chembl-search

Q: How do I install chembl-search?

Run npx skills add https://github.com/yorkeccak/scientific-skills --skill chembl-search in your project. The skills CLI detects the agents you use and copies the skill into the right folder. For Claude Code you can also place the skill folder at ~/.claude/skills/chembl-search/ (personal) or .claude/skills/chembl-search/ (project).

by yorkeccakData & Databases

Search ChEMBL bioactive molecules database with natural language queries. Find compounds and assay data with Valyu semantic search.

Installs: 125
Last 24h: —
Trending rank: —
Security: Not audited

Install

Works with every agent the skills CLI supports.

npx skills add https://github.com/yorkeccak/scientific-skills --skill chembl-search

01
Install
Run the command in your project. The CLI asks which agents to install for.
02
Describe the task
Ask your agent for something this skill covers. It loads chembl-search automatically when relevant.
03
Review the result
The agent follows the SKILL.md steps, scripts and references bundled with the skill.

SKILL.md

The instructions your agent reads when the skill is triggered.

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:

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:

$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:
```
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

{
  "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

# 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

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

Target Validation

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

SAR Analysis

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

Mechanism Research

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

Error Handling

All commands return JSON with success field:

{
  "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

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

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.

FAQ

What does the chembl-search skill do?

Search ChEMBL bioactive molecules database with natural language queries. Find compounds and assay data with Valyu semantic search.

How do I install chembl-search?

Run npx skills add https://github.com/yorkeccak/scientific-skills --skill chembl-search in your project. The skills CLI detects the agents you use and copies the skill into the right folder. For Claude Code you can also place the skill folder at ~/.claude/skills/chembl-search/ (personal) or .claude/skills/chembl-search/ (project).

Which AI agents can use chembl-search?

Any agent that supports the open Agent Skills format (a folder with a SKILL.md file), including Claude Code, Codex, Cursor, GitHub Copilot, Gemini CLI, Windsurf, Cline, OpenCode and more.

Is chembl-search safe to install?

No partner security audit is available yet. Skills can run commands and scripts, so read the SKILL.md and any bundled files before installing.

Who maintains chembl-search?

It is published by yorkeccak in yorkeccak/scientific-skills. It has 125 recorded installs.

Popular data & databases skills

View category →

supabase-postgres-best-practices

supabase/agent-skills

Postgres best practices maintained by Supabase, for Postgres running anywhere. Load this skill BEFORE writing or changing anything that lives in a Postgres database: creating or altering tables and columns (including choosing column types), schema design, migrations and declarative schema files, RLS policies and the tests that verify them, indexes, triggers, database functions, queues and scheduled jobs (pgcron, pgmq), vector/semantic search (pgvector), and restoring dumps (pgrestore) or importing data. Also load it when diagnosing slow queries, high CPU, timeouts, EXPLAIN plans, connection exhaustion, locking, bloat, or rows visible to the wrong user or tenant. This is not just a performance guide — schema, migration, security, and SQL authoring tasks need these rules too, even for a one-column change or a single query.

OfficialData & Databases462.2K installs

prisma-client-api

prisma/skills

Prisma Client API reference covering model queries, filters, operators, and client methods. Use when writing database queries, using CRUD operations, filtering data, or configuring Prisma Client. Triggers on "prisma query", "findMany", "create", "update", "delete", "$transaction".

OfficialData & Databases393.5K installs

prisma-database-setup

prisma/skills

Deprecated compatibility name for prisma-orm-setup. Use only when a user or existing integration explicitly invokes prisma-database-setup; otherwise select prisma-orm-setup.

OfficialData & Databases392.3K installs

prisma-cli

prisma/skills

Prisma ORM 7 CLI reference for existing Prisma 7 applications or explicitly selected Prisma 7 workflows. Covers prisma init, generate, migrate, db, dev, studio, and mcp. For setup, connection repair, or Prisma 8, use prisma-orm-setup; not the Prisma Platform CLI.

OfficialData & Databases390.8K installs

prisma-postgres

prisma/skills

Deprecated compatibility name for prisma-postgres-setup. Use only when a user or existing integration explicitly invokes prisma-postgres; otherwise select prisma-postgres-setup.

OfficialData & Databases384.4K installs

prisma-driver-adapter-implementation

prisma/skills

Required reference for Prisma ORM 7 SQL driver adapter work. Use when implementing or modifying adapters, adding database drivers, or touching SqlDriverAdapter, Transaction, savepoint, result mapping, or DriverAdapterError behavior. Covers current transaction lifecycle, optional savepoint hooks, original database-error preservation, and verification.

OfficialData & Databases378.9K installs

chembl-search

Install

Install

Describe the task

Review the result

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

FAQ

More from yorkeccak/scientific-skills

Popular data & databases skills