Agent skill

Chembl Search

Search ChEMBL bioactive molecules database with natural language queries.

Install Chembl Search

skills CLI

$ npx skills add wu-yc/LabClaw --skill chembl-search -a claude-code

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

GitHub CLI

$ gh skill install wu-yc/LabClaw chembl-search --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/wu-yc/LabClaw.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/pharma/chembl-search .claude/skills/chembl-search && 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 "chembl-search" agent skill from https://github.com/wu-yc/LabClaw/tree/main/skills/pharma/chembl-search into .claude/skills/chembl-search/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chembl-search", 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/wu-yc/LabClaw/tree/main/skills/pharma/chembl-search

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 wu-yc/LabClaw --skill chembl-search -a codex

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

GitHub CLI

$ gh skill install wu-yc/LabClaw chembl-search --agent codex

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

Manual copy

$ git clone --depth 1 https://github.com/wu-yc/LabClaw.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/pharma/chembl-search .agents/skills/chembl-search && 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 "chembl-search" agent skill from https://github.com/wu-yc/LabClaw/tree/main/skills/pharma/chembl-search into .agents/skills/chembl-search/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chembl-search", 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 wu-yc/LabClaw --skill chembl-search -a cursor

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

GitHub CLI

$ gh skill install wu-yc/LabClaw chembl-search --agent cursor

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

Manual copy

$ git clone --depth 1 https://github.com/wu-yc/LabClaw.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/pharma/chembl-search .cursor/skills/chembl-search && 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 "chembl-search" agent skill from https://github.com/wu-yc/LabClaw/tree/main/skills/pharma/chembl-search into .cursor/skills/chembl-search/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chembl-search", 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/wu-yc/LabClaw.git --path skills/pharma/chembl-search

--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 wu-yc/LabClaw --skill chembl-search -a gemini-cli

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

GitHub CLI

$ gh skill install wu-yc/LabClaw chembl-search --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/wu-yc/LabClaw.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/pharma/chembl-search .gemini/skills/chembl-search && 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 "chembl-search" agent skill from https://github.com/wu-yc/LabClaw/tree/main/skills/pharma/chembl-search into .gemini/skills/chembl-search/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chembl-search", 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 wu-yc/LabClaw chembl-search

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 wu-yc/LabClaw --skill chembl-search -a github-copilot

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

Manual copy

$ git clone --depth 1 https://github.com/wu-yc/LabClaw.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/pharma/chembl-search .github/skills/chembl-search && 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 "chembl-search" agent skill from https://github.com/wu-yc/LabClaw/tree/main/skills/pharma/chembl-search into .github/skills/chembl-search/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chembl-search", 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 wu-yc/LabClaw --skill chembl-search -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 wu-yc/LabClaw chembl-search --agent opencode

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

Manual copy

$ git clone --depth 1 https://github.com/wu-yc/LabClaw.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/pharma/chembl-search .opencode/skills/chembl-search && 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 "chembl-search" agent skill from https://github.com/wu-yc/LabClaw/tree/main/skills/pharma/chembl-search into .opencode/skills/chembl-search/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chembl-search", 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: chembl-search
GitHub stars: 1.1k
Used in: 2 other repos
Token cost: ~1.2k tokens
SKILL.md length: 314 words
Files: 1
Skills in repo: 68
Repo updated: Mar 19, 2026
First seen: Oct 9, 2026
Licence: MIT

At a glance

Search ChEMBL bioactive molecules database with natural language queries.

Works in 2 steps: Node.js 18+ (uses built-in fetch) → Valyu API key from…
Tasks that involve Drug discovery and cheminformatics
SKILL.md covers Why This Skill is Powerful, Requirements, CRITICAL: Script Path Resolution and API Key Setup Flow, plus 8 more sections
Calls jq; reaches api.valyu.ai and chembl.org

What it does

Chembl Search is an agent skill from wu-yc/LabClaw. Search ChEMBL bioactive molecules database with natural language queries. Find compounds and assay data with Valyu semantic search.

Its SKILL.md is about 1.2k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Research & Science, covering Drug discovery and cheminformatics. The repository describes itself as: LabClaw – Operating Layer for LabOS (Stanford-Princeton AI Co-Scientists). The licence is MIT.

