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Agent skill

Hmdb Database

by davila7 in davila7/claude-code-templates

Access Human Metabolome Database (220K+ metabolites). An agent skill from davila7/claude-code-templates.

MITAuto-check passed

Install Hmdb Database

skills CLI
$ npx skills add davila7/claude-code-templates --skill hmdb-database -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install davila7/claude-code-templates hmdb-database --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/davila7/claude-code-templates.git skills-src && mkdir -p .claude/skills && cp -r skills-src/cli-tool/components/skills/scientific/hmdb-database .claude/skills/hmdb-database && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
hmdb-database
GitHub stars
32k
Used in
11 other repos
Token cost
~1.9k tokens
SKILL.md length
872 words
Files
2 (incl. references)
Skills in repo
477
Repo updated
First seen
Licence
MIT

At a glance

Access Human Metabolome Database (220K+ metabolites). An agent skill from davila7/claude-code-templates.

  • Works in 5 steps: Web-Based Metabolite Searches → Accessing Metabolite Information → Downloadable Datasets → …
  • SKILL.md covers Overview, When to Use This Skill, Database Contents and Core Capabilities, plus 3 more sections
  • Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Hmdb Database is an agent skill from davila7/claude-code-templates. Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification.

Its SKILL.md is about 1.9k tokens, which your agent loads only when the skill is triggered. The skill folder holds 2 other files, including reference files (for example `references/hmdb_data_fields.md`).

The repository describes itself as: CLI tool for configuring and monitoring Claude Code. The licence is MIT.

Example prompts

  • “/hmdb-database”

Workflow steps

5 steps, taken from the step headings in SKILL.md.

  1. Web-Based Metabolite Searches
  2. Accessing Metabolite Information
  3. Downloadable Datasets
  4. Programmatic API Access
  5. Common Research Workflows

What it can do on your machine

Read from SKILL.md and the folder at commit 14680ec. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    No scripts in the folder and no shell commands in SKILL.md.

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    Links to these hosts (documentation or services it may open):

    • hmdb.ca

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Hmdb Database loads about 1.9k tokens when it runs, and up to ~4.1k if it reads all its reference files. Until then it costs about 51 tokens; SKILL.md has 872 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~51
When it runs · the whole SKILL.md, loaded when a task matches
~1.9k
With references · SKILL.md plus every file in references/, read only if the agent opens them
~4.1k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from davila7/claude-code-templates at commit 14680ec, republished under its MIT licence (© davila7). 872 words, ~1,884 tokens.

Download SKILL.mdSave it as .claude/skills/hmdb-database/SKILL.md (or your agent's skills folder). This skill also uses 1 other file; get the full folder from GitHub.
name
hmdb-database
description
Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification.

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.

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 (current as of 2025) contains:

  • 220,945 metabolite entries covering both water-soluble and lipid-soluble compounds
  • 8,610 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

Spectral Searches:

  • LC-MS spectral matching
  • GC-MS spectral matching
  • NMR spectral searches for metabolite identification

Advanced Searches:

  • Combine multiple criteria (name, properties, concentration ranges)
  • Filter by biological locations or specimen types
  • Search by protein/enzyme associations
2. Accessing Metabolite Information

When retrieving metabolite data, HMDB provides:

Chemical Information:

  • Systematic name, traditional names, and synonyms
  • Chemical formula and molecular weight
  • Structure representations (2D/3D, SMILES, InChI, MOL file)
  • Chemical taxonomy and classification

Biological Context:

  • Metabolic pathways and reactions
  • Associated enzymes and transporters
  • Subcellular locations
  • Biological roles and functions

Clinical Relevance:

  • Normal concentration ranges in biological fluids
  • Biomarker associations with diseases
  • Clinical significance
  • Toxicity information when applicable

Analytical Data:

  • Experimental and predicted NMR spectra
  • MS and MS-MS spectra
  • Retention times and chromatographic data
  • Reference peaks for identification
3. Downloadable Datasets

HMDB offers bulk data downloads at https://www.hmdb.ca/downloads in multiple formats:

Available Formats:

