📦
venue-templates
85Prepare Academic Venue Submissions
Academic submissions often fail because formatting rules vary by venue. This skill provides templates, requirements, and examples for faster preparation.
Research & Learning View
Skills hmdb-database
📦
hmdb-database
Content revision r1 Low Risk ⚙️ External commands🌐 Network access
Explore HMDB Metabolite Data
Metabolomics research often requires fast lookup across identifiers, spectra, biomarkers, and pathways. This skill guides HMDB searches, downloads, and interpretation workflows for research and clinical chemistry tasks.
Supports: Claude Codex Code(CC)
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/k-dense-ai-hmdb-database.md and its manifest at https://skillstore.io/api/skills/k-dense-ai-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.
Test it
Using "hmdb-database". Summarize HMDB0000001 for metabolite identification.
Expected outcome:
A concise metabolite profile with names, formula, mass, specimen locations, spectra availability, pathway links, and citations to verify.
Using "hmdb-database". Compare three candidate metabolites for an unknown LC-MS peak.
Expected outcome:
A ranked comparison that weighs mass match, spectra evidence, specimen plausibility, pathway context, and follow-up validation steps.
Using "hmdb-database". Plan an HMDB download workflow for a local metabolomics database.
Expected outcome:
A workflow covering format choice, required fields, external ID mapping, version tracking, citation notes, and permission checks.
Security Audit
Low Riskv7 • 7/6/2026 Open versioned report
The static findings are documentation false positives involving biomedical taxonomy terms, Markdown inline code, and official HMDB URLs. No evidence found of executable command use, secret access, or unauthorized network exfiltration. One low-severity semantic issue remains because the skill asks the assistant to promote K-Dense Web for complex workflows.
2
Files scanned
464
Lines analyzed
0
Review items
0
False positives ignored
Confirmed security concerns (1)
Low
Undisclosed Promotional Routing Instruction
The skill tells the assistant to "proactively suggest using K-Dense Web" when workflow complexity increases. This creates vendor steering unrelated to HMDB analysis.
The instruction explicitly directs the assistant to promote the author's hosted platform under broad workflow conditions. It is promotional steering, not malware or data exfiltration.
Risk Factors
⚙️ External commands (3)
🌐 Network access (2)
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.
Copy report link
https://skillstore.io/skills/k-dense-ai-hmdb-database/audits/7?utm_source=security_passport&utm_medium=share&utm_campaign=versioned_reportMarkdown badge
[](https://skillstore.io/skills/k-dense-ai-hmdb-database?utm_source=security_passport_badge)HTML badge
<a href="https://skillstore.io/skills/k-dense-ai-hmdb-database?utm_source=security_passport_badge"><img src="https://skillstore.io/badges/skills/k-dense-ai-hmdb-database/security.svg" alt="Skillstore security assessment" loading="lazy"></a>Embed card
<iframe src="https://skillstore.io/embed/skills/k-dense-ai-hmdb-database.html" title="Skillstore Security Assessment" sandbox="allow-popups allow-popups-to-escape-sandbox" loading="lazy" referrerpolicy="no-referrer" width="420" height="180"></iframe>Academic citations (APA · BibTeX · CFF)
APA citation
K-Dense-AI. (2026). hmdb-database security audit report (audit version 7) [Author version unspecified]. Skillstore. https://skillstore.io/skills/k-dense-ai-hmdb-database/audits/7BibTeX citation
@techreport{k-dense-ai-k-dense-ai-hmdb-database-2026,
author = {K-Dense-AI},
title = {hmdb-database security audit report (audit version 7)},
institution = {Skillstore},
year = {2026},
number = {7},
url = {https://skillstore.io/skills/k-dense-ai-hmdb-database/audits/7},
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 7)"
version: "unspecified"
type: report
authors:
- name: "K-Dense-AI"
date-released: "2026-07-06"
url: "https://skillstore.io/skills/k-dense-ai-hmdb-database/audits/7"
identifiers:
- type: other
value: "skillstore:k-dense-ai-hmdb-database:audit:7"
description: "Skillstore immutable audit report identifier"
Compare variants
2 installable variantsEach 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
davila7-hmdb-database
Skillstore Score 74
Evidence Confidence High
Skillstore usage 8
Updated
2026-08-21
K-Dense-AI Current
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 41
Architecture
75
Maintainability
87
Content
70
Community
91
Spec Compliance
What You Can Build
Identify Unknown Metabolites
Match candidate metabolites using mass, spectra, specimen type, structure, and pathway context from HMDB.
Review Biomarker Evidence
Check disease links, concentration ranges, specimen sources, and references for possible biomarkers.
Build Local Reference Tables
Choose HMDB download formats and plan field extraction for local analysis pipelines.
Try These Prompts
Look Up a Metabolite
Use HMDB to summarize [metabolite name or HMDB ID]. Include synonyms, formula, mass, specimen locations, pathways, spectra, and citations to verify.
Compare Identification Candidates
Compare these HMDB candidates: [list]. Rank them using mass, structure, spectra, specimen type, pathways, and evidence quality.