When your agent uses it

Tasks that involve Drug discovery and cheminformatics

Example prompts

“/chembl-search”

Requirements

Python 3
Node.js

Workflow steps

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

Node.js 18+ (uses built-in fetch)
Valyu API key from https://platform.valyu.ai ($10 free credits)

What it can do on your machine

Read from SKILL.md and the folder at commit df37802. 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
Shell commands in SKILL.md call:
- jq
From the folder's file list and the shell code blocks in SKILL.md.
Network
Hosts in commands or code, which the agent is likely to contact:
- api.valyu.ai
- chembl.org
Also links to:
- platform.valyu.ai
- docs.valyu.ai
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

Chembl Search loads about 1.2k tokens when it runs. Until then it costs about 36 tokens; SKILL.md has 314 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~36
When it runs · the whole SKILL.md, loaded when a task matches: ~1.2k

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 wu-yc/LabClaw at commit df37802, republished under its MIT licence (© wu-yc). 314 words, ~1,245 tokens.

Download SKILL.mdSave it as .claude/skills/chembl-search/SKILL.md (or your agent's skills folder).

name: chembl-search
description: Search ChEMBL bioactive molecules database with natural language queries. Find compounds and assay data with Valyu semantic search.
keywords: chembl, drug-discovery, bioactive-compounds, molecular-database, hit-identification, semantic-search
license: MIT

ChEMBL Search

Search the complete ChEMBL database of bioactive molecules, drug targets, and binding data using natural language queries powered by Valyu's semantic search API.

Why This Skill is Powerful

No API Parameter Parsing: Just pass natural language queries directly - no need to construct complex search parameters
Semantic Search: Understands the meaning of your query, not just keyword matching
Full-Text Access: Returns complete compound and target information
Image Links: Includes molecular structures and data visualizations
Comprehensive Coverage: Access to all ChEMBL bioactive molecule data for drug discovery

Requirements

Node.js 18+ (uses built-in fetch)
Valyu API key from https://platform.valyu.ai ($10 free credits)

CRITICAL: Script Path Resolution

The scripts/search commands in this documentation are relative to this skill's installation directory.

Before running any command, locate the script using:

bash

CHEMBL_SCRIPT=$(find ~/.claude/plugins/cache -name "search" -path "*/chembl-search/*/scripts/*" -type f 2>/dev/null | head -1)

Then use the full path for all commands:

bash

$CHEMBL_SCRIPT "kinase inhibitors" 15

API Key Setup Flow

When you run a search and receive "setup_required": true, follow this flow:

Ask the user for their API key: "To search ChEMBL, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai"
Once the user provides the key, run:
bash
```
scripts/search setup <api-key>
```
Retry the original search.

When to Use This Skill

Finding bioactive compounds for drug discovery
Target-based compound searching
Compound property optimization
Assay data and biological activity research
Structure-activity relationship studies
Lead compound identification

Output Format

json

{
  "success": true,
  "type": "chembl_search",
  "query": "kinase inhibitors",
  "result_count": 10,
  "results": [
    {
      "title": "Compound/Assay Title",
      "url": "https://chembl.org/...",
      "content": "Compound data, targets, assay results...",
      "source": "chembl",
      "relevance_score": 0.95,
      "images": ["https://example.com/structure.png"]
    }
  ],
  "cost": 0.025
}

Processing Results

With jq

bash

# Get compound titles
scripts/search "query" 10 | jq -r '.results[].title'

# Get URLs
scripts/search "query" 10 | jq -r '.results[].url'

# Extract full content
scripts/search "query" 10 | jq -r '.results[].content'

Common Use Cases

Drug Discovery

bash

# Find lead compounds
scripts/search "JAK2 selective inhibitors for myelofibrosis" 50

Target Validation

bash

# Search for target information
scripts/search "protein kinase B binding assays" 20

SAR Analysis

bash

# Find structure-activity relationships
scripts/search "benzimidazole derivatives anticancer activity" 15

Mechanism Research

bash

# Search for mechanism data
scripts/search "allosteric modulators of NMDA receptors" 25

Error Handling

All commands return JSON with success field:

json

{
  "success": false,
  "error": "Error message"
}

Exit codes:

0 - Success
1 - Error (check JSON for details)

API Endpoint

Base URL: https://api.valyu.ai/v1
Endpoint: /search
Authentication: X-API-Key header

Architecture

scripts/
├── search          # Bash wrapper
└── search.mjs      # Node.js CLI

Direct API calls using Node.js built-in fetch(), zero external dependencies.

Adding to Your Project

If you're building an AI project and want to integrate ChEMBL Search directly into your application, use the Valyu SDK:

Python Integration

python

from valyu import Valyu

client = Valyu(api_key="your-api-key")

response = client.search(
    query="your search query here",
    included_sources=["valyu/valyu-chembl"],
    max_results=20
)

for result in response["results"]:
    print(f"Title: {result['title']}")
    print(f"URL: {result['url']}")
    print(f"Content: {result['content'][:500]}...")

