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Agent skill

Biorxiv Database

by aipoch in aipoch/medical-research-skills

Search, retrieve metadata, and download PDFs for bioRxiv preprints; use when you need to discover biology preprints by keywords/authors/date ranges and programmatically fetch their details.

MITAuto-check passedDocuments & Office

Install Biorxiv Database

skills CLI
$ npx skills add aipoch/medical-research-skills --skill biorxiv-database -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install aipoch/medical-research-skills biorxiv-database --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/'scientific-skills/Evidence Insight/biorxiv-database' .claude/skills/biorxiv-database && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
biorxiv-database
GitHub stars
2k
Token cost
~1.4k tokens
SKILL.md length
563 words
Files
4 (incl. scripts, references)
Skills in repo
567
Repo updated
First seen
Licence
MIT

At a glance

Search, retrieve metadata, and download PDFs for bioRxiv preprints; use when you need to discover biology preprints by keywords/authors/date ranges and programmatically fetch their details.

  • Works in 4 steps: Validate the request against the skill… → Select the documented execution path and… → Produce the expected output using the… → …
  • You need to discover biology preprints by keywords/authors/date ranges and programmatically fetch their details
  • SKILL.md covers When to Use, Key Features, Dependencies and Example Usage, plus 8 more sections
  • Runs Python scripts from its folder; calls python and pip

What it does

Biorxiv Database is an agent skill from aipoch/medical-research-skills. Search, retrieve metadata, and download PDFs for bioRxiv preprints; use when you need to discover biology preprints by keywords/authors/date ranges and programmatically fetch their details.

Its SKILL.md is about 1.4k tokens, which your agent loads only when the skill is triggered. The skill folder holds 5 other files, including scripts and reference files (for example `biorxiv-database_audit_result_v2.json`, `references/api_reference.md` and `scripts/biorxiv_search.py`).

It sits in Documents & Office, covering Academic paper search. It works with Python. The repository describes itself as: Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing. The licence is MIT.

When your agent uses it

  • You need to discover biology preprints by keywords/authors/date ranges and programmatically fetch their details
  • Tasks that involve Academic paper search

Example prompts

  • “/biorxiv-database”

Requirements

  • Python 3

Workflow steps

4 steps, taken from the first numbered list in SKILL.md.

  1. Validate the request against the skill boundary and confirm all required inputs are present.
  2. Select the documented execution path and prefer the simplest supported command or procedure.
  3. Produce the expected output using the documented file format, schema, or narrative structure.
  4. Run a final validation pass for completeness, consistency, and safety before returning the result.

What it can do on your machine

Read from SKILL.md and the folder at commit 686e09d. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Ships 1 file in scripts/ (Python), which the agent can run.

    Shell commands in SKILL.md call:

    • python
    • pip

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md. Its commands use pip, which can reach the network depending on how they are called.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Biorxiv Database loads about 1.4k tokens when it runs, and up to ~1.6k if it reads all its reference files. Until then it costs about 52 tokens; SKILL.md has 563 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~52
When it runs · the whole SKILL.md, loaded when a task matches
~1.4k
With references · SKILL.md plus every file in references/, read only if the agent opens them
~1.6k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from aipoch/medical-research-skills at commit 686e09d, republished under its MIT licence (© aipoch). 563 words, ~1,378 tokens.

Download SKILL.mdSave it as .claude/skills/biorxiv-database/SKILL.md (or your agent's skills folder). This skill also uses 3 other files; get the full folder from GitHub.
name
biorxiv-database
description
Search, retrieve metadata, and download PDFs for bioRxiv preprints; use when you need to discover biology preprints by keywords/authors/date ranges and programmatically fetch their details.
license
MIT
author
AIPOCH

Source: https://github.com/aipoch/medical-research-skills

When to Use

  • You need to find recent bioRxiv preprints for a topic (e.g., "CRISPR") within a specific time window (last N days).
  • You want to build a literature monitoring pipeline that periodically searches bioRxiv and collects results.
  • You need structured preprint metadata (title, abstract, DOI, authors) for downstream analysis or indexing.
  • You want to automatically download full-text PDFs for a set of preprints identified by DOI.
  • You need a simple CLI tool to quickly query bioRxiv without writing additional code.

