# MyChem.info Drug Annotation Scraper (`parseforge/mychem-drug-annotation-scraper`) Actor

Scrapes curated drug annotations from MyChem.info for a search query or a list of drug names or InChIKeys. Returns each drug as one flat row with indications, mechanisms, targets, and identifiers.

- **URL**: https://apify.com/parseforge/mychem-drug-annotation-scraper.md
- **Developed by:** [ParseForge](https://apify.com/parseforge) (community)
- **Categories:** Developer tools, AI, Other
- **Stats:** 2 total users, 1 monthly users, 100.0% runs succeeded, 0 bookmarks
- **User rating**: No ratings yet

## Pricing

from $2.00 / 1,000 results

This Actor is paid per event. You are not charged for the Apify platform usage, but only a fixed price for specific events.
Since this Actor supports Apify Store discounts, the price gets lower the higher subscription plan you have.

Learn more: https://docs.apify.com/actors/running/actors-in-store.md#pay-per-event

## What's an Apify Actor?

Actors are web data automations that power AI and operations. They run on the Apify platform to scrape websites, process data, connect APIs, and automate workflows.
In Batch mode, an Actor accepts a well-defined JSON input, performs an action which can take anything from a few seconds to a few hours,
and optionally produces a well-defined JSON output, datasets with results, or files in key-value store.
In Standby mode, an Actor provides a web server which can be used as a website, API, or an MCP server.
Actors are written with capital "A".

## How to integrate an Actor?

If asked about integration, you help developers integrate Actors into their projects.
You adapt to their stack and deliver integrations that are safe, well-documented, and production-ready.
The best way to integrate Actors is as follows.

- **AI agents and MCP clients** — the [Apify MCP server](https://docs.apify.com/integrations/mcp.md) at `https://mcp.apify.com` (remote, streamable HTTP, OAuth on first use).
- **Agentic workflows and local Actor development** — [Agent Skills](https://apify.com/.well-known/agent-skills/index.json) with the [Apify CLI](https://docs.apify.com/cli/docs.md): `npm install -g apify-cli`, then `apify login`.
- **JavaScript/TypeScript projects** — the official [JS/TS client](https://docs.apify.com/api/client/js/docs.md): `npm install apify-client`.
- **Python projects** — the official [Python client](https://docs.apify.com/api/client/python/docs.md): `pip install apify-client`.
- **Any other language** — the [REST API](https://docs.apify.com/api/v2.md).

For usage examples, see the [API](#api) section below.

For more details, see Apify documentation as [Markdown index](https://docs.apify.com/llms.txt) and [Markdown full-text](https://docs.apify.com/llms-full.txt).

# README

[![ParseForge](https://raw.githubusercontent.com/ParseForge/apify-assets/main/banner.jpg)](https://apify.com/parseforge?fpr=vmoqkp)

### MyChem.info Drug Annotation Scraper

**Scrape curated drug annotations from MyChem.info by drug name, keyword, or InChIKey.** Each record returns the drug's indications, mechanisms, targets, and identifiers in one flat row. No API key required. Export to CSV, JSON, Excel, or XML.

MyChem.info aggregates drug annotations from ChEMBL, DrugBank, PharmGKB, and other sources, but querying it programmatically means writing your own API client and parsing deeply nested JSON. This Actor resolves drug names, keywords, or InChIKeys to the best-matching curated annotations and returns each drug as a flat, analysis-ready row.

| Who uses it | What they scrape MyChem.info for |
|---|---|
| Pharmacologists | Pull mechanism-of-action and target data for a set of compounds. |
| Bioinformaticians | Build a local dataset of drug annotations for enrichment analysis. |
| Clinical researchers | Gather indications and contraindications for drugs in a trial. |
| Data journalists | Investigate drug approvals and label changes across therapeutic areas. |

### What it does

This Actor collects curated drug annotations from MyChem.info for a search query or a list of drug names or InChIKeys, and returns each drug as one flat row.

- 🔍 **Search by keyword:** enter a therapeutic area or drug name and get the best-matching annotated compounds.
- 📋 **Batch by list:** paste up to a million drug names or InChIKeys and resolve each to its curated annotation.
- 🧬 **Identifier resolution:** accepts common drug names and InChIKeys, returning the canonical MyChem.info record.
- 📊 **Flat output:** every drug is returned as one row with indications, mechanisms, targets, and identifiers.

Results export to CSV, JSON, Excel, or XML, or straight from the API.

### What you can do with MyChem.info data

**🧪 Build a kinase inhibitor dataset.**

A pharmacologist enters 'kinase inhibitor' as the search query and exports the resulting drugs with their targets and mechanisms for a selectivity analysis.

**📋 Annotate a compound library.**

A bioinformatician pastes a list of InChIKeys from a screening hit list and gets back indications and targets for each compound to prioritize follow-up.

**📈 Track drug repurposing candidates.**

A clinical researcher searches for a disease keyword and collects all drugs annotated with that indication to identify candidates for repurposing.

