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 AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-hmdbgit clone --depth 1 https://github.com/AlterLab-IEU/AlterLab-Academic-SkillsWrote 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/alterlab-ieu/alterlab-academic-skills/alterlab-hmdb)<a href="https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-hmdb"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-hmdb/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/alterlab-ieu/alterlab-academic-skills/alterlab-hmdb"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-hmdb.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 | $0.01944 |
| Opus 5 | $0.00044 | $0.00972 |
| Sonnet 5 | $0.00018 | $0.00389 |
| Haiku 4.5 | $0.00009 | $0.00194 |
Grade A, and why
alterlab-hmdb 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 5d 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.
allowed-tools: Read WebFetch Bash(curl:*) Bash(python:*) How it starts
The opening of the file, as written. The whole thing — 203 lines — stays where its author put it; the contents beside it link to each section on GitHub.
HMDB Database
Overview
The Human Metabolome Database (HMDB) is a comprehensive, freely available resource containing detailed information about small molecule metabolites found in the human body.
Scripts
scripts/query_hmdb.py — fetch and parse an HMDB metabolite XML record by accession (stdlib only, JSON to stdout):
python scripts/query_hmdb.py HMDB0000001 # full accession
python scripts/query_hmdb.py 1 # bare number (zero-padded automatically)
Note: HMDB serves no public REST API and may rate-limit/block automated fetches; for bulk work download the XML/SDF dumps from https://www.hmdb.ca/downloads.
When to Use This Skill
This skill should be used when performing metabolomics research, clinical chemistry, biomarker discovery, or metabolite identification tasks.
Database Contents
HMDB version 5.0 (released 2022; latest major version as of mid-2026) contains:
- 220,945 metabolite entries covering both water-soluble and lipid-soluble compounds (the v5.0 paper reported 217,920; the live site count grows with curation)
- ~8,600 protein sequences for enzymes and transporters involved in metabolism
- 130+ data fields per metabolite including:
- Chemical properties (structure, formula, molecular weight, InChI, SMILES)
- Clinical data (biomarker associations, diseases, normal/abnormal concentrations)
- Biological information (pathways, reactions, locations)
- Spectroscopic data (NMR, MS, MS-MS spectra)
- External database links (KEGG, PubChem, MetaCyc, ChEBI, PDB, UniProt, GenBank)
Core Capabilities
1. Web-Based Metabolite Searches
Access HMDB through the web interface at https://www.hmdb.ca/ for:
Text Searches:
- Search by metabolite name, synonym, or identifier (HMDB ID)
- Example HMDB IDs: HMDB0000001, HMDB0001234
- Search by disease associations or pathway involvement
- Query by biological specimen type (urine, serum, CSF, saliva, feces, sweat)
Structure-Based Searches:
- Use ChemQuery for structure and substructure searches
- Search by molecular weight or molecular weight range
- Use SMILES or InChI strings to find compounds
What ships with it
3 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.
- 5d ago First seen · 203 lines · 89 tokens per session scan A d701e7f608b3
alterlab-hmdb is a skill published in the GitHub repository AlterLab-IEU/AlterLab-Academic-Skills (66 stars, last pushed 6d ago), licensed MIT. It adds 89 tokens to every session and 1,944 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 2026-09-05.
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