OpenBioMed is an agent platform and toolkit collection for biomedical research and drug discovery, covering areas such as molecular design, protein analysis, and single-cell data analysis. It is intended for researchers and provides the biomedical skills listed in the catalogue as workflows for Claude Code.
Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add PharMolix/OpenBioMed --skill biomedical-literature-searchgit clone --depth 1 https://github.com/PharMolix/OpenBioMedWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/pharmolix/openbiomed/biomedical-literature-search)<a href="https://agentmods.dev/skills/pharmolix/openbiomed/biomedical-literature-search"><img src="https://agentmods.dev/badge/skills/pharmolix/openbiomed/biomedical-literature-search/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/pharmolix/openbiomed/biomedical-literature-search"><img src="https://agentmods.dev/badge/skills/pharmolix/openbiomed/biomedical-literature-search.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector warn
SkillSpector: 2 findings, up to medium
These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →
- medium Data Exfiltration · line 51 Data is being sent to an external URL. This could be legitimate telemetry or data exfiltration. Manual review is recommended.Fix: Verify the destination URL is trusted and necessary. Remove or replace with documented APIs. Ensure no secrets, tokens, or PII are transmitted.
- medium Data Exfiltration · line 110 Data is being sent to an external URL. This could be legitimate telemetry or data exfiltration. Manual review is recommended.Fix: Verify the destination URL is trusted and necessary. Remove or replace with documented APIs. Ensure no secrets, tokens, or PII are transmitted.
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00075 | $0.00918 |
| Opus 5 | $0.00037 | $0.00459 |
| Sonnet 5 | $0.00015 | $0.00184 |
| Haiku 4.5 | $0.00007 | $0.00092 |
Grade A, and why
biomedical-literature-search scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 13d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
response = requests.get(search_url, params=params) How it starts
The opening of the file, as written. The whole thing — 120 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Biomedical Literature Search
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 |
What ships with it
1 file beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 13d ago First seen · 120 lines · 75 tokens per session scan A 07f8f5390132
biomedical-literature-search is a skill published in the GitHub repository PharMolix/OpenBioMed (1,105 stars, last pushed 1mo ago), licensed MIT. It adds 75 tokens to every session and 918 once invoked, about $0.0004 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
Other skills, from other repositories
literature_search
Search PubMed for biomedical research papers by topic, disease, or gene. Use this skill when: (1) User asks to find papers about a topic, (2) User wants recent literature on a disease or gene, (3) User needs citations for research, (4) User asks "papers about X" or "literature on Y".
academic-research
Nested swiss-knife reference for academic literature work — find papers, fetch full-text PDFs, trace citations, write LaTeX manuscripts. First action for any "get me this paper" request: python3 /scripts/fetchpaper.py — walks arXiv → Unpaywall → Europe PMC → CORE → in-house publisher-page extraction…
deep-science-writer
End-to-end scientific research pipeline combining Exa Search, Playwright, deep-research, text-humanization, and iterative Remi peer review.
remi
Strict peer reviewer for academic manuscripts (Nature/Science level). Evaluates 10 aspects without hallucinating citations.
biorxiv-search
Search bioRxiv biology preprints with natural language queries. Semantic search powered by Valyu.
research-agent
Project-first Research pipeline with live gates, source/PDF evidence, claim boundaries, compute and publication controls; includes an optional PubMed/arXiv standard-library helper.