Agent skill

Hmdb Database

by aipoch in aipoch/medical-research-skills

Install Hmdb Database

skills CLI

$ npx skills add aipoch/medical-research-skills --skill hmdb-database -a claude-code

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

GitHub CLI

$ gh skill install aipoch/medical-research-skills 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/aipoch/medical-research-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/'scientific-skills/Evidence Insight/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/

Paste into Claude Code

Install the "hmdb-database" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/hmdb-database into .claude/skills/hmdb-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "hmdb-database", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/hmdb-database

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add aipoch/medical-research-skills --skill hmdb-database -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install aipoch/medical-research-skills hmdb-database --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/'scientific-skills/Evidence Insight/hmdb-database' .agents/skills/hmdb-database && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "hmdb-database" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/hmdb-database into .agents/skills/hmdb-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "hmdb-database", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add aipoch/medical-research-skills --skill hmdb-database -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install aipoch/medical-research-skills hmdb-database --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/'scientific-skills/Evidence Insight/hmdb-database' .cursor/skills/hmdb-database && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "hmdb-database" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/hmdb-database into .cursor/skills/hmdb-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "hmdb-database", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/aipoch/medical-research-skills.git --path 'scientific-skills/Evidence Insight/hmdb-database'

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add aipoch/medical-research-skills --skill hmdb-database -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install aipoch/medical-research-skills hmdb-database --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/'scientific-skills/Evidence Insight/hmdb-database' .gemini/skills/hmdb-database && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "hmdb-database" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/hmdb-database into .gemini/skills/hmdb-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "hmdb-database", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install aipoch/medical-research-skills hmdb-database

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add aipoch/medical-research-skills --skill hmdb-database -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/'scientific-skills/Evidence Insight/hmdb-database' .github/skills/hmdb-database && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "hmdb-database" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/hmdb-database into .github/skills/hmdb-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "hmdb-database", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add aipoch/medical-research-skills --skill hmdb-database -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install aipoch/medical-research-skills hmdb-database --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/'scientific-skills/Evidence Insight/hmdb-database' .opencode/skills/hmdb-database && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "hmdb-database" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/hmdb-database into .opencode/skills/hmdb-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "hmdb-database", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: hmdb-database
GitHub stars: 2k
Token cost: ~985 tokens
SKILL.md length: 359 words
Files: 4 (incl. scripts, references)
Skills in repo: 567
Repo updated: Sep 17, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

Works in 3 steps: Download HMDB XML → Search and Extract Fields (Runnable… → Field Reference
Research & Science work in your project
SKILL.md covers When to Use, Key Features, Dependencies and Example Usage, plus 1 more section
Runs Python scripts from its folder

What it does

Hmdb Database is an agent skill from 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 mining.

Its SKILL.md is about 990 tokens, which your agent loads only when the skill is triggered. The skill folder holds 5 other files, including scripts and reference files (for example `hmdb-database_audit_result_v1.json`, `references/hmdb_data_fields.md` and `scripts/hmdb_parser.py`).

It sits in Research & Science. The repository describes itself as: Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing. The licence is MIT.

When your agent uses it

Research & Science work in your project

Example prompts

“/hmdb-database”

Requirements

Python 3

Workflow steps

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

Download HMDB XML
Search and Extract Fields (Runnable Example)
Field Reference

What it can do on your machine

Read from SKILL.md and the folder at commit 686e09d. 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
Ships 1 file in scripts/ (Python), which the agent can run.
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 985 tokens when it runs, and up to ~1.3k if it reads all its reference files. Until then it costs about 55 tokens; SKILL.md has 359 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~55
When it runs · the whole SKILL.md, loaded when a task matches: ~985
With references · SKILL.md plus every file in references/, read only if the agent opens them: ~1.3k

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); the scripts in this folder are not scanned.

SKILL.md

The full file from aipoch/medical-research-skills at commit 686e09d, republished under its MIT licence (© aipoch). 359 words, ~985 tokens.

Download SKILL.mdSave it as .claude/skills/hmdb-database/SKILL.md (or your agent's skills folder). This skill also uses 3 other files; get the full folder from GitHub.

name: hmdb-database
description: 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 mining.
license: MIT
author: AIPOCH

Source: https://github.com/aipoch/medical-research-skills

When to Use

You need to look up a metabolite by common name (e.g., “Caffeine”) and retrieve its HMDB entry data.
You have an HMDB ID (e.g., HMDB0000001) and want to extract standardized chemical/biological/clinical fields for downstream analysis.
You want to build a local, scriptable pipeline to mine the HMDB XML dump instead of manually browsing the website.
You need to map HMDB identifiers to external resources (e.g., KEGG, PubChem, ChEBI) for integration tasks.
You are preparing metabolomics datasets and need pathway/enzyme/transporter annotations from HMDB entries.

Key Features

Search metabolites by:
- Text name
- HMDB identifier (e.g., HMDB0000001)
- Structure-related query (as supported by the parser/search implementation)
Parse the HMDB XML dataset and extract:
- Chemical data (formula, molecular weight, InChI/SMILES where available)
- Biological data (pathways, enzymes, transporters)
- Clinical data (disease associations, biofluid concentrations)
Optional structuring of extracted results for analysis workflows (e.g., tabular outputs).
Supports integration workflows by exposing identifiers suitable for cross-database mapping.

