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bioRxiv access using API with support of time period and category

Name: bioRxiv access using API with support of time period and category
Author: aquaskyline

作者 aquaskyline · GitHub ↗ · v1.0.0 · MIT-0

cross-platform ✓ 安全检测通过

284

总下载

当前安装

版本数

在 OpenClaw 中安装

/install biorxiv-openclaw-skill

功能描述

Access and retrieve biology preprints from bioRxiv by category and date range, including paper metadata without needing authentication.

使用说明 (SKILL.md)

bioRxiv Skill

This skill provides access to the bioRxiv preprint repository using the official bioRxiv API.

When to Use

User asks for recent biology preprints
User wants papers from specific bioRxiv categories (bioinformatics, genomics, etc.)
User needs paper metadata (title, authors, DOI, date, category)
User asks for preprints from a specific date range

Quick Start

List Available Collections

python scripts/biorxiv.py --list

Fetch Recent Papers

# Default: bioinformatics papers
python scripts/biorxiv.py --collection bioinformatics

# Other collections
python scripts/biorxiv.py --collection genomics
python scripts/biorxiv.py --collection neuroscience
python scripts/biorxiv.py --collection microbiology

# Specific date range
python scripts/biorxiv.py --collection bioinformatics --start 2026-03-01 --end 2026-03-09

# Limit results
python scripts/biorxiv.py --collection bioinformatics --limit 10

Output as JSON

python scripts/biorxiv.py --collection bioinformatics --json

Available Collections

bioinformatics
genomics
molecular-biology
cell-biology
genetics
evolutionary-biology
ecology
neuroscience
plant-biology
microbiology
immunology
cancer-biology
biochemistry
biophysics
structural-biology
systems-biology
synthetic-biology
developmental-biology
computational-biology

API Notes

Official bioRxiv API

Base URL: https://api.biorxiv.org/details/biorxiv/{start_date}/{end_date}/{cursor}
No authentication required
Returns up to 100 papers per call
Supports category filtering via query parameter

API Endpoints

/details/biorxiv/[start]/[end]/[cursor] — Paper metadata
/pub/[start]/[end]/[cursor] — Published articles only

Usage Patterns

Summarize Recent Papers

Fetch papers from desired collection
Parse titles and abstracts
Group by theme if multiple
Provide concise summary

Find Papers by Topic

Search across multiple relevant collections
Filter by keywords in titles
Return most relevant results

安全使用建议

This skill appears coherent and low-risk: it only makes HTTPS requests to the public bioRxiv API and prints results, and it asks for no credentials or installs. Before installing: (1) Review the minor functional mismatches (the script defaults start_date to 2020-01-01 which may return a very large result set; if you expect 'last N days' behavior, the script may not do that), (2) Verify the collections/category names you need—the code maps hyphenated names to underscore API categories, which is fine but worth checking against the live API, (3) Run the script in a sandbox or with network monitoring if you want to confirm its outbound calls (it should call only api.biorxiv.org), and (4) If you need abstracts or summarization, note the shipped script may not return abstracts and additional processing would be required. Overall the skill is consistent with its stated purpose.

功能分析

Type: OpenClaw Skill Name: biorxiv-openclaw-skill Version: 1.0.0 The skill bundle is a legitimate tool for fetching scientific preprints from the official bioRxiv API. The Python script (scripts/biorxiv.py) uses standard libraries to perform HTTP GET requests and process JSON data without any evidence of malicious intent, data exfiltration, or unauthorized system access.

能力评估

ℹ Purpose & Capability

The name/description (fetch bioRxiv preprints by category/date) matches the included script and documentation; no credentials or installs are requested. Minor inconsistencies: SKILL.md and the script disagree about default date behavior (SKILL.md implies recent/last-N-days usage, while the script defaults to start_date="2020-01-01" if none provided), and the references/docs use slightly different example endpoint forms. These are implementation or documentation mismatches, not evidence of malicious intent.

ℹ Instruction Scope

Runtime instructions simply call the included Python script to query the public API and print JSON/text. The SKILL.md suggests parsing abstracts and grouping themes, but the shipped script returns title/author/doi/date/category/version and does not explicitly fetch or summarize abstracts—this is a functional mismatch rather than a security issue. The instructions do not ask the agent to read unrelated files, environment variables, or contact unknown endpoints.

✓ Install Mechanism

No install spec is provided (instruction-only with an included script). No external downloads, package installs, or archive extraction are performed by the skill.

✓ Credentials

The skill requests no environment variables or credentials. The Python script makes outbound HTTPS requests to api.biorxiv.org (the declared public API) and formats DOI links; it does not access secrets or local config files.

✓ Persistence & Privilege

always is false and the skill does not request persistent/system-wide changes. The default model-invocation behavior (agent may call the skill autonomously) is unchanged and appropriate for this kind of integration.

如何使用

确保已安装 OpenClaw（本地或 Docker 部署）
在对话框中输入安装命令：/install biorxiv-openclaw-skill
安装完成后，直接呼叫该 Skill 的名称或使用 /biorxiv-openclaw-skill 触发
根据 Skill 的参数说明提供必要输入，即可获得结构化输出

版本历史

v1.0.0

bio version 1.0.0 - Initial release with core functionality for writing and managing professional bios across various platforms and contexts. - Adapts bios for specific uses (LinkedIn, speaker introduction, website, press kit, conference, etc.), maintaining consistent voice and narrative. - Integrates credentials into narrative rather than lists, and generates multiple opening sentence options matched to context. - Tracks and prompts for bio updates when significant career changes occur. - Added: SKILL.md, references/api.md, scripts/biorxiv.py; Removed: skill.md.

元数据

Slug biorxiv-openclaw-skill

版本 1.0.0

许可证 MIT-0

累计安装 0

当前安装数 0

历史版本数 1

常见问题