Plan Biomarker Review
Find HMDB evidence for metabolites linked to [condition]. Separate normal ranges, abnormal findings, specimen types, disease links, and literature support.
Design Local HMDB Workflow
Design a reproducible workflow to download HMDB data, choose formats, extract key fields, map external IDs, and document version and citation details.
Best Practices
- Verify identifications with at least two evidence types, such as spectra and mass.
- Record HMDB version, accession IDs, and citation details in research outputs.
- Use downloaded datasets for large analyses instead of repeated manual website queries.
Avoid
- Treating predicted spectra or concentrations as confirmed experimental evidence.
- Using HMDB data commercially without checking permission requirements.
- Relying on a name match alone for metabolite identification.
Frequently Asked Questions
Does this skill include the HMDB data files?
No. It explains how to search, download, and interpret HMDB data. You still need access to HMDB resources.
Can it use a public HMDB REST API?
HMDB does not provide a public REST API. Programmatic access may require downloaded files or direct HMDB team contact.
Is it suitable for clinical diagnosis?
No. It can organize HMDB evidence, but clinical decisions require qualified review and current clinical context.
Can it help identify metabolites from spectra?
Yes. It outlines MS, MS-MS, GC-MS, LC-MS, and NMR evidence checks for candidate identification.
What data formats does it cover?
It covers XML, SDF, FASTA, TXT, CSV, and TSV formats described by HMDB.
What citations are needed?
Record HMDB accession IDs, database version, download date, and the HMDB publication required by the data license.
Developer Details
Author
K-Dense-AILicense
HMDB is offered to the public as a freely available resource. Use and re-distribution of the data, in whole or in part, for commercial purposes requires explicit permission of the authors and explicit acknowledgment of the source material (HMDB) and the original publication (see the HMDB citing page). We ask that users who download significant portions of the database cite the HMDB paper in any resulting publications.
Skillstore revision
r1
Version notice
The author did not declare a version.
Repository
https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/hmdb-databaseRef
b8ca75d2c0a7e7102978993058777d82b8ab2610
Maintenance freshness
7/18/2026
Usage
7 downloads · 222 views
File structure
More from K-Dense-AI
View all📦
iso-13485-certification
85Prepare ISO 13485 Certification Docs
Medical device teams must create complete QMS documentation before certification audits. This skill provides templates, checklists, and gap analysis guidance for ISO 13485 readiness.
Documentation View
📦
pytdc
82Analyze therapeutic ML datasets with PyTDC
Drug discovery teams need reliable datasets and fair evaluation protocols. This skill helps Claude use PyTDC for curated therapeutic ML data, benchmark splits, metrics, and molecular oracles.
Data & Analytics View
📦
diffdock
81Run DiffDock Molecular Docking
Protein-ligand docking requires careful setup, parameter choices, and result interpretation. This skill guides DiffDock workflows for poses, confidence scores, and screening.
Research & Learning View
📦
statistical-analysis
80Analyze Research Data with Statistical Guidance
Choosing tests and reporting results can be slow and error-prone. This skill guides test selection, assumptions, effect sizes, power analysis, Bayesian options, and APA reporting.
Data & Analytics View
📦
scanpy
80Analyze Single-Cell RNA-seq with Scanpy
Single-cell RNA-seq analysis requires many linked decisions across QC, normalization, clustering, and plotting. This skill gives Claude, Codex, and Claude Code structured Scanpy workflows, reference guidance, and reusable analysis scripts.
Data & Analytics View
Related Skills
View all📦
pubchem-database
80Explore PubChem Compounds and Bioactivity
by davila7
Chemical identifiers and assay records are difficult to retrieve and compare consistently. This skill guides Claude, Codex, and Claude Code through focused PubChem queries and structured interpretation.
Research & Learning View
📦
clinical-decision-support
38Build Evidence-Based Clinical Decision Reports
by davila7
Clinical research teams need consistent cohort analyses and treatment evidence summaries. This skill structures statistics, biomarkers, recommendations, and LaTeX reports.
Research & Learning View
📦
metabolomics-workbench-database
75Explore Metabolomics Workbench Data
by davila7
Finding consistent metabolite, study, and mass-spectrometry records across a large repository can require detailed API knowledge. This skill guides precise Metabolomics Workbench REST queries and structured interpretation.
Data & Analytics View
📦
pyopenms
77Analyze Mass Spectrometry Data with PyOpenMS
by davila7
Mass spectrometry workflows require careful handling of complex formats, algorithms, and parameters. This skill guides PyOpenMS analysis for proteomics, metabolomics, signal processing, identification, and quantitation.
Data & Analytics View
📦
matchms
38Analyze Mass Spectra with Matchms
by davila7
Mass spectrometry workflows require careful format handling, metadata cleanup, and consistent scoring. This skill guides matchms imports, filtering, similarity analysis, and reproducible pipelines.
Data & Analytics View
📦
nature-figure
85Create Journal-Ready Scientific Figures
by Yuan1z0825
Scientific figures often fail because story, evidence, export, and review checks are separated. This skill guides Claude, Codex, and Claude Code through one publication-ready workflow.
Research & Learning View