Key Features

  • Keyword-based search with a configurable lookback window (days).
  • Structured metadata retrieval in JSON-like dictionaries (e.g., Title, Abstract, DOI, Authors).
  • PDF download by DOI to a local file path.
  • Scriptable Python API via BioRxivSearcher.
  • Command-line interface for quick searches.

Dependencies

  • Python 3.8+
  • requests>=2.25.0

Example Usage

Install
bash
pip install requests
Python (end-to-end)
python
from scripts.biorxiv_search import BioRxivSearcher

def main():
    searcher = BioRxivSearcher()

    # 1) Search for papers (e.g., "CRISPR" in the last 30 days)
    papers = searcher.search_by_keywords(["CRISPR"], days_back=30)
    print(f"Found {len(papers)} papers")

    # 2) Print basic metadata and download the first PDF (if available)
    if papers:
        first = papers[0]
        print("First result:")
        print(f"  Title: {first.get('title')}")
        print(f"  DOI:   {first.get('doi')}")
        print(f"  Authors: {first.get('authors')}")

        out_path = "paper.pdf"
        print(f"Downloading PDF to: {out_path}")
        searcher.download_pdf(first["doi"], out_path)

if __name__ == "__main__":
    main()
CLI
bash
python scripts/biorxiv_search.py "CRISPR" 30

Implementation Details

  • Core entry point: BioRxivSearcher in scripts/biorxiv_search.py.
  • Search parameters:
    • keywords: list of strings used to match relevant preprints.
    • days_back: integer lookback window; the search is constrained to items within the last days_back days.
  • Returned data shape: search results are returned as a list of dictionaries containing key fields such as title, abstract, doi, and authors (exact keys depend on the API response mapping).
  • PDF download:
    • Uses the DOI from a search result to resolve and fetch the corresponding PDF.
    • Writes the downloaded content to the provided output file path.
  • API reference: See references/api_reference.md for endpoint/field details and response formats.

When Not to Use

  • Do not use this skill when the required source data, identifiers, files, or credentials are missing.
  • Do not use this skill when the user asks for fabricated results, unsupported claims, or out-of-scope conclusions.
  • Do not use this skill when a simpler direct answer is more appropriate than the documented workflow.

Required Inputs

  • A clearly specified task goal aligned with the documented scope.
  • All required files, identifiers, parameters, or environment variables before execution.
  • Any domain constraints, formatting requirements, and expected output destination if applicable.
Show full SKILL.md (243 more words)Show less
  1. Validate the request against the skill boundary and confirm all required inputs are present.
  2. Select the documented execution path and prefer the simplest supported command or procedure.
  3. Produce the expected output using the documented file format, schema, or narrative structure.
  4. Run a final validation pass for completeness, consistency, and safety before returning the result.

Output Contract

  • Return a structured deliverable that is directly usable without reformatting.
  • If a file is produced, prefer a deterministic output name such as biorxiv_database_result.md unless the skill documentation defines a better convention.
  • Include a short validation summary describing what was checked, what assumptions were made, and any remaining limitations.

Validation and Safety Rules

  • Validate required inputs before execution and stop early when mandatory fields or files are missing.
  • Do not fabricate measurements, references, findings, or conclusions that are not supported by the provided source material.
  • Emit a clear warning when credentials, privacy constraints, safety boundaries, or unsupported requests affect the result.
  • Keep the output safe, reproducible, and within the documented scope at all times.

Failure Handling

  • If validation fails, explain the exact missing field, file, or parameter and show the minimum fix required.
  • If an external dependency or script fails, surface the command path, likely cause, and the next recovery step.
  • If partial output is returned, label it clearly and identify which checks could not be completed.

Quick Validation

Run this minimal verification path before full execution when possible:

bash
python scripts/biorxiv_search.py --help

Expected output format:

text
Result file: biorxiv_database_result.md
Validation summary: PASS/FAIL with brief notes
Assumptions: explicit list if any

© aipoch, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 3 other files (scripts, references) in scientific-skills/Evidence Insight/biorxiv-database of aipoch/medical-research-skills.

