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openags

Paper Search MCP

by openags
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Python
Remote

read_pubmed_paper

Extract text content from PubMed papers using PMID identifiers to access scientific literature for research and analysis purposes.

Instructions

Read and extract text content from a PubMed paper.

Args: paper_id: PubMed ID (PMID). save_path: Directory where the PDF would be saved (unused). Returns: str: Message indicating that direct paper reading is not supported.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
paper_idYes
save_pathNo./downloads

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes

Implementation Reference

  • paper_search_mcp/server.py:538-547 (handler)
    The MCP tool wrapper function 'read_pubmed_paper' which delegates the request to the 'pubmed_searcher' instance.
    async def read_pubmed_paper(paper_id: str, save_path: str = "./downloads") -> str:
    """Read and extract text content from a PubMed paper.

    Args:
        paper_id: PubMed ID (PMID).
        save_path: Directory where the PDF would be saved (unused).
    Returns:
        str: Message indicating that direct paper reading is not supported.
    """
    return pubmed_searcher.read_paper(paper_id, save_path)
  • paper_search_mcp/academic_platforms/pubmed.py:111-124 (handler)
    The actual implementation of 'read_paper' within the 'PubMedSearcher' class, which returns a message explaining that reading full text is not supported.
    def read_paper(self, paper_id: str, save_path: str = "./downloads") -> str:
    """Attempt to read and extract text from a PubMed paper.

    Args:
        paper_id: PubMed ID (PMID)
        save_path: Directory for potential PDF storage (unused)

    Returns:
        str: Error message indicating PDF reading is not supported
    """
    message = ("PubMed papers cannot be read directly through this tool. "
              "Only metadata and abstracts are available through PubMed's API. "
              "Please use the paper's DOI or URL to access the full text on the publisher's website.")
    return message

Tool Definition Quality

C2.4/5.0
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 discloses that 'direct paper reading is not supported' in the returns, which is a critical behavioral trait, but fails to explain what the tool actually does (e.g., does it fetch metadata, return an error, or provide alternative content?). This leaves the agent uncertain about the tool's real behavior.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is appropriately sized and front-loaded, with the purpose stated first, followed by args and returns in a structured format. Every sentence adds value, such as the critical note in returns, though it could be more concise by integrating the 'unused' detail into the args section more smoothly.

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 complexity (a tool that claims to read but doesn't support it), no annotations, and low schema coverage, the description is incomplete. It hints at limitations in returns but doesn't fully explain the tool's functionality, error handling, or what it actually returns (e.g., a string message). With an output schema present, it doesn't need to detail return values, but the overall context is lacking for effective use.

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

Parameters2/5

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

Schema description coverage is 0%, so the description must compensate. It adds minimal semantics: 'paper_id' is explained as 'PubMed ID (PMID)' and 'save_path' as 'Directory where the PDF would be saved (unused),' but this is insufficient for 2 parameters. The 'unused' note is helpful but doesn't clarify why the parameter exists or its implications, leaving gaps in understanding.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose3/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description states the tool's purpose as 'Read and extract text content from a PubMed paper,' which is clear but vague about what 'read and extract' entails. It does not differentiate from siblings like 'download_pubmed' or 'read_arxiv_paper' in terms of functionality or scope, leaving ambiguity about its specific role.

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 is provided on when to use this tool versus alternatives. With many sibling tools for downloading or reading papers from various sources, the description lacks context on prerequisites, exclusions, or comparisons, such as when to choose this over 'download_pubmed' or other read tools.

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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