# PubChem-MCP

> Use this tool when you need to retrieve detailed information on chemical compounds, substances, and molecular properties from the PubChem database. It solves problems related to chemical classification, cross-referencing, and data retrieval through natural language searches by name, structure, or identifier. The tool provides outputs such as chemical classifications and cross-references, making it ideal for use cases involving chemical research, analysis, and discovery.

Canonical page: https://skillsregistry.net/skills/biocontext-pubchem-mcp  
JSON: https://api.skillsregistry.net/v1/skills/biocontext-pubchem-mcp

## Description

An MCP server that provides tools for querying the PubChem database for detailed information on chemical compounds, substances, bioassays, and molecular properties. It enables users to search by name, structure, or identifier to retrieve chemical classifications and cross-references through natural language.

## Trust

- **Trust score (0–1):** 0.71
- **Verification tier:** verified
- **Last scanned:** 2026-09-19

## Facts

- **Version:** 1.0.0
- **Skill type:** atomic
- **Execution layer:** mcp-remote
- **Runtime environment:** api
- **Category:** database
- **Updated:** 2026-09-19

## Source

- **Source listing:** [Glama](https://glama.ai/mcp/servers/p26mit8yu0)
- **Repository:** <https://github.com/BioContext/PubChem-MCP>

## Use it

Resolve this record through the SkillsRegistry MCP server (no auth, read-only):

```
claude mcp add --transport http --scope user skillsregistry https://api.skillsregistry.net/mcp
```

```json
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "get_skill",
    "arguments": {
      "slug": "biocontext-pubchem-mcp"
    }
  }
}
```

REST: `GET https://api.skillsregistry.net/v1/skills/biocontext-pubchem-mcp` · pull for local use: `GET https://api.skillsregistry.net/v1/skills/biocontext-pubchem-mcp/pull`

---
SkillsRegistry indexes agent skills from public registries and GitHub. Skills we have analysed are scanned with Circle-IR and scored on six dimensions; each listing states its scan coverage. More: https://skillsregistry.net/llms.txt