**🗞️ Investigate drug safety signals.**

A data journalist pulls annotations for a set of drugs and compares their listed contraindications and adverse effects across sources.

### Why choose this scraper

|  | What you get |
|---|---|
| **No API coding** | The Actor handles MyChem.info's query and response parsing for you. |
| **Curated annotations** | Each record aggregates data from ChEMBL, DrugBank, PharmGKB, and more. |
| **Flat schema** | Nested JSON is flattened into one row per drug for easy analysis. |
| **Batch friendly** | Resolve up to a million drugs in a single run. |

### How it compares

No other Store actor targets MyChem.info the same way, so the honest comparison is with the alternatives teams actually weigh.

| | MyChem.info Drug Annotation Scraper | Build it in-house | By hand |
|---|---|---|---|
| Setup | Run it now, zero config | Days of engineering | None, but hours per pull |
| When MyChem.info changes | Maintained for you | You fix it | You re-learn the page |
| Proxies, retries, anti-bot | Built in | Your problem | Browser only |
| Output | Fixed JSON schema, CSV/Excel export | Whatever you build | Copy-paste |
| Cost | Pay per result | Engineering time | Analyst hours |

### Configure the run

Drive the Actor from a search query, a list of drug names or InChIKeys, or both, and cap how many drugs are collected per run. The Input tab lists every parameter.

A first run with the defaults:

```json
{
  "searchQuery": "leukemia",
  "drugList": [
    "imatinib",
    "dasatinib",
    "nilotinib",
    "aspirin",
    "metformin"
  ],
  "maxItems": 10
}
```

A larger pull:

```json
{
  "searchQuery": "leukemia",
  "drugList": [
    "imatinib",
    "dasatinib",
    "nilotinib",
    "aspirin",
    "metformin"
  ],
  "maxItems": 200
}
```

### Pricing

Pay-per-result: **$0.004 per result** collected. You pay only for the results written to your dataset.

| Results collected | Approximate cost |
|---|---|
| 100 results | $0.40 |
| 1,000 results | $4.00 |
| 10,000 results | $40.00 |

New Apify accounts start with $5 in free credit.

### Free users

Free-plan runs return up to 10 results as a preview. [Upgrade your Apify plan](https://console.apify.com/sign-up?fpr=vmoqkp) to collect up to 1,000,000 results per run.

### Run it

1. [Create a free Apify account with $5 in credit](https://console.apify.com/sign-up?fpr=vmoqkp).
2. Open the [MyChem.info Drug Annotation Scraper](https://apify.com/parseforge/mychem-drug-annotation-scraper?fpr=vmoqkp).
3. Set your inputs and any filters, then click **Start**.
4. Export the results as CSV, Excel, JSON, or XML from the **Dataset** tab.

Run it programmatically through the [Apify API](https://docs.apify.com/api/v2) (`run-sync-get-dataset-items`) or the [ApifyClient](https://docs.apify.com/api/client/js) for JavaScript and Python.

### Use with AI agents (MCP)

Give an AI agent live access to MyChem.info through the Model Context Protocol. Add the Actor to Claude, Cursor, or any MCP client:

```bash
claude mcp add --transport http apify "https://mcp.apify.com/?tools=parseforge/mychem-drug-annotation-scraper"
```

Then prompt it in plain language to run the scraper and read back the results.

### Troubleshooting

**Why am I getting no results?**

Check that your search query or drug list is not empty. If using a keyword, try a broader term. If using drug names, verify the spelling or try the InChIKey instead.

**Why does my drug name return the wrong drug?**

MyChem.info may match a different compound with a similar name. Use the InChIKey for unambiguous resolution, or refine your search query.

**Why is the run slow with a large drug list?**

The Actor queries MyChem.info for each drug individually. For very large lists, consider splitting them into smaller batches or increasing the run timeout.

**Why are some fields empty in the output?**

Not all drugs have annotations for every field. MyChem.info only returns data that is available from its sources.

### FAQ

| Question | Answer |
|---|---|
| What is MyChem.info? | MyChem.info is a free API that provides integrated drug annotations from sources like ChEMBL, DrugBank, PharmGKB, and the FDA. It is maintained by The Su Lab at The Scripps Research Institute. |
| Do I need an API key? | No. The Actor queries the public MyChem.info endpoint directly, so no registration or key is required. |
| What input formats does it accept? | You can provide a free-text search query, a list of drug names, a list of InChIKeys, or any combination of these. |
| What does the output look like? | Each drug is returned as one flat row with fields for indications, mechanisms, targets, identifiers, and more. The exact fields are shown in the sample output. |
| How many drugs can I collect in one run? | You can set the maximum number of drugs per run, up to 1,000,000. |
| What if a drug name is ambiguous? | The Actor uses MyChem.info's best-match resolution, which returns the most relevant curated annotation for the query. |
| Can I search by therapeutic area? | Yes. Enter a keyword like 'leukemia' or 'diabetes' and the Actor returns drugs annotated with that indication. |
| Does it support InChIKeys? | Yes. You can paste a list of InChIKeys and each will be resolved to its drug annotation. |
| What export formats are available? | You can export the results as CSV, JSON, Excel, or XML. |
| Is the data updated? | The Actor fetches live data from MyChem.info on each run, so you always get the current annotations. |

### Related actors

- [clinicaltrials-scraper](https://apify.com/parseforge/clinicaltrials-scraper?fpr=vmoqkp): Use this to scrape clinical trial records from ClinicalTrials.gov.