Dependencies

Python >=3.9
Standard library:
- xml.etree.ElementTree (built-in)
Optional:
- pandas >= 1.5

Example Usage

1) Download HMDB XML

Download the HMDB metabolite XML dataset from:

https://hmdb.ca/downloads

Assume you saved it as:

text

data/hmdb_metabolites.xml

2) Search and Extract Fields (Runnable Example)

python

from scripts.hmdb_parser import HMDBParser

def main():
    # Path to the HMDB XML dump downloaded from hmdb.ca/downloads
    xml_path = "data/hmdb_metabolites.xml"

    parser = HMDBParser(xml_path)

    # Search by metabolite name (text query)
    results = parser.search("Caffeine")

    # Print basic information from the first match (structure depends on implementation)
    if not results:
        print("No results found.")
        return

    first = results[0]
    print("Top match:")
    print(first)

if __name__ == "__main__":
    main()

3) Field Reference

For a curated list of extractable fields and how they map to HMDB XML elements, see:

references/hmdb_data_fields.md

Show full SKILL.md (149 more words)Show less

Implementation Details

Data acquisition
- Primary workflow uses the official HMDB downloadable XML dataset (recommended for bulk parsing).
- Single-entry lookups can be done via the HMDB website, but this skill is designed around XML parsing.
Parsing approach
- The parser reads the HMDB XML and traverses metabolite entries using xml.etree.ElementTree.
- Extracted fields should follow the definitions documented in references/hmdb_data_fields.md.
Search behavior
- Name/ID search typically matches against key textual identifiers (e.g., common name, synonyms, HMDB accession).
- Structure-based search is dependent on what structural fields are indexed/exposed by HMDBParser (e.g., SMILES/InChI).
Integration / cross-references
- HMDB entries often include cross-references to external databases (e.g., KEGG, PubChem, ChEBI).
- A common workflow is to extract these identifiers and build mapping tables for downstream joins.
Spectral analysis (conceptual)
- HMDB contains NMR/MS references for some metabolites; this skill can be extended to link parsed entries to spectral metadata.
- Actual spectral matching/identification is not guaranteed unless implemented in the codebase.

Files

SKILL.md and 3 other files (scripts, references) in scientific-skills/Evidence Insight/hmdb-database of aipoch/medical-research-skills.

SKILL.md
hmdb-database_audit_result_v1.json
references/hmdb_data_fields.md
scripts/hmdb_parser.py

Open the folder on GitHubat commit 686e09d

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
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GitHub Deep Researchbytedance/deer-flow	83k	5 repos	~1.3k	Automated safety check: Pass	MIT	today
Nature Paper CardYuan1z0825/nature-skills	46k	2 repos	~2.1k	Automated safety check: Pass	Apache-2.0	yesterday
Read arXiv Paperkarpathy/nanochat	58k	2 repos	~494	Automated safety check: Pass	MIT	1 mo ago
Content Research Writerweapp-tailwindcss/weapp-tailwindcss	1.9k	25 repos	~3.5k	Automated safety check: Pass	MIT	today

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Questions about Hmdb Database

What does Hmdb Database do?

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…. Hmdb Database is an agent skill from 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 mining.

When should I use Hmdb Database?

Hmdb Database fits situations like: research & Science work in your project.

How do I install Hmdb Database in Claude Code?

Run `npx skills add aipoch/medical-research-skills --skill hmdb-database -a claude-code`. Or copy the skill folder (scientific-skills/Evidence Insight/hmdb-database in aipoch/medical-research-skills) 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 aipoch/medical-research-skills --skill hmdb-database -a codex`. Or copy the skill folder (scientific-skills/Evidence Insight/hmdb-database in aipoch/medical-research-skills) 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 aipoch/medical-research-skills --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?

Going by SKILL.md and its folder, Hmdb Database needs Python for the scripts in its folder. Our summary lists: Python 3.

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. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Hmdb Database use?

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

How many tokens does Hmdb Database use?

About 985 tokens (SKILL.md is roughly 3.9k 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 312 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: Hypothesis Generation (spacering-net/codeg, 3.8k stars), GitHub Deep Research (bytedance/deer-flow, 83k stars), Nature Paper Card (Yuan1z0825/nature-skills, 46k stars) and Read arXiv Paper (karpathy/nanochat, 58k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Hmdb Database?

aipoch (a GitHub organization) maintains it in aipoch/medical-research-skills, which has 1,974 GitHub stars. The repository holds 567 skills in this directory. The repository was last updated on September 17, 2026.

Source: aipoch/medical-research-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Hmdb Database

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

When to Use

Key Features

Dependencies

Example Usage

1) Download HMDB XML

2) Search and Extract Fields (Runnable Example)

3) Field Reference

Implementation Details

Files

Compare with similar skills

Similar skills

More from aipoch/medical-research-skills

Related

Questions about Hmdb Database