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PubMed MCP — wraps the NCBI E-utilities API (biomedical literature, free, no auth)

Status
Healthy
Last Tested
Transport
Streamable HTTP
URL
Repository
pipeworx-io/mcp-pubmed
GitHub Stars
0

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Tool DescriptionsA

Average 4/5 across 3 of 3 tools scored.

Server CoherenceA
Disambiguation5/5

Each tool has a clearly distinct purpose: get_abstract retrieves detailed abstract text, get_summary provides metadata summaries, and search_pubmed finds articles via queries. There is no overlap in functionality, making tool selection straightforward for an agent.

Naming Consistency5/5

All tool names follow a consistent verb_noun pattern (get_abstract, get_summary, search_pubmed) with clear, descriptive verbs and nouns. There are no deviations or mixed conventions, ensuring predictable naming throughout.

Tool Count4/5

With 3 tools, the server is well-scoped for basic PubMed operations, but it feels slightly thin as it lacks update or delete functions typical in CRUD workflows. However, for a focused literature search and retrieval service, the count is reasonable and each tool earns its place.

Completeness4/5

The tools cover core PubMed workflows: search, retrieve metadata, and get abstracts, with no dead ends as search results feed into the other tools. A minor gap exists in not supporting article creation or modification, but this aligns with PubMed's read-only nature, and agents can work effectively with the provided surface.

Available Tools

3 tools
get_abstractAInspect

Get the full abstract text for a single PubMed article by its PubMed ID. Returns structured abstract with section labels when available.

ParametersJSON Schema
NameRequiredDescriptionDefault
idYesA single PubMed ID (e.g., "33579999")
Behavior3/5

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

No annotations are provided, so the description carries the full burden. It discloses the return format ('structured abstract with section labels when available'), which is valuable behavioral context, but does not mention potential errors, rate limits, or authentication needs.

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 appropriately sized and front-loaded, with two clear sentences that efficiently convey the tool's purpose and return behavior without any 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?

Given the tool's low complexity (1 parameter, no annotations, no output schema), the description is reasonably complete. It explains what the tool does and what it returns, though it could benefit from more behavioral details like error handling or limitations.

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 the single parameter 'id'. The description adds marginal value by reinforcing that it's for a 'single PubMed article' but does not provide additional syntax or format details 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 purpose with specific verb ('Get') and resource ('full abstract text for a single PubMed article'), and distinguishes it from sibling tools by specifying it retrieves abstracts rather than summaries or search results.

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 clear context for when to use this tool ('by its PubMed ID'), but does not explicitly state when not to use it or name alternatives like the sibling tools get_summary or search_pubmed.

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

get_summaryAInspect

Get metadata summaries for one or more PubMed articles by their PubMed IDs. Returns title, authors, journal, publication date, and DOI.

ParametersJSON Schema
NameRequiredDescriptionDefault
idsYesComma-separated PubMed IDs (e.g., "33579999,34567890")
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 the tool's behavior by specifying what it returns (title, authors, journal, publication date, DOI) and the input format, but does not mention potential limitations like rate limits, error conditions, or authentication needs. It adequately describes the core operation without contradictions.

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 front-loaded with the core purpose, followed by specific return details, all in two efficient sentences with zero wasted words. Every sentence adds essential information without redundancy.

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 low complexity (single parameter, no annotations, no output schema), the description is mostly complete for a read-only retrieval tool. It clearly states the purpose, input, and return fields. However, without an output schema, it could benefit from more detail on response structure or error handling, but the essentials are covered.

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 fully documents the single parameter 'ids'. The description adds no additional parameter semantics beyond what the schema provides (e.g., it doesn't clarify format beyond 'comma-separated' or discuss validation), meeting the baseline for high schema coverage.

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 specific action ('Get metadata summaries'), target resource ('PubMed articles'), and scope ('by their PubMed IDs'), distinguishing it from sibling tools like 'get_abstract' (which likely returns full abstracts) and 'search_pubmed' (which searches rather than retrieves by ID).

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 usage context (retrieving metadata for known PubMed IDs) but does not explicitly state when to use this tool versus alternatives like 'get_abstract' or 'search_pubmed'. It provides clear input requirements but lacks explicit exclusions or comparative guidance.

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

search_pubmedAInspect

Search the PubMed biomedical literature database by keyword, author, or MeSH term. Returns a list of PubMed IDs that can be used with get_summary or get_abstract.

ParametersJSON Schema
NameRequiredDescriptionDefault
limitNoNumber of results to return (1-100, default 10)
queryYesSearch query (e.g., "CRISPR cancer therapy", "Smith J[Author]", "COVID-19[MeSH]")
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 states the tool returns a list of PubMed IDs, which implies a read-only operation, but doesn't specify other behaviors like rate limits, authentication requirements, or error handling. The description adds some context about the output format but lacks details on pagination or result ordering.

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 zero waste: the first sentence states the purpose and search methods, and the second explains the output and connection to sibling tools. It is appropriately sized, front-loaded with key information, and every sentence earns its place by adding distinct value.

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 moderate complexity (search operation with 2 parameters), no annotations, and no output schema, the description is reasonably complete. It covers the purpose, usage context with siblings, and output format. However, it could improve by addressing potential limitations like result ordering or default behaviors beyond the limit parameter.

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 fully documents both parameters (query and limit). The description adds minimal value beyond the schema by mentioning search types (keyword, author, MeSH) that align with the query parameter examples, but doesn't provide additional syntax or format details. This meets the baseline for high schema coverage.

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 specific action ('Search'), resource ('PubMed biomedical literature database'), and search methods ('by keyword, author, or MeSH term'). It distinguishes this tool from its siblings by explaining that it returns PubMed IDs that can be used with get_summary or get_abstract, establishing its role in a workflow.

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 clear context by mentioning the types of searches (keyword, author, MeSH) and explicitly naming sibling tools (get_summary, get_abstract) that should be used after obtaining IDs. However, it lacks explicit guidance on when NOT to use this tool or alternatives for different search needs, such as filtering by date or journal.

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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