Biomedical Literature Search

Search biomedical literature from PubMed and bioRxiv for research papers. Use this skill when: (1) Finding research papers on a specific topic or disease, (2...

Security Scan

The skill's code and instructions match its stated purpose (searching PubMed and bioRxiv) and do not request unrelated credentials, privileged installs, or access to local secrets.

Purpose & Capability

Name/description ask for PubMed and bioRxiv searches; SKILL.md and examples only call NCBI E-utilities and the bioRxiv API and return titles/abstracts/metadata — all directly relevant.

Instruction Scope

Instructions and example Python code only perform HTTP GETs to public APIs (eutils.ncbi.nlm.nih.gov, api.biorxiv.org, biorxiv.org) and parse responses. They do not read local files, access unrelated env vars, or send data to unexpected endpoints. Error-handling/rate-limit notes align with API usage.

Install Mechanism

No install spec (instruction-only plus an example script). This is low risk; example requires the common 'requests' library but no package installation is forced by the skill.

Credentials

The skill requests no environment variables, credentials, or config paths. That is proportionate to the documented functionality (public API queries).

Persistence & Privilege

always is false and the skill does not request permanent presence or modify other skills or system settings. Autonomous invocation is enabled by default but is not combined with any other red flags.

Assessment

This skill is coherent and low-risk: it simply issues HTTP requests to public PubMed and bioRxiv APIs and parses results. Before installing or running, consider: (1) source/homepage is unknown — you may wish to verify the publisher or review the example code; (2) the example script requires outbound network access and the Python 'requests' package — ensure your environment permits outbound HTTP and that you review/approve network calls; (3) NCBI recommends including an email or API key for higher rate limits and abiding by their rate limits (SKILL.md mentions rate limiting); (4) the skill does not request or exfiltrate secrets, but if you adapt it to include private queries or store results, review that behavior. Overall it appears to do what it claims.

Search PubMed and bioRxiv for biomedical research papers with titles and abstracts.

When to Use

• Find research papers on a specific biomedical topic
• Retrieve recent preprints from bioRxiv
• Get paper titles, abstracts, authors, and links
• Literature review for drug discovery or biomedical research

Workflow

PubMed Search (Keyword-based)

import requests
import xml.etree.ElementTree as ET

# Step 1: Search for PMIDs
search_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
params = {"db": "pubmed", "term": "PD-1 inhibitor cancer", "retmax": 10, "retmode": "json"}
response = requests.get(search_url, params=params)
pmids = response.json()["esearchresult"]["idlist"]

# Step 2: Fetch paper details
fetch_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"
response = requests.get(fetch_url, params={"db": "pubmed", "id": ",".join(pmids), "rettype": "abstract", "retmode": "xml"})

bioRxiv Fetch (Date-range based)

import requests

# Fetch papers by date range
url = "https://api.biorxiv.org/details/biorxiv/2026-02-01/2026-03-01"
response = requests.get(url)
papers = response.json()["collection"]

for paper in papers[:5]:
    print(f"Title: {paper['title']}")
    print(f"Abstract: {paper['abstract'][:200]}...")

Expected Outputs

PubMed Results

Returns list of papers with:

Field	Description
title	Paper title
authors	Author list
abstract	Full abstract
doi	DOI identifier
pmid	PubMed ID
date	Publication date
link	PubMed URL

bioRxiv Results

Returns list of papers with:

Field	Description
title	Paper title
authors	Author list
abstract	Full abstract
doi	DOI identifier
date	Publication date
category	Subject category
link	bioRxiv URL

Category Filters for bioRxiv

Category	Description
cancer_biology	Cancer research
immunology	Immune system studies
cell_biology	Cellular processes
bioinformatics	Computational biology
neuroscience	Nervous system research
microbiology	Microbial studies
genomics	Genome analysis

Error Handling

Error	Solution
No PubMed results	Broaden search terms, check spelling
bioRxiv timeout	Reduce date range, retry
Empty abstract	Paper may not have abstract available
Rate limiting	Add delay between requests (NCBI: 3 req/sec)

API References

• PubMed E-utilities: https://www.ncbi.nlm.nih.gov/books/NBK25500/
• bioRxiv API: https://api.biorxiv.org/

Notes

• PubMed: Keyword search via NCBI E-utilities API
• bioRxiv: Date-range or category-based fetch via bioRxiv API
• bioRxiv does not support direct keyword search
• For comprehensive search, use both sources together

See examples/basic_example.py for complete runnable examples.