  • SKILL.md
  • biorxiv-database_audit_result_v2.json
  • references/api_reference.md
  • scripts/biorxiv_search.py

Open the folder on GitHubat commit 686e09d

Compare with similar skills

Biorxiv Database next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Biorxiv Database compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Biorxiv Database this skillaipoch/medical-research-skills2k—~1.4kAutomated safety check: PassMIT
Literature PDF OCR Library BuilderLigphiDonk/Oh-my--paper738—~1.1kAutomated safety check: PassMIT
Nature Paper2pptCitrus-bit/Anaxa1201 repos~5.9kAutomated safety check: PassMIT
Ref Downloaderltczding-gif/ref-downloader139—~5.9kAutomated safety check: PassMIT
Agent Survey CorpusWILLOSCAR/research-units-pipeline-skills513—~628Automated safety check: PassNone
Papers Skillmajiayu000/claude-skill-registry6662 repos~2.1kAutomated safety check: PassMIT

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Works with

Categories

Questions about Biorxiv Database

What does Biorxiv Database do?

Search, retrieve metadata, and download PDFs for bioRxiv preprints; use when you need to discover biology preprints by keywords/authors/date ranges and programmatically fetch their details. Biorxiv Database is an agent skill from aipoch/medical-research-skills. Search, retrieve metadata, and download PDFs for bioRxiv preprints; use when you need to discover biology preprints by keywords/authors/date ranges and programmatically fetch their details.

When should I use Biorxiv Database?

Biorxiv Database fits situations like: you need to discover biology preprints by keywords/authors/date ranges and programmatically fetch their details; tasks that involve Academic paper search.

How do I install Biorxiv Database in Claude Code?

Run `npx skills add aipoch/medical-research-skills --skill biorxiv-database -a claude-code`. Or copy the skill folder (scientific-skills/Evidence Insight/biorxiv-database in aipoch/medical-research-skills) into .claude/skills/biorxiv-database in your project. Claude Code loads it when a task matches its description.

How do I install Biorxiv Database in Codex?

Run `npx skills add aipoch/medical-research-skills --skill biorxiv-database -a codex`. Or copy the skill folder (scientific-skills/Evidence Insight/biorxiv-database in aipoch/medical-research-skills) into .agents/skills/biorxiv-database in your project. Codex loads it when a task matches its description.

Can I use Biorxiv Database in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add aipoch/medical-research-skills --skill biorxiv-database -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/biorxiv-database, .gemini/skills/biorxiv-database, .github/skills/biorxiv-database and .opencode/skills/biorxiv-database in your project.

What does Biorxiv Database need to run?

Going by SKILL.md and its folder, Biorxiv Database needs Python for the scripts in its folder and the command-line tools its instructions call (python and pip). Our summary lists: Python 3.

Does Biorxiv Database access the network?

SKILL.md contains no URLs. Its commands use pip, which can reach the network depending on how they are called. This is read from the text; nothing was executed.

Is Biorxiv Database safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Biorxiv Database use?

Biorxiv Database is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Biorxiv Database use?

About 1.4k tokens (SKILL.md is roughly 5.5k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 212 tokens, read only when the agent opens those files.

What are the alternatives to Biorxiv Database?

Skills that share tags, products or a category with Biorxiv Database: Literature PDF OCR Library Builder (LigphiDonk/Oh-my--paper, 738 stars), Nature Paper2ppt (Citrus-bit/Anaxa, 120 stars), Ref Downloader (ltczding-gif/ref-downloader, 139 stars) and Agent Survey Corpus (WILLOSCAR/research-units-pipeline-skills, 513 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Biorxiv Database?

aipoch (a GitHub organization) maintains it in aipoch/medical-research-skills, which has 1,974 GitHub stars. The repository holds 567 skills in this directory. The repository was last updated on September 17, 2026.

Source: aipoch/medical-research-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.