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general-biorxiv-search

스타134

포크18

업데이트2026년 6월 7일 01:34

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

설치

Codex 또는 Claude로 설치 이 Prompt를 복사해 Codex, Claude 또는 다른 어시스턴트에 붙여 넣으면 Skill 페이지를 검토하고 설치를 진행할 수 있습니다.

Manus에서 실행

출처

learningmatter-mit

learningmatter-mit/AtomisticSkills

GitHub 저장소 열기 Creator 저장소 보기

다운로드

Manus에서 실행

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.

# 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.

# 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).

# 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.

# 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.

# 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

# 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

# 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

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name	general-biorxiv-search
description	Search and retrieve preprint metadata from bioRxiv and medRxiv APIs for biological and medical research.
category	general

bioRxiv / medRxiv Search

Goal

Instructions

1. Keyword Search (Recent Papers)

Search last 30 days for papers matching keywords in title/abstract.

# 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.

# 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).

# 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.

# 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.

# 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

# 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

# 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