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 molecule-biochemical-significance-query-biot5git 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/molecule-biochemical-significance-query-biot5)<a href="https://agentmods.dev/skills/pharmolix/openbiomed/molecule-biochemical-significance-query-biot5"><img src="https://agentmods.dev/badge/skills/pharmolix/openbiomed/molecule-biochemical-significance-query-biot5/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/molecule-biochemical-significance-query-biot5"><img src="https://agentmods.dev/badge/skills/pharmolix/openbiomed/molecule-biochemical-significance-query-biot5.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 | $0.00089 | $0.00787 |
| Opus 5 | $0.00044 | $0.00394 |
| Sonnet 5 | $0.00018 | $0.00157 |
| Haiku 4.5 | $0.00009 | $0.00079 |
Grade A, and why
molecule-biochemical-significance-query-biot5 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 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.
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 — 107 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Molecule Biochemical Significance Query
Query a molecule's biochemical significance using BioT5 multi-modal model.
When to Use
- User asks about a molecule's biological roles or functions
- User wants to understand what a molecule is used for
- User requests natural language description of molecular properties
- User asks about a molecule's metabolic or chemical significance
Workflow
Step 1: Create Molecule
Create molecule from SMILES string.
from open_biomed.data import Molecule
molecule = Molecule.from_smiles("CCCCCCCc1ccco1") # Heptylfuran
Step 2: Ask About Biochemical Significance
Use the molecule_question_answering tool with the default question.
from open_biomed.data import Text
from open_biomed.tools.tool_registry import TOOLS
qa_tool = TOOLS["molecule_question_answering"]
question = Text.from_str(
"I am interested in understanding the molecule biochemical significance; "
"can you describe its roles in biology and chemistry?"
)
outputs, _ = qa_tool.run(molecule=molecule, text=question)
print(outputs[0]) # Natural language answer
Alternative: Get Molecule by Name
If you have a molecule name instead of SMILES:
from open_biomed.tools.tool_registry import TOOLS
# Get molecule from name
name_tool = TOOLS["molecule_name_request"]
molecules, _ = name_tool.run("aspirin")
molecule = molecules[0]
# Then proceed with QA
qa_tool = TOOLS["molecule_question_answering"]
question = Text.from_str(
"I am interested in understanding the molecule biochemical significance; "
"can you describe its roles in biology and chemistry?"
)
outputs, _ = qa_tool.run(molecule=molecule, text=question)
Expected Outputs
| Output | Description |
|---|---|
| Natural language text | Description of biochemical roles, applications, and significance |
Example Outputs
| Molecule | Output |
|---|---|
CCCCCCCc1ccco1 (heptylfuran) |
"flavouring agent; fragrance; metabolite" |
CC(=O)OC1=CC=CC=C1C(=O)O (aspirin) |
"analgesic; anti-inflammatory; antipyretic" |
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.
- 13d ago First seen · 107 lines · 89 tokens per session scan A 3830c4c88d3c
molecule-biochemical-significance-query-biot5 is a skill published in the GitHub repository PharMolix/OpenBioMed (1,105 stars, last pushed 1mo ago), licensed MIT. It adds 89 tokens to every session and 787 once invoked, about $0.0004 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.
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