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biomedical-search

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Chinese

Biomedical Search

生物医学搜索

Search across all major biomedical databases (PubMed, bioRxiv, medRxiv, ClinicalTrials.gov, FDA drug labels) simultaneously using natural language queries powered by Valyu's semantic search API.
借助Valyu的语义搜索API，使用自然语言查询同时搜索所有主要生物医学数据库（PubMed、bioRxiv、medRxiv、ClinicalTrials.gov、FDA药物标签）。

Why This Skill is Powerful

本工具的强大之处

  • No API Parameter Parsing: Just pass natural language queries directly - no need to construct complex search parameters
  • Semantic Search: Understands the meaning of your query, not just keyword matching
  • Full-Text Access: Returns complete content from literature, trials, and drug labels
  • Image Links: Includes figures and images when available
  • Comprehensive Coverage: Search across PubMed, bioRxiv, medRxiv, clinical trials, and drug labels simultaneously
  • Unified Results: Get results from all biomedical sources in a single query
  • 无需解析API参数：直接传入自然语言查询即可，无需构建复杂的搜索参数
  • 语义搜索：理解查询的含义，而非仅进行关键词匹配
  • 全文访问：返回文献、试验和药物标签的完整内容
  • 图片链接：在可用时包含图表和图片
  • 全面覆盖：同时搜索PubMed、bioRxiv、medRxiv、临床试验和药物标签
  • 统一结果：一次查询获取所有生物医学来源的结果

Requirements

要求

  1. Node.js 18+ (uses built-in fetch)
  2. Valyu API key from https://platform.valyu.ai ($10 free credits)
  1. Node.js 18+（使用内置的fetch）
  2. 从https://platform.valyu.ai获取Valyu API密钥（赠送10美元免费额度）

CRITICAL: Script Path Resolution

重要提示：脚本路径解析

The 
scripts/search
commands in this documentation are relative to this skill's installation directory.
Before running any command, locate the script using:
bash
BIOMEDICAL_SCRIPT=$(find ~/.claude/plugins/cache -name "search" -path "*/biomedical-search/*/scripts/*" -type f 2>/dev/null | head -1)
Then use the full path for all commands:
bash
$BIOMEDICAL_SCRIPT "CAR-T cell therapy" 20
本文档中的
scripts/search
命令是相对于本工具的安装目录的。
在运行任何命令之前，使用以下命令定位脚本：
bash
BIOMEDICAL_SCRIPT=$(find ~/.claude/plugins/cache -name "search" -path "*/biomedical-search/*/scripts/*" -type f 2>/dev/null | head -1)
然后使用完整路径执行所有命令：
bash
$BIOMEDICAL_SCRIPT "CAR-T cell therapy" 20

API Key Setup Flow

API密钥设置流程

When you run a search and receive 
"setup_required": true
, follow this flow:
  1. Ask the user for their API key: "To search biomedical databases, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai"
  2. Once the user provides the key, run:
    bash
    scripts/search setup <api-key>
  3. Retry the original search.
当你运行搜索并收到
"setup_required": true
时，请按照以下流程操作：
  1. 向用户索要API密钥： "要搜索生物医学数据库，我需要你的Valyu API密钥。可在https://platform.valyu.ai免费获取（含10美元额度）"
  2. 用户提供密钥后，运行：
    bash
    scripts/search setup <api-key>
  3. 重试原搜索。

When to Use This Skill

使用场景

  • Complete biomedical information gathering
  • Clinical research combined with basic science
  • Finding trials, literature, and official drug info together
  • Evidence-based medicine research
  • Disease understanding from multiple angles
  • 完整的生物医学信息收集
  • 结合基础科学的临床研究
  • 同时查找试验、文献和官方药物信息
  • 循证医学研究
  • 从多角度了解疾病

Output Format

输出格式

json
{
  "success": true,
  "type": "biomedical_search",
  "query": "CAR-T cell therapy",
  "result_count": 20,
  "results": [
    {
      "title": "Title",
      "url": "https://...",
      "content": "Full content...",
      "source": "pubmed|biorxiv|medrxiv|clinical-trials|drug-labels",
      "relevance_score": 0.95,
      "images": ["https://example.com/figure1.jpg"]
    }
  ],
  "cost": 0.035
}
json
{
  "success": true,
  "type": "biomedical_search",
  "query": "CAR-T cell therapy",
  "result_count": 20,
  "results": [
    {
      "title": "Title",
      "url": "https://...",
      "content": "Full content...",
      "source": "pubmed|biorxiv|medrxiv|clinical-trials|drug-labels",
      "relevance_score": 0.95,
      "images": ["https://example.com/figure1.jpg"]
    }
  ],
  "cost": 0.035
}

Processing Results

结果处理

With jq

使用jq

bash
undefined
bash
undefined

Get titles

获取标题

scripts/search "query" 20 | jq -r '.results[].title'
scripts/search "query" 20 | jq -r '.results[].title'

Get URLs

获取URL

scripts/search "query" 20 | jq -r '.results[].url'
scripts/search "query" 20 | jq -r '.results[].url'

Extract full content

提取完整内容

scripts/search "query" 20 | jq -r '.results[].content'
scripts/search "query" 20 | jq -r '.results[].content'

