoIf true and citing_source='pubmed', include the list of citing PMIDs

TDQS

A4.4/5.0
Behavior4/5

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

With no annotations provided, the description carries the full transparency burden. It clearly states that iCite returns counts only and includes external citations, while pubmed uses elink and can return citing PMIDs. It also implies that include_citing_pmids is only effective with pubmed. It does not cover error handling or output format, but the core behavior is well disclosed.

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. The first sentence states the core purpose; the second explains the key parameter choice and its benefit. Every clause adds value and the information is front-loaded.

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?

The tool is relatively simple, has no output schema, and lacks annotations. The description covers the main use cases, the source distinction, and what to expect from each mode. It omits details like return structure or failure behavior, but these are less critical for a simple lookup tool and the description is otherwise adequate.

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?

Schema coverage is 100%, so baseline is 3. The description adds meaning beyond the schema by explaining what 'icite' and 'pubmed' mean conceptually (external vs. internal citations, snowballing) and how they affect both the output and the include_citing_pmids parameter. This enriches the raw schema definitions.

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 opens with a specific verb and resource: 'Get citation counts for PMIDs.' It clearly distinguishes between the two sources (iCite vs. PubMed), which differentiates this tool from sibling tools like 'count' or 'fetch'. The purpose is unambiguous and actionable.

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

Usage Guidelines4/5

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

The description gives explicit guidance on which source to use: default iCite for broad counts, and citing_source='pubmed' when PubMed-internal citations or citing PMIDs are needed. It explains the trade-off and a concrete use case (backward snowballing), but it does not explicitly contrast with sibling tools, so it falls short of full when/when-not guidance.

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

get_full_textA

Retrieve full text of articles from PubMed Central (PMC) by PMC ID. Supports section filtering to reduce token usage.

ParametersJSON Schema
NameRequiredDescriptionDefault
pmcIdsYesPMC IDs (with or without 'PMC' prefix). Max 20 per request.
sectionsNoSections to extract. Use specific sections to reduce token usage.

TDQS

A3.6/5.0
Behavior3/5

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

With no annotations provided, the description carries the full burden. It discloses that the operation retrieves full text and offers section filtering to reduce token usage, which is a useful behavioral detail. However, it does not mention response format, error handling, or rate limits, leaving some gaps typical of a read operation.

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 a brief two-sentence definition that front-loads the core functionality and adds only one additional feature. It is succinct and to the point, with no redundant content.

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 simple retrieval tool with two well-documented parameters and no output schema, the description covers the essential 'what' and hints at a key usage trait (section filtering). It lacks explicit statements about output format or relationship to siblings, but given the simplicity, it is mostly complete.

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?

The input schema provides detailed descriptions for both parameters, covering PMIC ID format and section options. The description adds no further parameter semantics; its mention of token usage is already in the schema. Given high schema coverage, the baseline of 3 is appropriate.

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 retrieves full text from PMC by PMC ID, specifying the verb and resource. It also mentions section filtering, which adds purpose. However, it does not explicitly differentiate from sibling tools like fetch or fetch_batch, so it does not achieve a perfect 5.

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 when full text from PMC is needed, and the section filtering note suggests a use case for reducing token usage. However, there is no explicit comparison to alternatives or exclusion criteria, leaving the guidance implicit rather than explicit.

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

Tool Schema Changelog

Recent tool additions, removals, and schema changes observed during successful MCP inspections.

  1. 10 tool updatesv2.0.0
    • First observedbatch_process
    • First observedconvert_ids
    • First observedcount
    • First observedexport_to_ris
    • First observedfetch
    • First observedfetch_batch
    • First observedfind_similar_articles
    • First observedget_citation_counts
    • First observedget_full_text
    • First observedsearch

TDQS

A4.2/5.0

Scored across 10 tools

Disambiguation5/5

Each tool serves a distinct purpose: search, abstract retrieval (single/batch), full-text, count, similarity, export, citations, ID conversion, and batch processing. Overlapping tools like fetch/fetch_batch and search/count are clearly differentiated by scope and description.

Naming Consistency5/5

All tool names use lowercase snake_case and follow a predictable verb-first pattern (e.g., search, fetch, get_full_text, export_to_ris). The naming style is consistent and readable across the entire set.

Tool Count5/5

10 tools is well-scoped for a PubMed server, covering essential operations without redundancy. Each tool adds meaningful functionality, and the count feels appropriate for the domain.

Completeness5/5

The tool set covers the full research workflow: search, retrieval, full-text access, counting, similarity discovery, citation analysis, ID conversion, citation export, and batch processing. There are no obvious dead ends or missing core operations for a read-only biomedical literature server.

Maintenance

ActivityInactive
ResponsivenessNo issues

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