  • XML: Complete metabolite, protein, and spectra data
  • SDF: Metabolite structure files for cheminformatics
  • FASTA: Protein and gene sequences
  • TXT: Raw spectra peak lists
  • CSV/TSV: Tabular data exports

Dataset Categories:

  • All metabolites or filtered by specimen type
  • Protein/enzyme sequences
  • Experimental and predicted spectra (NMR, GC-MS, MS-MS)
  • Pathway information

Best Practices:

  • Download XML format for comprehensive data including all fields
  • Use SDF format for structure-based analysis and cheminformatics workflows
  • Parse CSV/TSV formats for integration with data analysis pipelines
  • Check version dates to ensure up-to-date data (current: v5.0, 2023-07-01)

Usage Requirements:

  • Free for academic and non-commercial research
  • Commercial use requires explicit permission (contact samackay@ualberta.ca)
  • Cite HMDB publication when using data
4. Programmatic API Access

API Availability: HMDB does not provide a public REST API. Programmatic access requires contacting the development team:

Alternative Programmatic Access:

  • R/Bioconductor: Use the hmdbQuery package for R-based queries
    • Install: BiocManager::install("hmdbQuery")
    • Provides HTTP-based querying functions
  • Downloaded datasets: Parse XML or CSV files locally for programmatic analysis
  • Web scraping: Not recommended; contact team for proper API access instead
Show full SKILL.md (358 more words)Show less
5. Common Research Workflows

Metabolite Identification in Untargeted Metabolomics:

  1. Obtain experimental MS or NMR spectra from samples
  2. Use HMDB spectral search tools to match against reference spectra
  3. Verify candidates by checking molecular weight, retention time, and MS-MS fragmentation
  4. Review biological plausibility (expected in specimen type, known pathways)

Biomarker Discovery:

  1. Search HMDB for metabolites associated with disease of interest
  2. Review concentration ranges in normal vs. disease states
  3. Identify metabolites with strong differential abundance
  4. Examine pathway context and biological mechanisms
  5. Cross-reference with literature via PubMed links

Pathway Analysis:

  1. Identify metabolites of interest from experimental data
  2. Look up HMDB entries for each metabolite
  3. Extract pathway associations and enzymatic reactions
  4. Use linked SMPDB (Small Molecule Pathway Database) for pathway diagrams
  5. Identify pathway enrichment for biological interpretation

Database Integration:

  1. Download HMDB data in XML or CSV format
  2. Parse and extract relevant fields for local database
  3. Link with external IDs (KEGG, PubChem, ChEBI) for cross-database queries
  4. Build local tools or pipelines incorporating HMDB reference data

The HMDB ecosystem includes related databases:

  • DrugBank: ~2,832 drug compounds with pharmaceutical information
  • T3DB (Toxin and Toxin Target Database): ~3,670 toxic compounds
  • SMPDB (Small Molecule Pathway Database): Pathway diagrams and maps
  • FooDB: ~70,000 food component compounds

These databases share similar structure and identifiers, enabling integrated queries across human metabolome, drug, toxin, and food databases.

Best Practices

Data Quality:

  • Verify metabolite identifications with multiple evidence types (spectra, structure, properties)
  • Check experimental vs. predicted data quality indicators
  • Review citations and evidence for biomarker associations

Version Tracking:

  • Note HMDB version used in research (current: v5.0)
  • Databases are updated periodically with new entries and corrections
  • Re-query for updates when publishing to ensure current information

Citation:

  • Always cite HMDB in publications using the database
  • Reference specific HMDB IDs when discussing metabolites
  • Acknowledge data sources for downloaded datasets

Performance:

  • For large-scale analysis, download complete datasets rather than repeated web queries
  • Use appropriate file formats (XML for comprehensive data, CSV for tabular analysis)
  • Consider local caching of frequently accessed metabolite information

Reference Documentation

See references/hmdb_data_fields.md for detailed information about available data fields and their meanings.

© davila7, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 1 other file (references) in cli-tool/components/skills/scientific/hmdb-database of davila7/claude-code-templates.