Filter by source type

按来源类型筛选

scripts/search "query" 20 | jq -r '.results[] | select(.source == "clinical-trials") | .title'
undefined
scripts/search "query" 20 | jq -r '.results[] | select(.source == "clinical-trials") | .title'
undefined

Common Use Cases

常见使用案例

Clinical Research Planning

临床研究规划

bash
undefined
bash
undefined

Gather evidence for clinical study design

收集临床研究设计的证据

scripts/search "phase 2 trials checkpoint inhibitors melanoma" 50
undefined
scripts/search "phase 2 trials checkpoint inhibitors melanoma" 50
undefined

Drug Safety Assessment

药物安全性评估

bash
undefined
bash
undefined

Search literature, labels, and trials for safety data

搜索文献、标签和试验中的安全性数据

scripts/search "SGLT2 inhibitors cardiovascular safety" 40
undefined
scripts/search "SGLT2 inhibitors cardiovascular safety" 40
undefined

Treatment Protocol Development

治疗方案开发

bash
undefined
bash
undefined

Find current practice and emerging approaches

查找当前实践和新兴方法

scripts/search "pembrolizumab dosing regimens NSCLC" 30
undefined
scripts/search "pembrolizumab dosing regimens NSCLC" 30
undefined

Medical Writing

医学写作

bash
undefined
bash
undefined

Comprehensive research for medical communications

为医学传播进行全面研究

scripts/search "JAK inhibitors rheumatoid arthritis efficacy" 60
undefined
scripts/search "JAK inhibitors rheumatoid arthritis efficacy" 60
undefined

Error Handling

错误处理

All commands return JSON with 
success
field:
json
{
  "success": false,
  "error": "Error message"
}
Exit codes:
  • 0
    - Success
  • 1
    - Error (check JSON for details)
所有命令返回的JSON中包含
success
字段：
json
{
  "success": false,
  "error": "Error message"
}
退出码：
  • 0
    - 成功
  • 1
    - 错误（查看JSON获取详情）

API Endpoint

API端点

  • Base URL: 
    https://api.valyu.ai/v1
  • Endpoint: 
    /search
  • Authentication: X-API-Key header
  • 基础URL: 
    https://api.valyu.ai/v1
  • 端点: 
    /search
  • 认证: X-API-Key请求头

Architecture

架构

scripts/
├── search          # Bash wrapper
└── search.mjs      # Node.js CLI
Direct API calls using Node.js built-in 
fetch()
, zero external dependencies.
scripts/
├── search          # Bash包装器
└── search.mjs      # Node.js命令行工具
使用Node.js内置的
fetch()
直接调用API，无外部依赖。

Adding to Your Project

添加到你的项目中

If you're building an AI project and want to integrate Biomedical Search directly into your application, use the Valyu SDK:
如果你正在构建AI项目，并希望将生物医学搜索直接集成到应用中，请使用Valyu SDK：

Python Integration

Python集成

python
from valyu import Valyu

client = Valyu(api_key="your-api-key")

response = client.search(
    query="your search query here",
    included_sources=["valyu/valyu-pubmed", "valyu/valyu-biorxiv", "valyu/valyu-medrxiv", "valyu/valyu-clinical-trials", "valyu/valyu-drug-labels"],
    max_results=20
)

for result in response["results"]:
    print(f"Title: {result['title']}")
    print(f"URL: {result['url']}")
    print(f"Content: {result['content'][:500]}...")
python
from valyu import Valyu

client = Valyu(api_key="your-api-key")

response = client.search(
    query="your search query here",
    included_sources=["valyu/valyu-pubmed", "valyu/valyu-biorxiv", "valyu/valyu-medrxiv", "valyu/valyu-clinical-trials", "valyu/valyu-drug-labels"],
    max_results=20
)

for result in response["results"]:
    print(f"Title: {result['title']}")
    print(f"URL: {result['url']}")
    print(f"Content: {result['content'][:500]}...")

TypeScript Integration

TypeScript集成

typescript
import { Valyu } from "valyu-js";

const client = new Valyu("your-api-key");

const response = await client.search({
  query: "your search query here",
  includedSources: ["valyu/valyu-pubmed", "valyu/valyu-biorxiv", "valyu/valyu-medrxiv", "valyu/valyu-clinical-trials", "valyu/valyu-drug-labels"],
  maxResults: 20
});

response.results.forEach((result) => {
  console.log(`Title: ${result.title}`);
  console.log(`URL: ${result.url}`);
  console.log(`Content: ${result.content.substring(0, 500)}...`);
});
See the Valyu docs for full integration examples and SDK reference.
typescript
import { Valyu } from "valyu-js";

const client = new Valyu("your-api-key");

const response = await client.search({
  query: "your search query here",
  includedSources: ["valyu/valyu-pubmed", "valyu/valyu-biorxiv", "valyu/valyu-medrxiv", "valyu/valyu-clinical-trials", "valyu/valyu-drug-labels"],
  maxResults: 20
});

response.results.forEach((result) => {
  console.log(`Title: ${result.title}`);
  console.log(`URL: ${result.url}`);
  console.log(`Content: ${result.content.substring(0, 500)}...`);
});
查看Valyu文档获取完整的集成示例和SDK参考。