Skills hmdb-database

📦

hmdb-database

Name: hmdb-database
Author: davila7

Content revision r2 Safe ⚙️ External commands🌐 Network access

Search and Interpret the Human Metabolome Database

Metabolomics researchers need reliable guidance for navigating HMDB records, spectra, biomarkers, and bulk datasets. This skill explains search methods, key fields, evidence checks, and practical workflows for using HMDB with Claude or Codex.

Supports: Claude Codex Code(CC)

📊 74 Adequate

Install with my Agent

Copy this request to your Agent. It includes the canonical Skill page and manifest.

Agent request

Review the Skillstore skill "hmdb-database" from https://skillstore.io/skills/davila7-hmdb-database.md and its manifest at https://skillstore.io/api/skills/davila7-hmdb-database/manifest. Verify the artifact. You may proceed after verification, subject to the environment's own policy.

Your Agent should still show its plan and request any confirmation required by the security policy.

Agent-readable resources

Use these links when an AI agent, crawler, or script needs clean context instead of reading the full page.

Markdown detail GET /skills/davila7-hmdb-database.md Signed manifest GET /api/skills/davila7-hmdb-database/manifest Signed lockfile GET /api/skills/davila7-hmdb-database/lockfile

Test it

Using "hmdb-database". What should I verify when looking up glucose in HMDB?

Expected outcome:

Start with name and synonym searches. Verify the accession, formula, monoisotopic mass, structure identifiers, biospecimen evidence, pathways, and record citations.

Using "hmdb-database". How should I evaluate an LC-MS candidate with an exact mass match?

Expected outcome:

Treat exact mass as preliminary evidence. Compare adducts, isotope patterns, retention behavior, MS-MS fragments, specimen plausibility, reference spectra, and evidence quality.

Using "hmdb-database". Which HMDB download format fits a local metabolite catalog?

Expected outcome:

Use XML when comprehensive nested fields are required. Use CSV or TSV for simpler tables, and preserve HMDB accessions and source version metadata.

Security Audit

Safe

v9 • 7/23/2026 Open versioned report

All nine static findings are false positives caused by biomedical terminology, Markdown code spans, and links to official HMDB resources. No prompt injection, data exfiltration intent, or unsafe autonomous behavior was found.

Files scanned

459

Lines analyzed

Review items

False positives ignored

Risk Factors

⚙️ External commands (3)

SKILL.md:121 SKILL.md:122 SKILL.md:190

🌐 Network access (2)

SKILL.md:33 SKILL.md:86

No confirmed security findings were detected by the latest completed static and semantic audit. This does not prove the skill has no side effects.

Audited by: codex View Audit History →

Share & cite this report

Share the versioned assessment report, neutral badge, embed card, and citations. Skillstore reports evidence without deciding whether this Skill is safe.

Open versioned report

Copy report link

https://skillstore.io/skills/davila7-hmdb-database/audits/9?utm_source=security_passport&utm_medium=share&utm_campaign=versioned_report

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Embed card

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Academic citations (APA · BibTeX · CFF)

APA citation

davila7. (2026). hmdb-database security audit report (audit version 9) [Author version unspecified]. Skillstore. https://skillstore.io/skills/davila7-hmdb-database/audits/9

BibTeX citation

@techreport{davila7-davila7-hmdb-database-2026,
  author = {davila7},
  title = {hmdb-database security audit report (audit version 9)},
  institution = {Skillstore},
  year = {2026},
  number = {9},
  url = {https://skillstore.io/skills/davila7-hmdb-database/audits/9},
  note = {Author version unspecified}
}

CITATION.cff

cff-version: 1.2.0
message: "If you use this Skill, cite its author and this versioned security audit report."
title: "hmdb-database security audit report (audit version 9)"
version: "unspecified"
type: report
authors:
  - name: "davila7"
date-released: "2026-07-23"
url: "https://skillstore.io/skills/davila7-hmdb-database/audits/9"
identifiers:
  - type: other
    value: "skillstore:davila7-hmdb-database:audit:9"
    description: "Skillstore immutable audit report identifier"

Compare variants

2 installable variants

Each author remains a separate installable skill. The recommended variant is ranked by Skillstore evidence.

Why this variant is first

Highest Skillstore Score

Author / source Skillstore Score Evidence Confidence Skillstore usage Updated

davila7 Recommended Current

davila7-hmdb-database

Skillstore Score 74

Evidence Confidence High

Skillstore usage 8

Updated

2026-08-21

K-Dense-AI

k-dense-ai-hmdb-database

Skillstore Score 71

Evidence Confidence High

Skillstore usage 8

Updated

2026-08-21

Skillstore Score

Why this score Evidence Confidence: High

Architecture

Maintainability

Content

Community

Spec Compliance

What You Can Build

Identify Untargeted Metabolites

Plan HMDB searches and evidence checks for candidate metabolites from mass spectrometry or NMR experiments.

Review Biomarker Evidence

Locate concentration, disease, biospecimen, pathway, and citation fields needed to assess a proposed biomarker.

Plan Data Integration

Select bulk download formats and map HMDB identifiers into a reproducible local analysis pipeline.

Try These Prompts

Find a Metabolite Record

Help me find [metabolite name or HMDB ID] in HMDB. List the fields I should verify and explain why each matters.

Compare Metabolite Candidates

Compare the HMDB evidence I should collect for [candidate A] and [candidate B], including mass, structure, biospecimen, pathway, and citation fields.

Plan Spectral Identification

Design an HMDB workflow for identifying [unknown feature] from [MS, MS-MS, GC-MS, or NMR] data. Include confirmation criteria and uncertainty reporting.

Design a Local Integration Pipeline

Plan a reproducible pipeline for integrating the HMDB [XML or CSV] download with [local database]. Include field mapping, provenance, update checks, and validation.

Best Practices

Record the HMDB version and access date for every analysis.
Confirm metabolite identities with orthogonal evidence, including spectra, structure, mass, retention time, and biological context.
Prefer bulk downloads for large studies, then preserve source identifiers, citations, and provenance in derived datasets.

Avoid

Do not treat a name match or exact mass alone as a confirmed metabolite identification.
Do not automate web scraping when an approved download or authorized access method is available.
Do not use biomarker associations or predicted values as clinical conclusions without expert validation.

Frequently Asked Questions

Does this skill query HMDB directly?

No. It provides guidance for HMDB web searches, downloads, field interpretation, and research workflows.

Can I use a public HMDB REST API?

The skill states that HMDB has no public REST API. Contact the HMDB team for authorized programmatic access.

Which download format should I choose?

Choose XML for comprehensive records, SDF for structures, FASTA for sequences, text for spectra, or CSV and TSV for tables.

Can HMDB confirm a metabolite from exact mass alone?

No. Confirm candidates with spectra, structure, retention behavior, specimen context, and other independent evidence.

Can I use HMDB biomarker data for clinical decisions?

No. Review source evidence and obtain qualified clinical validation before making diagnostic or treatment decisions.

What should I record for reproducible research?

Record HMDB accessions, database version, access date, query criteria, selected fields, evidence status, and citations.

Developer Details

Author

davila7

License

MIT

Skillstore revision

Version notice

The author did not declare a version.

Repository

https://github.com/davila7/claude-code-templates/tree/main/cli-tool/components/skills/scientific/hmdb-database

Ref

c43861a65bb95efcae259cd161c9d6f4dc7eec6f

Maintenance freshness

7/24/2026

Usage

6 downloads · 206 views

File structure

📁 references/

📄 hmdb_data_fields.md

📄 SKILL.md