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Agent skill

Ukb Navigator

by ClawBio in ClawBio/ClawBio

Semantic search across UK Biobank's 12,000+ data fields and publications — find the right variables for your research question.

MITAuto-check passedResearch & Science

Install Ukb Navigator

skills CLI
$ npx skills add ClawBio/ClawBio --skill ukb-navigator -a claude-code

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

GitHub CLI
$ gh skill install ClawBio/ClawBio ukb-navigator --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/ClawBio/ClawBio.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/ukb-navigator .claude/skills/ukb-navigator && 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
ukb-navigator
GitHub stars
1.2k
Used in
2 other repos
Token cost
~1k tokens
SKILL.md length
404 words
Files
3
Skills in repo
104
Repo updated
First seen
Licence
MIT

At a glance

Semantic search across UK Biobank's 12,000+ data fields and publications — find the right variables for your research question.

  • Works in 5 steps: Semantic field search: Query 12,000+ UK… → Category navigation: Browse field… → Field lookup: Direct lookup by UK… → …
  • Tasks that involve Hypothesis generation
  • SKILL.md covers Core Capabilities, Input Formats, Data Sources and Workflow, plus 6 more sections
  • Runs Python scripts from its folder; calls python

What it does

Ukb Navigator is an agent skill from ClawBio/ClawBio. Semantic search across UK Biobank's 12,000+ data fields and publications — find the right variables for your research question.

Its SKILL.md is about 1k tokens, which your agent loads only when the skill is triggered. The skill folder holds 3 other files (for example `tests/test_ukb_navigator.py` and `ukb_navigator.py`).

It sits in Research & Science, covering Hypothesis generation and Embeddings. It works with Chroma. The repository describes itself as: 🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free. The licence is MIT.

When your agent uses it

  • Tasks that involve Hypothesis generation
  • Tasks that involve Embeddings

Example prompts

  • “/ukb-navigator”

Requirements

  • Python 3

Workflow steps

5 steps, taken from the first numbered list in SKILL.md.

  1. Semantic field search: Query 12,000+ UK Biobank data fields by natural language description
  2. Category navigation: Browse field categories (imaging, genomics, health records, etc.)
  3. Field lookup: Direct lookup by UK Biobank field ID (e.g., field 21001 = BMI)
  4. Publication search: Find UK Biobank publications related to a research topic
  5. Schema embedding: One-time indexing of UKB schema into ChromaDB for fast retrieval

What it can do on your machine

Read from SKILL.md and the folder at commit dece754. 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 script files (Python), which the agent can run.

    Shell commands in SKILL.md call:

    • python

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

  • Network

    No URLs in SKILL.md.

    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

Ukb Navigator loads about 1k tokens when it runs. Until then it costs about 35 tokens; SKILL.md has 404 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~35
When it runs · the whole SKILL.md, loaded when a task matches
~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 ClawBio/ClawBio at commit dece754, republished under its MIT licence (© ClawBio). 404 words, ~1,015 tokens.

Download SKILL.mdSave it as .claude/skills/ukb-navigator/SKILL.md (or your agent's skills folder). This skill also uses 2 other files; get the full folder from GitHub.
name
ukb-navigator
description
Semantic search across UK Biobank's 12,000+ data fields and publications — find the right variables for your research question.
license
MIT
metadata.version
0.1.0

🏥 UKB Navigator

You are UKB Navigator, a specialised ClawBio agent for searching the UK Biobank data schema. Your role is to take a natural language research question and find the most relevant UK Biobank data fields, categories, and publications using semantic search over embedded schema documentation.

Core Capabilities

  1. Semantic field search: Query 12,000+ UK Biobank data fields by natural language description
  2. Category navigation: Browse field categories (imaging, genomics, health records, etc.)
  3. Field lookup: Direct lookup by UK Biobank field ID (e.g., field 21001 = BMI)
  4. Publication search: Find UK Biobank publications related to a research topic
  5. Schema embedding: One-time indexing of UKB schema into ChromaDB for fast retrieval

Input Formats

  • Natural language query: "blood pressure measurements", "cognitive function tests", "imaging-derived phenotypes"
  • Field ID: Any valid UK Biobank field ID (e.g., 21001, 22009, 41270)
  • Research question: "What fields relate to cardiovascular risk factors?"

Data Sources

SourceDescription
ukb_schema.csvFull UK Biobank data showcase schema (fields, categories, descriptions)
schema_27.txtApplication-specific schema documentation

Workflow

When the user asks about UK Biobank data:

  1. Embed (first use): Index UKB schema into ChromaDB with Voyage AI embeddings
  2. Search: Semantic search against the embedded schema
  3. Rank: Return top matches by cosine similarity
  4. Report: Generate markdown report with field IDs, descriptions, and relevance scores

Example Queries

  • "What UK Biobank fields measure kidney function?"
  • "Find all imaging-derived brain phenotypes"
  • "Look up UKB field 21001"
  • "Which fields capture medication use?"
  • "Blood biomarkers related to inflammation"
Show full SKILL.md (161 more words)Show less

Output Structure

output_directory/
├── report.md                    # Full markdown report with matched fields
├── matched_fields.csv           # Structured table of matching fields
└── reproducibility/
    ├── commands.sh              # Portable replay command ($CLAWBIO_ROOT / $OUTPUT_DIR)
    ├── environment.yml          # Conda recipe (chromadb + voyageai)
    └── checksums.sha256         # SHA-256 of report.md and matched_fields.csv

Demo Mode

Run --demo to search using pre-cached schema results without requiring UKB data files:

bash
python ukb_navigator.py --demo --output /tmp/ukb_demo

The demo searches for "blood pressure and hypertension" and returns sample field matches.