  • SKILL.md
  • references/hmdb_data_fields.md

Open the folder on GitHubat commit 14680ec

Used in 11 other repositories

We found 23 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 11 other GitHub owners. This page covers the copy in davila7/claude-code-templates, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Hmdb Database next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Hmdb Database compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Hmdb Database this skilldavila7/claude-code-templates32k11 repos~1.9kAutomated safety check: PassMIT
Bio Metabolomics Metabolite AnnotationGPTomics/bioSkills1.2k1 repos~4.4kAutomated safety check: PassMIT
Hmdb Databaseaipoch/medical-research-skills2k—~985Automated safety check: PassMIT
Bio Metabolomics Metabolite Annotationmajiayu000/claude-skill-registry6662 repos~1.6kAutomated safety check: PassMIT
Tooluniverse Metabolomicswu-yc/LabClaw1.1k2 repos~3kAutomated safety check: NotesNone
Hmdb Databasejaechang-hits/SciAgent-Skills3701 repos~6.1kAutomated safety check: PassCC-BY-4.0

Similar skills

  • Bio Metabolomics Metabolite Annotation

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    1.2k GitHub starsUsed in 1 repo~4.4k tokens
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  • Hmdb Database

    aipoch/medical-research-skills

    Access the Human Metabolome Database (HMDB) to search metabolites by name/structure/ID and extract chemical/biological/clinical fields when you need metabolomics research data or automated HMDB XML…

    2k GitHub stars~985 tokensUpdated 21 days ago
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  • Bio Metabolomics Metabolite Annotation

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  • Hmdb Database

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    Parse HMDB (Human Metabolome Database) local XML for metabolite info, chemical properties, biological context, disease links, spectra, and cross-DB mapping.

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Questions about Hmdb Database

What does Hmdb Database do?

Access Human Metabolome Database (220K+ metabolites). An agent skill from davila7/claude-code-templates. Hmdb Database is an agent skill from davila7/claude-code-templates. Access Human Metabolome Database (220K+ metabolites).

How do I install Hmdb Database in Claude Code?

Run `npx skills add davila7/claude-code-templates --skill hmdb-database -a claude-code`. Or copy the skill folder (cli-tool/components/skills/scientific/hmdb-database in davila7/claude-code-templates) into .claude/skills/hmdb-database in your project. Claude Code loads it when a task matches its description.

How do I install Hmdb Database in Codex?

Run `npx skills add davila7/claude-code-templates --skill hmdb-database -a codex`. Or copy the skill folder (cli-tool/components/skills/scientific/hmdb-database in davila7/claude-code-templates) into .agents/skills/hmdb-database in your project. Codex loads it when a task matches its description.

Can I use Hmdb Database in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add davila7/claude-code-templates --skill hmdb-database -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/hmdb-database, .gemini/skills/hmdb-database, .github/skills/hmdb-database and .opencode/skills/hmdb-database in your project.

What does Hmdb Database need to run?

SKILL.md names no scripts, command-line tools or credentials: Hmdb Database is instructions for the agent only.

Does Hmdb Database access the network?

SKILL.md names 1 domain. As links in the text: hmdb.ca. This is read from the text; nothing was executed.

Is Hmdb Database safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Hmdb Database use?

Hmdb Database is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Hmdb Database use?

About 1.9k tokens (SKILL.md is roughly 7.5k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 2.2k tokens, read only when the agent opens those files.

What are the alternatives to Hmdb Database?

Skills that share tags, products or a category with Hmdb Database: Bio Metabolomics Metabolite Annotation (GPTomics/bioSkills, 1.2k stars), Hmdb Database (aipoch/medical-research-skills, 2k stars), Bio Metabolomics Metabolite Annotation (majiayu000/claude-skill-registry, 666 stars) and Tooluniverse Metabolomics (wu-yc/LabClaw, 1.1k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Hmdb Database?

davila7 (a GitHub user) maintains it in davila7/claude-code-templates, which has 32,463 GitHub stars. The repository holds 477 skills in this directory. The repository was last updated on October 8, 2026.

Source: davila7/claude-code-templates on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.