Browse the full [ParseForge collection](https://apify.com/parseforge?fpr=vmoqkp) for more scrapers.

🆘 **Need help?** Email parseforge@protonmail.com with your run ID, your input, and what you expected.

⚠️ **Disclaimer.** This Actor is unofficial and is not affiliated with, endorsed by, or sponsored by The Su Lab at The Scripps Research Institute. It collects only publicly available data. You are responsible for using the collected data in compliance with the source's terms of service and applicable data-protection laws, including GDPR, CCPA, and PIPL. Do not use it to collect personal data unlawfully.

# Actor input Schema

## `searchQuery` (type: `string`):

A free-text search term such as a therapeutic area or drug name (for example imatinib, leukemia, kinase). The Actor returns the curated annotations for the best-matching drug-annotated compounds. Leave blank when supplying a drug list below.

## `drugList` (type: `array`):

One or more drug names (for example imatinib, aspirin) or InChIKeys (for example KTUFNOKKBVMGRW-UHFFFAOYSA-N). Each entry is resolved to its curated MyChem.info annotation.

## `maxItems` (type: `integer`):

How many drugs to collect per run.

## Actor input object example

```json
{
  "searchQuery": "leukemia",
  "drugList": [
    "imatinib",
    "dasatinib",
    "nilotinib",
    "aspirin",
    "metformin"
  ],
  "maxItems": 10
}
```

# Actor output Schema

## `results` (type: `string`):

No description

# API

You can run this Actor programmatically using our API. Below are code examples in JavaScript, Python, and CLI, as well as the OpenAPI specification and MCP server setup.

## JavaScript example

```javascript
import { ApifyClient } from 'apify-client';

// Initialize the ApifyClient with your Apify API token
// Replace the '<YOUR_API_TOKEN>' with your token
const client = new ApifyClient({
    token: '<YOUR_API_TOKEN>',
});

// Prepare Actor input
const input = {
    "searchQuery": "leukemia",
    "drugList": [
        "imatinib",
        "dasatinib",
        "nilotinib",
        "aspirin",
        "metformin"
    ],
    "maxItems": 10
};

// Run the Actor and wait for it to finish
const run = await client.actor("parseforge/mychem-drug-annotation-scraper").call(input);

// Fetch and print Actor results from the run's dataset (if any)
console.log('Results from dataset');
console.log(`💾 Check your data here: https://console.apify.com/storage/datasets/${run.defaultDatasetId}`);
const { items } = await client.dataset(run.defaultDatasetId).listItems();
items.forEach((item) => {
    console.dir(item);
});

// 📚 Want to learn more 📖? Go to → https://docs.apify.com/api/client/js/docs

```

## Python example

```python
from apify_client import ApifyClient

# Initialize the ApifyClient with your Apify API token
# Replace '<YOUR_API_TOKEN>' with your token.
client = ApifyClient("<YOUR_API_TOKEN>")

# Prepare the Actor input
run_input = {
    "searchQuery": "leukemia",
    "drugList": [
        "imatinib",
        "dasatinib",
        "nilotinib",
        "aspirin",
        "metformin",
    ],
    "maxItems": 10,
}

# Run the Actor and wait for it to finish
run = client.actor("parseforge/mychem-drug-annotation-scraper").call(run_input=run_input)

# Fetch and print Actor results from the run's dataset (if there are any)
print(f"💾 Check your data here: https://console.apify.com/storage/datasets/{run.default_dataset_id}")
for item in client.dataset(run.default_dataset_id).iterate_items():
    print(item)

# 📚 Want to learn more 📖? Go to → https://docs.apify.com/api/client/python/docs/quick-start

```

## CLI example

```bash
echo '{
  "searchQuery": "leukemia",
  "drugList": [
    "imatinib",
    "dasatinib",
    "nilotinib",
    "aspirin",
    "metformin"
  ],
  "maxItems": 10
}' |
apify call parseforge/mychem-drug-annotation-scraper --silent --output-dataset

```

## MCP server setup

```json
{
    "mcpServers": {
        "apify": {
            "type": "http",
            "url": "https://mcp.apify.com/?tools=fetch-actor-details,parseforge/mychem-drug-annotation-scraper"
        }
    }
}

```

The hosted server signs you in with OAuth on first connect, so no API token belongs in this config. Clients without OAuth support can send an `Authorization: Bearer <APIFY_API_TOKEN>` header instead, using a token from API & Integrations in Apify Console (https://console.apify.com/settings/integrations).

## OpenAPI specification

Download the OpenAPI definition: https://api.apify.com/v2/actors/snSnBJkV9UoePrSRq/builds/bdHPniupTgvUORwb0/openapi.json