biorxiv-database

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bioRxiv Database

bioRxiv数据库

A Python toolkit for programmatic access to bioRxiv preprints. Supports comprehensive metadata retrieval with structured JSON output for integration into research workflows.

一个用于程序化访问bioRxiv预印本的Python工具包。支持全面的元数据检索，并输出结构化JSON格式，以便集成到研究工作流中。

Use Cases

使用场景

Query recent preprints by topic or research domain
Monitor publications from specific researchers
Perform systematic literature reviews
Analyze publication trends across time periods
Retrieve citation metadata and DOIs
Download preprint PDFs for text analysis
Filter results by subject category

按主题或研究领域查询近期预印本
监控特定研究人员的出版物
进行系统性文献综述
分析不同时间段的出版趋势
检索引用元数据和DOI
下载预印本PDF用于文本分析
按学科类别筛选结果

Quick Start

快速开始

bash

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bash

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Install dependencies

安装依赖

pip install requests

Search by keywords

按关键词搜索

python scripts/biorxiv_client.py --terms "protein folding" --recent 30 --out results.json

Search by author

按作者搜索

python scripts/biorxiv_client.py --author "Chen" --recent 180

Get specific paper by DOI

通过DOI获取特定论文

python scripts/biorxiv_client.py --doi "10.1101/2024.05.22.594321"

Download PDF

下载PDF

python scripts/biorxiv_client.py --doi "10.1101/2024.05.22.594321" --fetch-pdf paper.pdf

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python scripts/biorxiv_client.py --doi "10.1101/2024.05.22.594321" --fetch-pdf paper.pdf

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Command-Line Options

命令行选项

Option	Description
`-t, --terms`	Search keywords (multiple allowed)
`-a, --author`	Author name to search
`--doi`	Specific DOI to retrieve
`--since`	Start date (YYYY-MM-DD)
`--until`	End date (YYYY-MM-DD)
`--recent`	Search last N days
`-s, --subject`	Subject category filter
`--fields`	Fields to search: title, abstract, authors
`-o, --out`	Output file (default: stdout)
`--max`	Maximum results to return
`--fetch-pdf`	Download PDF (requires --doi)
`-v, --verbose`	Enable debug output

选项	描述
`-t, --terms`	搜索关键词（可输入多个）
`-a, --author`	要搜索的作者姓名
`--doi`	要检索的特定DOI
`--since`	起始日期（YYYY-MM-DD）
`--until`	结束日期（YYYY-MM-DD）
`--recent`	搜索最近N天的内容
`-s, --subject`	学科类别筛选器
`--fields`	要搜索的字段：标题、摘要、作者
`-o, --out`	输出文件（默认：标准输出）
`--max`	要返回的最大结果数
`--fetch-pdf`	下载PDF（需要搭配--doi使用）
`-v, --verbose`	启用调试输出

Programmatic API

程序化API

python

from scripts.biorxiv_client import PreprintClient

client = PreprintClient(debug=True)

python

from scripts.biorxiv_client import PreprintClient

client = PreprintClient(debug=True)

Search by keywords

按关键词搜索

results = client.find_by_terms( terms=["enzyme engineering"], since="2024-01-01", until="2024-12-31", subject="biochemistry" )

Search by author

按作者搜索

papers = client.find_by_author(name="Garcia", since="2023-01-01")

Get paper by DOI

通过DOI获取论文

metadata = client.get_by_doi("10.1101/2024.05.22.594321")

Download PDF

下载PDF

client.fetch_pdf(doi="10.1101/2024.05.22.594321", destination="paper.pdf")

Normalize output

标准化输出

formatted = client.normalize(metadata, include_abstract=True)

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formatted = client.normalize(metadata, include_abstract=True)