TypeScript Integration

typescript

import { Valyu } from "valyu-js";

const client = new Valyu("your-api-key");

const response = await client.search({
  query: "your search query here",
  includedSources: ["valyu/valyu-chembl"],
  maxResults: 20
});

response.results.forEach((result) => {
  console.log(`Title: ${result.title}`);
  console.log(`URL: ${result.url}`);
  console.log(`Content: ${result.content.substring(0, 500)}...`);
});

See the Valyu docs for full integration examples and SDK reference.

Files

Just SKILL.md in skills/pharma/chembl-search of wu-yc/LabClaw.

Open the folder on GitHubat commit df37802

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 wu-yc/LabClaw, which our catalogue first saw on October 9, 2026.

Compare with similar skills

Chembl Search 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.

Chembl Search compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Chembl Search this skillwu-yc/LabClaw	1.1k	2 repos	~1.2k	Automated safety check: Pass	MIT	6 mo ago
MolecodeAtomFlow-AI/MoleCode	306	—	~1.9k	Automated safety check: Pass	MIT	4 mo ago
Drug DiscoveryTommy-yw/RunbookHermes	546	1 repos	~2.3k	Automated safety check: Pass	MIT	4 mo ago
DiffDock Molecular DockingK-Dense-AI/scientific-agent-skills	48k	1 repos	~3k	Automated safety check: Notes	MIT	6 days ago
Biomedical Analysis Dispatchxjtulyc/MedgeClaw	617	1 repos	~2k	Automated safety check: Pass	None	7 mo ago
Biopipelineslocbp-uzh/biopipelines	109	—	~2.4k	Automated safety check: Pass	MIT	10 days ago

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Questions about Chembl Search

What does Chembl Search do?

Search ChEMBL bioactive molecules database with natural language queries. Chembl Search is an agent skill from wu-yc/LabClaw. Search ChEMBL bioactive molecules database with natural language queries.

When should I use Chembl Search?

Chembl Search fits situations like: tasks that involve Drug discovery and cheminformatics.

How do I install Chembl Search in Claude Code?

Run `npx skills add wu-yc/LabClaw --skill chembl-search -a claude-code`. Or copy the skill folder (skills/pharma/chembl-search in wu-yc/LabClaw) into .claude/skills/chembl-search in your project. Claude Code loads it when a task matches its description.

How do I install Chembl Search in Codex?

Run `npx skills add wu-yc/LabClaw --skill chembl-search -a codex`. Or copy the skill folder (skills/pharma/chembl-search in wu-yc/LabClaw) into .agents/skills/chembl-search in your project. Codex loads it when a task matches its description.

Can I use Chembl Search 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 wu-yc/LabClaw --skill chembl-search -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/chembl-search, .gemini/skills/chembl-search, .github/skills/chembl-search and .opencode/skills/chembl-search in your project.

What does Chembl Search need to run?

Going by SKILL.md and its folder, Chembl Search needs the command-line tools its instructions call (jq). Our summary lists: Python 3; Node.js.

Does Chembl Search access the network?

SKILL.md names 4 domains. In commands or code: api.valyu.ai and chembl.org; the agent is likely to contact these when it follows the instructions. As links in the text: platform.valyu.ai and docs.valyu.ai. This is read from the text; nothing was executed.

Is Chembl Search 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 Chembl Search use?

Chembl Search 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 Chembl Search use?

About 1.2k tokens (SKILL.md is roughly 5k 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 Chembl Search?

Skills that share tags, products or a category with Chembl Search: Molecode (AtomFlow-AI/MoleCode, 306 stars), Drug Discovery (Tommy-yw/RunbookHermes, 546 stars), DiffDock Molecular Docking (K-Dense-AI/scientific-agent-skills, 48k stars) and Biomedical Analysis Dispatch (xjtulyc/MedgeClaw, 617 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Chembl Search?

wu-yc (a GitHub user) maintains it in wu-yc/LabClaw, which has 1,055 GitHub stars. The repository holds 68 skills in this directory. The repository was last updated on March 19, 2026.

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

Install Chembl Search

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

ChEMBL Search

Why This Skill is Powerful

Requirements

CRITICAL: Script Path Resolution

API Key Setup Flow

When to Use This Skill

Output Format

Processing Results

With jq

Common Use Cases

Drug Discovery

Target Validation

SAR Analysis

Mechanism Research

Error Handling

API Endpoint

Architecture

Adding to Your Project

Python Integration

TypeScript Integration

Files

Used in 2 other repositories

Compare with similar skills

Similar skills

More from wu-yc/LabClaw

Related

Questions about Chembl Search