# General Biorxiv Search

> Search and retrieve preprint metadata from bioRxiv and medRxiv APIs for biological and medical research.

- **Type:** Skill
- **Install:** `agentstack add skill-learningmatter-mit-atomisticskills-general-biorxiv-search`
- **Verified:** Yes — security-reviewed for prompt injection and unsafe behavior
- **Seller:** [learningmatter-mit](https://agentstack.voostack.com/s/learningmatter-mit)
- **Installs:** 0
- **Category:** [Search](https://agentstack.voostack.com/c/search)
- **Latest version:** 0.1.0
- **License:** MIT
- **Upstream author:** [learningmatter-mit](https://github.com/learningmatter-mit)
- **Source:** https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/general-biorxiv-search
- **Website:** https://arxiv.org/abs/2605.24002

## Install

```sh
agentstack add skill-learningmatter-mit-atomisticskills-general-biorxiv-search
```

Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent.

## About

# bioRxiv / medRxiv Search

## Goal
Search and retrieve preprint metadata (title, authors, abstract, DOI, category, etc.) from bioRxiv and medRxiv using the official REST API. Supports keyword filtering, subject category filtering, date-range search, and DOI lookup.

## Instructions

### 1. Keyword Search (Recent Papers)
Search last 30 days for papers matching keywords in title/abstract.

```bash
# Env: base-agent
python .agents/skills/general-biorxiv-search/scripts/biorxiv_search.py "protein folding" --max_results 5 --output protein_folding.json
```

### 2. Date Range Search
Retrieve preprints posted in a specific date range, with optional keyword/category filter.

```bash
# Env: base-agent
python .agents/skills/general-biorxiv-search/scripts/biorxiv_search.py "CRISPR" --start 2025-01-01 --end 2025-06-01 --max_results 10 --output crispr_2025.json
```

### 3. Category Filter
Filter by subject category (use shortcuts or full names).

```bash
# Env: base-agent
python .agents/skills/general-biorxiv-search/scripts/biorxiv_search.py --category neuroscience --days 14 --max_results 10
```

**Supported Category Shortcuts:**
- `biochemistry`, `bioinformatics`, `biophysics`
- `cancer` → cancer_biology
- `cell-bio` → cell_biology
- `dev-bio` → developmental_biology
- `ecology`, `epidemiology`, `evolution`
- `genetics`, `genomics`, `immunology`
- `microbiology`, `molecular-bio` → molecular_biology
- `neuroscience`, `pharmacology`, `physiology`
- `plant-bio` → plant_biology
- `synthetic-bio` → synthetic_biology
- `systems-bio` → systems_biology

### 4. Search medRxiv
Use `--server medrxiv` for medical preprints.

```bash
# Env: base-agent
python .agents/skills/general-biorxiv-search/scripts/biorxiv_search.py "COVID vaccine efficacy" --server medrxiv --max_results 5 --output covid_vaccine.json
```

### 5. DOI Lookup
Retrieve metadata for a specific preprint by DOI.

```bash
# Env: base-agent
python .agents/skills/general-biorxiv-search/scripts/biorxiv_search.py --doi 10.1101/2021.01.01.000000 --output paper.json
```

## Examples

### Recent Neuroscience Papers
```bash
# Env: base-agent
python .agents/skills/general-biorxiv-search/scripts/biorxiv_search.py --category neuroscience --days 7 --max_results 5
```

### Genomics Papers with Keyword Filter
```bash
# Env: base-agent
python .agents/skills/general-biorxiv-search/scripts/biorxiv_search.py "single cell sequencing" --category genomics --start 2024-01-01 --end 2024-12-31 --max_results 10 --output scrna_2024.json
```

## Constraints
- **No official rate limit** specified by bioRxiv API; script includes 0.5s delay per request as courtesy.
- **Pagination**: API returns 30 results per page; script paginates automatically up to `--max_results`.
- **Keyword filtering**: Done client-side (API lacks full-text search); date range must be broad enough to surface relevant papers.
- **Environment**: Requires `base-agent` conda environment.
- **Dependencies**: Uses `requests`.
- **Metadata fields**: DOI, URL, title, authors, abstract, date, category, server, version, license, published journal (if available).

---

**Author:** mlederbauer
**Contact:** [GitHub @learningmatter-mit](https://github.com/learningmatter-mit)

## Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

- **Author:** [learningmatter-mit](https://github.com/learningmatter-mit)
- **Source:** [learningmatter-mit/AtomisticSkills](https://github.com/learningmatter-mit/AtomisticSkills)
- **License:** MIT
- **Homepage:** https://arxiv.org/abs/2605.24002

Install and usage instructions live in the source repository linked above.

## Pricing

- **Free** — Free

## Security capabilities

Automated source analysis of v0.1.0 — what this tool can access:

- **Network access:** no
- **Filesystem access:** no
- **Shell / process execution:** no
- **Environment & secrets:** no
- **Dynamic code execution:** no

*"Yes" means the capability is present in the source — more access means more to trust, not that it is unsafe.*


## Versions

- **0.1.0** — security scan: passed — Imported from the upstream source.

## Links

- Listing page: https://agentstack.voostack.com/l/skill-learningmatter-mit-atomisticskills-general-biorxiv-search
- Seller: https://agentstack.voostack.com/s/learningmatter-mit
- Browse the marketplace: https://agentstack.voostack.com/browse

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Listed on AgentStack — the marketplace for AI agent skills and MCP servers. Every listing is security-reviewed. Creators keep 70%.