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Subject Categories

学科类别

Category	Category
animal-behavior-and-cognition	molecular-biology
biochemistry	neuroscience
bioengineering	paleontology
bioinformatics	pathology
biophysics	pharmacology-and-toxicology
cancer-biology	physiology
cell-biology	plant-biology
clinical-trials	scientific-communication-and-education
developmental-biology	synthetic-biology
ecology	systems-biology
epidemiology	zoology
evolutionary-biology
genetics
genomics
immunology
microbiology

类别	类别
animal-behavior-and-cognition	molecular-biology
biochemistry	neuroscience
bioengineering	paleontology
bioinformatics	pathology
biophysics	pharmacology-and-toxicology
cancer-biology	physiology
cell-biology	plant-biology
clinical-trials	scientific-communication-and-education
developmental-biology	synthetic-biology
ecology	systems-biology
epidemiology	zoology
evolutionary-biology
genetics
genomics
immunology
microbiology

Response Structure

响应结构

json

{
  "query": {
    "terms": ["protein folding"],
    "since": "2024-03-01",
    "until": "2024-09-30",
    "subject": "biophysics"
  },
  "count": 87,
  "papers": [
    {
      "doi": "10.1101/2024.05.22.594321",
      "title": "Example Preprint Title",
      "authors": "Chen L, Patel R, Kim S",
      "corresponding_author": "Chen L",
      "institution": "Research Institute",
      "posted": "2024-05-22",
      "revision": "1",
      "category": "biophysics",
      "license": "cc_by",
      "paper_type": "new results",
      "abstract": "Abstract content here...",
      "pdf_link": "https://www.biorxiv.org/content/10.1101/2024.05.22.594321v1.full.pdf",
      "web_link": "https://www.biorxiv.org/content/10.1101/2024.05.22.594321v1",
      "journal_ref": ""
    }
  ]
}

json

{
  "query": {
    "terms": ["protein folding"],
    "since": "2024-03-01",
    "until": "2024-09-30",
    "subject": "biophysics"
  },
  "count": 87,
  "papers": [
    {
      "doi": "10.1101/2024.05.22.594321",
      "title": "Example Preprint Title",
      "authors": "Chen L, Patel R, Kim S",
      "corresponding_author": "Chen L",
      "institution": "Research Institute",
      "posted": "2024-05-22",
      "revision": "1",
      "category": "biophysics",
      "license": "cc_by",
      "paper_type": "new results",
      "abstract": "Abstract content here...",
      "pdf_link": "https://www.biorxiv.org/content/10.1101/2024.05.22.594321v1.full.pdf",
      "web_link": "https://www.biorxiv.org/content/10.1101/2024.05.22.594321v1",
      "journal_ref": ""
    }
  ]
}

Best Practices

最佳实践

Recommendation	Details
Date ranges	Narrow ranges improve response time. Split large queries into chunks.
Category filters	Use `--subject` to reduce bandwidth and improve precision.
Rate limiting	Built-in 0.5s delay between requests. Add more for bulk operations.
Result caching	Save JSON outputs to avoid redundant API calls.
Version awareness	Preprints may have multiple versions. PDF URLs encode version numbers.
Error checking	Verify `count` in outputs. Zero results may indicate date or connectivity issues.
Debug mode	Use `--verbose` for detailed request/response logging.

建议	详情
日期范围	缩小日期范围可提升响应速度。将大型查询拆分为多个小查询。
类别筛选	使用 `--subject` 选项减少带宽占用并提高检索精度。
请求频率限制	内置0.5秒的请求间隔。批量操作时可增加间隔时间。
结果缓存	保存JSON输出以避免重复调用API。
版本意识	预印本可能有多个版本。PDF链接中包含版本号。
错误检查	验证输出中的 `count` 值。结果为零可能表示日期设置或连接问题。
调试模式	使用 `--verbose` 选项查看详细的请求/响应日志。

Reference Files

参考文件

File	Contents
api-reference.md	Complete bioRxiv REST API documentation
examples.md	Extended code examples and workflow patterns

文件	内容
api-reference.md	完整的bioRxiv REST API文档
examples.md	扩展代码示例和工作流模式