Dependencies

Required:

  • chromadb >= 0.4 (vector database)
  • Python 3.10+

Optional:

  • voyageai (Voyage AI embeddings — falls back to ChromaDB default if absent)

Safety

  • All processing is local — no data leaves this machine
  • UK Biobank schema is publicly available metadata (not patient data)
  • No individual-level UKB data is included or transmitted
  • Requires valid UKB data access application for actual research use

Integration with Bio Orchestrator

This skill is invoked by the Bio Orchestrator when:

  • User mentions "UK Biobank", "UKB", "Biobank fields", "UKB schema"
  • User asks about finding variables or fields in a large biobank
  • Query contains keywords: "ukb", "uk biobank", "biobank navigator"

It can be chained with:

  • gwas-prs: Use discovered field IDs to define phenotypes for PRS analysis
  • gwas-lookup: Look up GWAS associations for variants in UKB-identified phenotypes
  • lit-synthesizer: Find publications about UKB-derived phenotypes

© ClawBio, 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 2 other files in skills/ukb-navigator of ClawBio/ClawBio.

  • SKILL.md
  • tests/test_ukb_navigator.py
  • ukb_navigator.py

Open the folder on GitHubat commit dece754

Used in 2 other repositories

We found 2 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 2 other GitHub owners. This page covers the copy in ClawBio/ClawBio, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Ukb Navigator 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.

Ukb Navigator compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Ukb Navigator this skillClawBio/ClawBio1.2k2 repos~1kAutomated safety check: PassMIT
Chroma Vector DatabaseOrchestra-Research/AI-Research-SKILLs13k7 repos~2.3kAutomated safety check: PassMIT
CLIP Image-Text MatchingOrchestra-Research/AI-Research-SKILLs13k7 repos~1.7kAutomated safety check: PassMIT
HypoGeniC Hypothesis GenerationK-Dense-AI/scientific-agent-skills48k1 repos~3.6kAutomated safety check: NotesMIT
Evo2JimLiu/science-skills2274 repos~1.3kAutomated safety check: PassApache-2.0
ScgptJimLiu/science-skills2274 repos~1.3kAutomated safety check: PassApache-2.0

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Works with

Categories

Questions about Ukb Navigator

What does Ukb Navigator do?

Semantic search across UK Biobank's 12,000+ data fields and publications — find the right variables for your research question. Ukb Navigator is an agent skill from ClawBio/ClawBio. Semantic search across UK Biobank's 12,000+ data fields and publications — find the right variables for your research question.

When should I use Ukb Navigator?

Ukb Navigator fits situations like: tasks that involve Hypothesis generation; tasks that involve Embeddings.

How do I install Ukb Navigator in Claude Code?

Run `npx skills add ClawBio/ClawBio --skill ukb-navigator -a claude-code`. Or copy the skill folder (skills/ukb-navigator in ClawBio/ClawBio) into .claude/skills/ukb-navigator in your project. Claude Code loads it when a task matches its description.

How do I install Ukb Navigator in Codex?

Run `npx skills add ClawBio/ClawBio --skill ukb-navigator -a codex`. Or copy the skill folder (skills/ukb-navigator in ClawBio/ClawBio) into .agents/skills/ukb-navigator in your project. Codex loads it when a task matches its description.

Can I use Ukb Navigator 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 ClawBio/ClawBio --skill ukb-navigator -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/ukb-navigator, .gemini/skills/ukb-navigator, .github/skills/ukb-navigator and .opencode/skills/ukb-navigator in your project.

What does Ukb Navigator need to run?

Going by SKILL.md and its folder, Ukb Navigator needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.

Does Ukb Navigator access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Ukb Navigator 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 Ukb Navigator use?

Ukb Navigator 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 Ukb Navigator use?

About 1k tokens (SKILL.md is roughly 4.1k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Ukb Navigator?

Skills that share tags, products or a category with Ukb Navigator: Chroma Vector Database (Orchestra-Research/AI-Research-SKILLs, 13k stars), CLIP Image-Text Matching (Orchestra-Research/AI-Research-SKILLs, 13k stars), HypoGeniC Hypothesis Generation (K-Dense-AI/scientific-agent-skills, 48k stars) and Evo2 (JimLiu/science-skills, 227 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Ukb Navigator?

ClawBio (a GitHub organization) maintains it in ClawBio/ClawBio, which has 1,154 GitHub stars. The repository holds 104 skills in this directory. The repository was last updated on October 8, 2026.

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