io.github.helena-bioinformatics由 GitHub 账号 helena-bioinformatics 发布v0.2.1更新于 Oct 24, 2026
Search biomedical papers, inspect publication records, and traverse citation or semantic graphs.
一个只读的远程 MCP 服务器，用于检索公开的 PubMed 衍生生物医学文献库，并探索论文之间的引用与语义邻域。
Web executable，通过 Streamable HTTP。 远程服务在工作区中配置后即可从网页运行时运行。
把这段提示词粘贴到 Claude Code、Codex、Cursor 等智能体，或 SourceWeft 对话中。智能体会读取该服务器的安装指南，先向你展示发布者、端点和登录方式，经你同意后再把它添加到你的客户端。密钥不会写进任何命令。
阅读 https://sourceweft.com/mcp/io.github.helena-bioinformatics%2Fnoodle/install.md，并按其中说明把这个 MCP 服务器接入我的客户端。修改任何配置之前，先告诉我它的发布者、端点和登录方式，等我确认。不要把 API 密钥写进命令或我会提交的文件；问我密钥应从哪里获取。把它添加到你客户端的 mcpServers 配置中。
{
"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.
来源：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.
无需输入参数。
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.
无需输入参数。
已满足适用检查项的 100%
该评分衡量此收录条目的完整程度，依据注册中心条目、端点与公开来源计算得出。它不是对服务器本身的评价，也不表示服务器安全或当前可用：可连通性是带日期的检查结果，评分也不包含安装量或用户评价。
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