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ncukondo

PubMed MCP Server

by ncukondo

Server Quality Checklist

58%
Profile completionA complete profile improves this server's visibility in search results.
  • Latest release: v1.0.0

  • Disambiguation5/5

    Each tool has a clearly distinct purpose with no overlap: fetch_summary retrieves article metadata, get_fulltext provides full content, and search_pubmed finds articles. The descriptions make it easy for an agent to choose the right tool for each task without confusion.

    Naming Consistency5/5

    All tool names follow a consistent verb_noun pattern (fetch_summary, get_fulltext, search_pubmed) with clear, action-oriented verbs. The naming is uniform and predictable across the set, making it easy to understand each tool's function.

    Tool Count3/5

    With only 3 tools, the count feels thin for a PubMed domain that typically involves more operations like filtering, citation management, or advanced search. While the tools cover basic needs, the scope could benefit from additional functionality to be fully robust.

    Completeness3/5

    The tools cover core functions (search, summary, fulltext) but lack operations for updating, deleting, or managing articles, as well as advanced features like filtering by date or author. This creates minor gaps that agents might need to work around for complex workflows.

  • Average 2.9/5 across 3 of 3 tools scored.

    See the Tool Scores section below for per-tool breakdowns.

    • No community issues in the last 6 months
    • 0 commits in the last 12 weeks
    • No stable releases found
    • No critical vulnerability alerts
    • No high-severity vulnerability alerts
    • No code scanning findings
    • CI status not available
  • This repository is licensed under MIT License.

  • This repository includes a README.md file.

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How is the quality score calculated?

The overall quality score combines two components: Tool Definition Quality (70%) and Server Coherence (30%).

Tool Definition Quality measures how well each tool describes itself to AI agents. Every tool is scored 1–5 across six dimensions: Purpose Clarity (25%), Usage Guidelines (20%), Behavioral Transparency (20%), Parameter Semantics (15%), Conciseness & Structure (10%), and Contextual Completeness (10%). The server-level definition quality score is calculated as 60% mean TDQS + 40% minimum TDQS, so a single poorly described tool pulls the score down.

Server Coherence evaluates how well the tools work together as a set, scoring four dimensions equally: Disambiguation (can agents tell tools apart?), Naming Consistency, Tool Count Appropriateness, and Completeness (are there gaps in the tool surface?).

Tiers are derived from the overall score: A (≥3.5), B (≥3.0), C (≥2.0), D (≥1.0), F (<1.0). B and above is considered passing.

Tool Scores

  • Behavior2/5

    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 mentions 'detailed article information' but doesn't specify what that includes (e.g., title, authors, abstract), whether there are rate limits, authentication needs, or error handling. This leaves significant gaps in understanding the tool's behavior beyond basic 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, efficient sentence that directly states the tool's purpose without unnecessary words. It's front-loaded with the core action and resource, making it easy to parse. There's no wasted information, earning a high score for conciseness.

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

    Completeness2/5

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

    Given the lack of annotations and output schema, the description is incomplete. It doesn't explain what 'detailed article information' entails, potential limitations (e.g., batch size, availability), or error cases. For a tool with no structured behavioral data, this leaves too many unknowns for effective agent use.

    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 the parameter 'pmids' clearly documented as an array of PubMed IDs. The description adds minimal value beyond the schema by mentioning 'using PMIDs', which reinforces but doesn't expand on the parameter's purpose. The baseline score of 3 is appropriate since the schema does the heavy lifting.

    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 verb ('fetch') and resource ('detailed article information from PubMed'), making the purpose understandable. It specifies the mechanism ('using PMIDs'), which helps distinguish it from general search operations. However, it doesn't explicitly differentiate from sibling tools like 'get_fulltext' or 'search_pubmed' beyond the 'detailed article information' phrasing.

    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?

    The description provides no guidance on when to use this tool versus alternatives. It doesn't mention sibling tools like 'get_fulltext' or 'search_pubmed' or explain scenarios where this tool is preferred (e.g., for known PMIDs vs. keyword searches). The usage context is implied but not explicitly stated.

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

  • Behavior2/5

    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 states the tool retrieves full text but doesn't disclose behavioral traits such as rate limits, authentication needs, error handling (e.g., for invalid PMIDs), or output format (e.g., plain text, HTML). For a tool with no annotation coverage, this is a significant gap.

    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, efficient sentence with zero waste. It front-loads the purpose clearly and uses straightforward language, making it easy to parse. Every word earns its place.

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

    Completeness2/5

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

    Given the lack of annotations and output schema, the description is incomplete. It doesn't explain what the tool returns (e.g., full text content in what format?), potential limitations (e.g., availability of full text), or error cases. For a tool with no structured support, more context is needed to be fully helpful.

    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 description coverage is 100%, with the parameter 'pmids' clearly documented in the schema as an array of PubMed IDs. The description adds minimal value beyond the schema by mentioning 'using PMIDs', but doesn't provide additional semantics like format examples or constraints. Baseline 3 is appropriate when the schema does the heavy lifting.

    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 action ('Get full text content') and resource ('PubMed articles') with a specific mechanism ('using PMIDs'). It distinguishes from sibling tools like 'fetch_summary' (which presumably provides summaries) and 'search_pubmed' (which searches rather than retrieves full text). However, it doesn't explicitly mention how it differs from siblings beyond the verb, keeping it at 4 rather than 5.

    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?

    The description provides no guidance on when to use this tool versus alternatives like 'fetch_summary' or 'search_pubmed'. It doesn't specify prerequisites (e.g., needing valid PMIDs) or exclusions (e.g., not for abstracts). Without any usage context, it scores low.

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

  • Behavior2/5

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

    With no annotations provided, the description carries full burden for behavioral disclosure. It states what the tool does but doesn't describe important behaviors like pagination handling (implied by retMax/retStart), rate limits, authentication requirements, error conditions, or what the response format looks like. For a search tool with complex parameters, this is inadequate.

    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, efficient sentence that communicates the core purpose without unnecessary words. It's appropriately sized for a search tool and front-loads the essential information.

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

    Completeness2/5

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

    For a search tool with 2 parameters (one being a complex nested object), no annotations, and no output schema, the description is insufficient. It doesn't explain what the tool returns, how results are structured, or important behavioral aspects like pagination. The agent would need to guess about the response format and operational constraints.

    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 fully documents both parameters and their sub-properties. The description adds no parameter-specific information beyond what's in the schema, maintaining the baseline score. It doesn't explain how parameters interact or provide usage examples.

    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 action ('Search') and resource ('PubMed for scientific articles'), making the purpose immediately understandable. However, it doesn't differentiate this search tool from sibling tools like 'fetch_summary' or 'get_fulltext', which presumably retrieve specific article details rather than perform searches.

    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?

    The description provides no guidance on when to use this tool versus the sibling tools 'fetch_summary' or 'get_fulltext'. It doesn't mention prerequisites, limitations, or alternative approaches, leaving the agent to infer usage context from tool names alone.

    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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