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h-lu

Paper Search MCP Server

by h-lu

read_biorxiv_paper

Download and extract full text from bioRxiv papers by providing a DOI, with optional PDF saving, to obtain the paper content in Markdown format.

Instructions

Download and extract full text from bioRxiv paper.

Args:
    paper_id: bioRxiv DOI.
    save_path: Directory to save PDF.

Returns:
    Full paper text in Markdown format.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
paper_idYes
save_pathNo
Behavior3/5

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

Discloses side effect of saving PDF to directory and return format (Markdown). But no annotations exist; description doesn't mention read-only nature, error handling, or network usage.

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?

Concise with three lines plus structured Args/Returns. No unnecessary words, front-loaded with main action.

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 2-param tool with no output schema or annotations, the description covers inputs, output format, and side effects. Lacks error handling and differentiation from siblings, but overall sufficient.

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?

Adds meaning to both parameters: paper_id is DOI, save_path is save directory. This compensates for 0% schema coverage. However, optionality of save_path is not clarified.

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 'download and extract' and the resource 'bioRxiv paper'. However, it does not distinguish from siblings like 'download_biorxiv' (which might only download PDF) or other read_* tools, missing specificity.

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?

No guidance on when to use this tool over siblings (e.g., download_biorxiv, read_arxiv_paper). Lacks context on prerequisites or exclusions.

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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