MyChem.info Drug Annotation Scraper

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:

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

A larger pull:

{
  "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 to collect up to 1,000,000 results per run.

Run it

1. Create a free Apify account with $5 in credit.
2. Open the MyChem.info Drug Annotation Scraper.
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 (run-sync-get-dataset-items) or the ApifyClient 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:

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: Use this to scrape clinical trial records from ClinicalTrials.gov.

Browse the full ParseForge collection 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.