このリポジトリには、BioPythonのEntrezモジュールを使用してPubMedの論文抄録を検索するMCPサーバーが含まれています。FastMCPフレームワークを活用して、PubMedの非同期検索機能を提供します。
**PubMed を検索:**検索用語に基づいて記事を検索します。
抄録の取得: PubMed から返された記事の抄録を取得します。
**非同期操作:**サーバーのブロックを回避するために、非同期実行 ( asyncio.to_thread経由) を使用します。
Related MCP server: PubMed MCP Server
Python 3.8以上
mcp[cli]
バイオパイソン
リポジトリをクローンします。
git clone https://github.com/AIAnytime/MCP-Servers
cd pubmed-mcp-server依存関係をインストールします:
uv を使用して必要なパッケージをインストールできます。
uv add -r requirements.txtEntrez メールの設定:
コード ( main.py内) に有効なメール アドレスが設定されていることを確認します。
Entrez.email = "give an email address"次のコマンドを実行して PubMed MCP サーバーを起動します。
uv run main.pyこのコマンドは、 uvコマンドライン ツール (構成で指定されたとおり) を使用してサーバーを起動します。
MCP クライアントを PubMed MCP サーバーに接続するように構成するには、次のようにconfig.jsonファイルを作成または更新します。
{
"mcpServers": {
"pubmed": {
"command": "C:/Users/aiany/.local/bin/uv",
"args": [
"--directory",
"C:/Users/aiany/OneDrive/Desktop/YT Video/pubmed-mcp-server",
"run",
"main.py"
]
}
}
}指示：
MCP サーバーを実行するために使用されるコマンドライン ツールへのフル パス (この場合はuv )。
引数:
--directory : サーバーが配置されている作業ディレクトリを指定します。
"C:/Users/aiany/OneDrive/Desktop/YT Video/pubmed-mcp-server" : サーバーのルート ディレクトリへのパス。
"run"と"main.py" : PubMed MCP サーバーを起動するためのコマンドとエントリ ポイント。
サーバーが実行中になり、MCP クライアントが設定されると、提供されているツールを使用できます。
ツール: search_pubmed
パラメータ:
query : PubMedの検索用語（デフォルトは"endocarditis" ）。
max_results : 取得する記事の最大数 (デフォルトは10 )。
使用例:
search_pubmed(query="endocarditis", max_results=10)これにより、改行で区切られた記事の要約を含む文字列が返されます。
このプロジェクトはMIT ライセンスに基づいてライセンスされています。
特定の設定に応じて、必要に応じてパスと詳細を調整できます。
Search PubMed for articles matching the query.
Args:
query: The search term for PubMed.
max_results: Maximum number of articles to retrieve.
Returns:
A string containing the abstracts of found articles, separated by two newlines.
| Name | Required | Description | Default |
|---|---|---|---|
| max_results | No | ||
| query | No | endocarditis |
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 the tool 'searches' and 'retrieves' articles, implying a read-only operation, but doesn't clarify if it's safe, requires authentication, has rate limits, or details the search behavior (e.g., relevance ranking, filters). The return format is described, but key behavioral traits like error handling or performance are omitted.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is well-structured and front-loaded with the core purpose, followed by clear sections for Args and Returns. Every sentence adds value: the first states the purpose, and the others explain parameters and output. There's no redundancy or unnecessary information, making it highly efficient.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the tool's moderate complexity (2 parameters, no output schema, no annotations), the description is minimally adequate. It covers the purpose, parameters, and return format, but lacks behavioral context like error handling, search constraints, or performance details. Without annotations or output schema, more completeness would be beneficial, but it meets basic requirements.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
The description adds basic meaning for both parameters: 'query' is described as 'the search term for PubMed,' and 'max_results' as 'maximum number of articles to retrieve.' This compensates for the 0% schema description coverage by providing semantic context. However, it lacks details on query syntax, result limits, or default behaviors, keeping it at a baseline level.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states the tool's purpose: 'Search PubMed for articles matching the query.' This specifies the verb ('search'), resource ('PubMed articles'), and scope ('matching the query'). It's not a tautology and is unambiguous. However, with no sibling tools mentioned, there's no explicit differentiation from alternatives, preventing a perfect score.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
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 lacks context about prerequisites, limitations, or scenarios where it's most appropriate. While it implies usage for searching PubMed articles, there's no explicit when/when-not advice or mention of other tools, leaving the agent with minimal usage direction.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Recent tool additions, removals, and schema changes observed during successful MCP inspections.
v1.0.0search_pubmedScored across 1 tool
With only one tool, there is no possibility of confusion or overlap between tools. The tool 'search_pubmed' has a clear, singular purpose of searching PubMed for articles, making disambiguation trivial.
Since there is only one tool, naming consistency is inherently perfect. The tool name 'search_pubmed' follows a clear verb_noun pattern, and there are no other tools to compare it against for inconsistency.
A single tool for a PubMed server is too few for the apparent scope. PubMed typically involves operations like fetching article details, filtering by date or author, or retrieving citations, which are missing. This minimal set limits functionality and feels incomplete for the domain.
The tool set is severely incomplete for a PubMed server. While 'search_pubmed' covers basic searching, there are obvious gaps such as retrieving full article metadata, accessing citations, filtering results, or managing user queries. This will likely cause agent failures when more complex tasks are required.
Search 36M+ PubMed biomedical articles and ClinicalTrials.gov studies.
Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms.
Search PubMed with precision using keyword and journal filters and smart sorting. Uncover MeSH ter…
Search biomedical literature, get article details, find related articles, and explore MeSH terms