io.github.helena-bioinformatics由 GitHub 帳號 helena-bioinformatics 發布v0.2.1更新於 Oct 24, 2026
Search biomedical papers, inspect publication records, and traverse citation or semantic graphs.
一個唯讀的遠端 MCP 伺服器，用來檢索公開的 PubMed 衍生生物醫學文獻庫，並探索論文之間的引用與語意鄰域。
Web executable，透過 Streamable HTTP。 遠端服務在工作區中設定後即可從網頁執行環境執行。
把這段提示詞貼上到 Claude Code、Codex、Cursor 等代理程式，或 SourceWeft 對話中。代理程式會讀取該伺服器的安裝指南，先向你展示發布者、端點和登入方式，經你同意後再把它新增到你的客戶端。金鑰不會寫進任何命令。
閱讀 https://sourceweft.com/mcp/io.github.helena-bioinformatics%2Fnoodle/install.md，並按其中說明把這個 MCP 伺服器接入我的客戶端。修改任何設定之前，先告訴我它的發布者、端點和登入方式，等我確認。不要把 API 金鑰寫進命令或我會提交的檔案；問我金鑰應從哪裡取得。把它新增到你客戶端的 mcpServers 設定中。
{
"mcpServers": {
"noodle-biomedical-literature-discovery": {
"type": "http",
"url": "https://api.helena.bio/noodle/v1/mcp"
}
}
}[DOI] [AllMCPs Verified] [OpenSSF Scorecard] [RRID]
The official public, read-only Model Context Protocol adapter for biomedical literature discovery from Helena Bioinformatics. Agents can select it from a user task even when the user does not know the Noodle brand.
Public endpoint: https://api.helena.bio/noodle/v1/mcp
Official Registry identity: io.github.helena-bioinformatics/noodle
No account, API key, patient data, or private content is required or accepted.
The seven published tools are search_biomedical_literature,
get_publication_details, get_work_details,
get_publication_neighborhood, get_work_neighborhood,
get_corpus_summary, and the separate explicit opt-in support_helena
information action.
Any MCP client that supports remote Streamable HTTP can use the endpoint. Exact
recipes for ChatGPT, Claude, Codex, VS Code, Cursor, Windsurf, Gemini CLI,
Grok, Perplexity, Microsoft Copilot Studio, Biomni, and Biorouter live under
registry/platforms and integrations.
Ready-to-use ecosystem packages are included for:
.difypkg;The companion Agent Skill is in
skills/noodle-biomedical-literature-discovery. It enables implicit,
task-first selection for requests such as:
Build the deterministic skill archive with:
Start from a resolved PMID or work ID and request one bounded neighborhood at a time. Report edges exactly as returned, keep a visited-ID set, and stop at a missing neighborhood. Search rank, citation proximity, semantic similarity, co-mention, and graph distance are discovery signals. They do not establish causality, scientific validity, diagnosis, or treatment.
Python 3.12 is required.
Run the brand-blind contract audit with:
The benchmark contains 60 prompts that omit Noodle, Helena, and MCP.
It covers all six scientific routes plus negative and safety controls.
This repository is also a portable Agent Plugin and Kiro Power. plugin.json
provides brand-blind activation keywords, the existing Agent Skill supplies the
scientific routing and safety boundary, and mcp.json connects directly to the
canonical hosted Streamable HTTP endpoint. The Power does not proxy, repackage,
or reimplement Noodle.
Privacy policy: https://noodle.helena.bio/privacy
The persistent Research Resource Identifier is
RRID:SCR_028920. Cite the resource in a
methods section as Noodle (RRID:SCR_028920). Use the
version DOI when a version-specific
software citation is also needed. The RRID identifies the resource across
publications, while the DOI identifies the archived 0.2.0 release.
Support: https://noodle.helena.bio/contact or [email protected]
Apache License 2.0. Report vulnerabilities privately as described in
SECURITY.md. Do not submit patient, private case, clinical-record, credential,
or private uploaded content to the public service or issue tracker.
來源：README.md，提交 a0c92ae
Search biomedical literature
Semantically search Noodle's public PubMed-derived biomedical corpus. Include known PMID, DOI, or PMCID identifiers in the query so they can act as exact anchors. Results are for literature discovery and professional review, not diagnosis or treatment.
sortlimitquery必填cursorGet publication details by PMID
Retrieve one complete public bibliographic record by PMID after search. Results are for literature discovery and professional review, not diagnosis or treatment.
pmid必填Get publication details by work ID
Retrieve one complete public bibliographic record by Noodle work identifier. Results are for literature discovery and professional review, not diagnosis or treatment.
work_id必填Explore a PMID literature neighborhood
Retrieve the bounded citation and semantic neighborhood around one PMID. Results are for literature discovery and professional review, not diagnosis or treatment.
pmid必填from_work_idExplore a work literature neighborhood
Retrieve the bounded citation and semantic neighborhood around one Noodle work identifier. Results are for literature discovery and professional review, not diagnosis or treatment.
work_id必填from_work_idGet corpus summary
Return public corpus coverage, source, freshness, and count metadata. Results are for literature discovery and professional review, not diagnosis or treatment.
無需輸入參數。
Support Helena's free scientific infrastructure
Learn about the separate Helena Good MCP. This opt-in information action initiates no payment or outreach and changes no scientific result.
無需輸入參數。
已滿足適用檢查項的 100%
該評分衡量此收錄條目的完整程度，依據註冊中心條目、端點與公開來源計算得出。它不是對伺服器本身的評價，也不表示伺服器安全或目前可用：可連通性是帶日期的檢查結果，評分也不包含安裝量或使用者評價。
python3 ops/package_agent_skill.pypython -m venv .venv. .venv/bin/activatepython -m pip install -r requirements-dev.lockpython -m pip install --no-deps -e .pytestruff check .ruff format --check .python benchmarks/agent-discovery/audit_skill.py