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 chembl-querygit 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/chembl-query)<a href="https://agentmods.dev/skills/pharmolix/openbiomed/chembl-query"><img src="https://agentmods.dev/badge/skills/pharmolix/openbiomed/chembl-query/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/chembl-query"><img src="https://agentmods.dev/badge/skills/pharmolix/openbiomed/chembl-query.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector pass
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 | $0.00069 | $0.01277 |
| Opus 5 | $0.00034 | $0.00639 |
| Sonnet 5 | $0.00014 | $0.00255 |
| Haiku 4.5 | $0.00007 | $0.00128 |
Grade A, and why
chembl-query scanned grade A with 0 findings 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 11d 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.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 164 lines — stays where its author put it; the contents beside it link to each section on GitHub.
ChEMBL Query
Query ChEMBL database for bioactivity data on drug-like compounds.
When to Use
- Find compounds active against a protein target (target-based search)
- Get bioactivity profile for a molecule (molecule-based search)
- Find drugs for a disease indication (indication-based search)
Workflow
Use Case 1: Target-Based Compound Search
Find compounds with activity against a protein target.
from open_biomed.tools.tool_registry import TOOLS
tool = TOOLS["chembl_query"]
# Search by target name
results, _ = tool.run(
query_type="target",
target_name="EGFR",
standard_type="IC50",
standard_value_lte=100, # nM
limit=20
)
# Or search by UniProt ID
results, _ = tool.run(
query_type="target",
uniprot_id="P00533",
standard_type="IC50",
limit=20
)
Use Case 2: Molecule Bioactivity Profile
Get all known targets and activity data for a compound.
# Search by molecule name
results, _ = tool.run(
query_type="molecule",
molecule_name="imatinib",
limit=50
)
# Or search by SMILES
results, _ = tool.run(
query_type="molecule",
smiles="CC(=O)Oc1ccccc1C(=O)O",
limit=20
)
# Or search by ChEMBL ID
results, _ = tool.run(
query_type="molecule",
chembl_id="CHEMBL25",
limit=20
)
Use Case 3: Disease/Indication-Based Drug Search
Find drugs studied for a specific disease.
# Find all drugs for diabetes
results, _ = tool.run(
query_type="indication",
disease="diabetes",
limit=50
)
# Filter for approved drugs only (max_phase=4)
results, _ = tool.run(
query_type="indication",
disease="diabetes",
max_phase=4, # Approved drugs only
limit=20
)
Expected Outputs
| Query Type | Output Fields |
|---|---|
| Target | molecule_chembl_id, molecule_name, target_chembl_id, target_name, standard_type, standard_value, standard_units, pchembl_value |
| Molecule | molecule_chembl_id, molecule_name, target_chembl_id, target_name, target_organism, standard_type, standard_value, standard_units, pchembl_value |
| Indication | molecule_chembl_id, molecule_name, indication, max_phase_for_ind, phase_description |
What ships with it
2 files 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.
- 11d ago First seen · 164 lines · 69 tokens per session scan A aff17526a3c1
chembl-query is a skill published in the GitHub repository PharMolix/OpenBioMed (1,106 stars, last pushed 1mo ago), licensed MIT. It adds 69 tokens to every session and 1,277 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
Other skills, from other repositories
chembl-bioactivity
Use this Skill to query ChEMBL for bioactivity data: target lookup, IC50/Ki retrieval, activity cliffs, SAR tables, and pChEMBL-normalized values.
compound-profile
Generate comprehensive compound profiles including structure, properties, bioactivity, and development status. Use for drug analysis, SAR studies, and competitive profiling. Keywords: compound, drug, molecule, structure, SMILES, bioactivity, IC50.
molecular-rag
Retrieve structurally similar compounds with known properties from ChEMBL/ZINC to ground predictions and inform optimization. Based on MolRAG (Xian 2025, ACL).
chembl-search
Search ChEMBL bioactive molecules database with natural language queries. Find compounds and assay data with Valyu semantic search.
chembl-search
Search ChEMBL bioactive molecules database with natural language queries. Find compounds and assay data with Valyu semantic search.
design-mcp-server
Design the tool surface, resources, and service layer for a new MCP server. Use when starting a new server, planning a major feature expansion, or when the user describes a domain/API they want to expose via MCP. Produces a design doc at docs/design.md that drives implementation.