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bioRxiv Search

bioRxiv搜索

Search the complete bioRxiv database of biological sciences preprints using natural language queries powered by Valyu's semantic search API.
使用由Valyu语义搜索API提供支持的自然语言查询，搜索生物科学领域的完整bioRxiv预印本数据库。

Why This Skill is Powerful

此工具的强大之处

  • 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 article content, not just abstracts
  • Image Links: Includes figures and images from papers
  • Comprehensive Coverage: Access to all bioRxiv preprints in biological sciences
  • 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：返回完整的文章内容，而非仅摘要
  • 图片链接：包含论文中的图表和图片
  • 全面覆盖：可访问生物科学领域的所有bioRxiv预印本

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
BIORXIV_SCRIPT=$(find ~/.claude/plugins/cache -name "search" -path "*/biorxiv-search/*/scripts/*" -type f 2>/dev/null | head -1)
Then use the full path for all commands:
bash
$BIORXIV_SCRIPT "CRISPR gene editing" 15
本文档中的
scripts/search
命令是相对于此工具的安装目录的路径。
运行任何命令前，请使用以下命令定位脚本：
bash
BIORXIV_SCRIPT=$(find ~/.claude/plugins/cache -name "search" -path "*/biorxiv-search/*/scripts/*" -type f 2>/dev/null | head -1)
然后使用完整路径执行所有命令：
bash
$BIORXIV_SCRIPT "CRISPR基因编辑" 15

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 bioRxiv, 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bioRxiv，我需要你的Valyu API密钥。可前往https://platform.valyu.ai免费获取（赠送10美元额度）"
  2. 用户提供密钥后，运行：
    bash
    scripts/search setup <api-key>
  3. 重试最初的搜索。

Example Flow:

示例流程：

User: Search bioRxiv for CRISPR advances
→ Response: {"success": false, "setup_required": true, ...}
→ Claude asks: "Please provide your Valyu API key from https://platform.valyu.ai"
→ User: "val_abc123..."
→ Claude runs: scripts/search setup val_abc123...
→ Response: {"success": true, "type": "setup", ...}
→ Claude retries: scripts/search "CRISPR advances" 10
→ Success!
用户：搜索bioRxiv中关于CRISPR进展的内容
→ 响应：{"success": false, "setup_required": true, ...}
→ Claude询问："请提供你从https://platform.valyu.ai获取的Valyu API密钥"
→ 用户："val_abc123..."
→ Claude运行：scripts/search setup val_abc123...
→ 响应：{"success": true, "type": "setup", ...}
→ Claude重试：scripts/search "CRISPR进展" 10
→ 成功！

When to Use This Skill

适用场景

  • Finding biology research not yet published in journals
  • Cross-disciplinary life sciences research
  • Rapid access to unpublished experimental data
  • Disease mechanism research
  • Evolutionary and developmental biology studies
  • Ecological research and conservation biology
  • 查找尚未在期刊上发表的生物学研究
  • 跨学科生命科学研究
  • 快速获取未发表的实验数据
  • 疾病机制研究
  • 进化与发育生物学研究
  • 生态学研究与保护生物学

Output Format

输出格式

json
{
  "success": true,
  "type": "biorxiv_search",
  "query": "CRISPR gene editing",
  "result_count": 10,
  "results": [
    {
      "title": "Article Title",
      "url": "https://biorxiv.org/content/...",
      "content": "Full article text with figures...",
      "source": "biorxiv",
      "relevance_score": 0.95,
      "images": ["https://example.com/figure1.jpg"]
    }
  ],
  "cost": 0.025
}
json
{
  "success": true,
  "type": "biorxiv_search",
  "query": "CRISPR基因编辑",
  "result_count": 10,
  "results": [
    {
      "title": "文章标题",
      "url": "https://biorxiv.org/content/...",
      "content": "包含图表的完整文章文本...",
      "source": "biorxiv",
      "relevance_score": 0.95,
      "images": ["https://example.com/figure1.jpg"]
    }
  ],
  "cost": 0.025
}

Processing Results

结果处理

With jq

使用jq

bash
undefined
bash
undefined

Get article titles

获取文章标题

scripts/search "query" 10 | jq -r '.results[].title'
scripts/search "查询内容" 10 | jq -r '.results[].title'

Get URLs

获取URL

scripts/search "query" 10 | jq -r '.results[].url'
scripts/search "查询内容" 10 | jq -r '.results[].url'

Extract full content

提取完整内容

scripts/search "query" 10 | jq -r '.results[].content'
undefined
scripts/search "查询内容" 10 | jq -r '.results[].content'
undefined

Common Use Cases

常见使用场景

Molecular Biology

分子生物学

bash
undefined
bash
undefined

Find recent molecular biology papers

查找近期的分子生物学论文

scripts/search "protein-protein interaction networks" 50
undefined
scripts/search "蛋白质-蛋白质相互作用网络" 50
undefined

Neuroscience

神经科学

bash
undefined
bash
undefined

Search for neuroscience research

搜索神经科学研究

scripts/search "optogenetics in behavior studies" 20
undefined
scripts/search "行为研究中的光遗传学" 20
undefined

Genomics

基因组学

bash
undefined
bash
undefined

Find genomics papers

查找基因组学论文

scripts/search "single cell RNA sequencing analysis" 15
undefined
scripts/search "单细胞RNA测序分析" 15
undefined

Developmental Biology

发育生物学

bash
undefined
bash
undefined

Search for developmental biology papers

搜索发育生物学论文

scripts/search "embryonic stem cell differentiation" 25
undefined
scripts/search "胚胎干细胞分化" 25
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)
所有命令均返回包含
success
字段的JSON：
json
{
  "success": false,
  "error": "错误信息"
}
退出码：
  • 0
    - 成功
  • 1
    - 错误（查看JSON获取详细信息）

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
  • 认证方式: 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

集成到你的项目中

If you're building an AI project and want to integrate bioRxiv Search directly into your application, use the Valyu SDK:
如果你正在构建AI项目，并希望将bioRxiv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-biorxiv"],
    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="你的搜索查询内容",
    included_sources=["valyu/valyu-biorxiv"],
    max_results=20
)

for result in response["results"]:
    print(f"标题: {result['title']}")
    print(f"URL: {result['url']}")
    print(f"内容: {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-biorxiv"],
  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: "你的搜索查询内容",
  includedSources: ["valyu/valyu-biorxiv"],
  maxResults: 20
});

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