BioModels Models Scraper

BioModels Models Scraper

Scrape BioModels model records by keyword, up to a million per run. Every record comes with its ID, name, URL, format, submitter, and submission date. No API key or registration. Export to JSON, CSV, Excel, or XML.

BioModels is a repository of curated mathematical models of biological systems, but browsing it manually or writing custom scripts takes time. This Actor searches the public BioModels database by keyword and returns each matching model record in a flat, structured row. You get the model ID, name, URL, format, submitter, and submission date for every result, ready for analysis.

Who uses it	What they scrape BioModels for
Bioinformatics researchers	Gathering a list of published models for a specific disease or pathway.
Systems biology modelers	Finding reusable SBML or CellML models by topic before building their own.
Data curators	Auditing model metadata across a domain for completeness and consistency.
Academic groups	Building a searchable internal catalog of models relevant to their lab's focus.

What it does

This Actor searches BioModels by keyword and returns each matching model record as a flat row with its ID, name, URL, format, submitter, and submission date.

• 🔍 Keyword search: feed the Actor any biological term, gene name, or disease and it returns every matching model record.
• 📊 Structured output: each row is a flat record with model ID, name, URL, format, submitter, and submission date, consistent across runs.
• 📈 Scalable collection: set a maximum from 1 to 1,000,000 models per run to control scope and cost.

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

What you can do with BioModels data

🧬 Map models for a disease area.

A bioinformatician searches 'cancer' and collects every curated model to identify which pathways and species are most represented.

📋 Audit model metadata.

A data curator runs a keyword for a pathway of interest and exports the submitter and submission date fields to check for outdated or unmaintained entries.

🔁 Feed a modeling pipeline.

A systems biologist scrapes all models tagged with a specific gene, then downloads the SBML files from the URLs for parameterization and simulation.

📚 Build a lab knowledge base.

A research group searches their organism of interest, collects the model list, and stores it as a shared CSV for new lab members.

Why choose this scraper

	What you get
Consistent schema	Every model record arrives with the same fields, so your analysis script never breaks.
No API key	Reads the public search interface directly, no registration or token management.
Bulk export	Save results as JSON, CSV, Excel, or XML for direct use in R, Python, or spreadsheets.

How it compares

This Actor and the original Biomodels Models Scraper collect the same core metadata fields from BioModels search results.

Feature	ParseForge	Biomodels Models Scraper
Keyword search	Yes	Yes
Model ID field	Yes	Yes
Submitter field	Yes	Yes
Submission date field	Yes	Yes
Format field	Yes	Yes

Configure the run

Drive the Actor with a single keyword or phrase, and set a maximum number of models to cap the run. The Input tab lists every parameter.

A first run with the defaults:

{
 "query": "cancer",
 "maxItems": 10
}

A larger pull:

{
 "query": "cancer",
 "maxItems": 200
}

Pricing

Pay-per-result: $0.0085 per result collected. You pay only for the results written to your dataset.

Results collected	Approximate cost
100 results	$0.85
1,000 results	$8.50
10,000 results	$85.00

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 BioModels Models 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 BioModels 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/biomodels-models-scraper"

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

Troubleshooting

Why am I getting no results?

Check your query spelling. Try a broader term or a known model ID. If the BioModels website returns no results for that term, the Actor will also return nothing.

The run stopped before reaching my maxItems limit.

The Actor stops when BioModels has no more results for your query. Your keyword may have fewer matching models than the limit you set.

Some fields are empty in my output.

BioModels records do not always have every field populated. If a model lacks a submitter or format, that cell will be blank in your dataset.

The run is taking a long time.

Large maxItems values mean more requests. Reduce the maximum models per run, or run the Actor on an Apify plan with higher memory if you need speed.

I got an error during the run.

Check the run log for details. Temporary issues with the BioModels website can cause failures. Retry the run after a few minutes.

FAQ

Question	Answer
Do I need an API key or account to scrape BioModels?	No. This Actor reads the public BioModels search interface directly, so no registration, API key, or authentication is required.
What fields does each model record contain?	Each row includes the model ID, name, URL, format, submitter, and submission date. The exact field list is shown in the sample output on this page.
Can I scrape all models on BioModels?	You can search by keyword. To collect a large portion of the database, use a broad or empty query and set a high maxItems value.
What export formats are supported?	You can export your dataset as JSON, CSV, Excel, or XML from the Apify platform.
How many models can I collect in one run?	You set the maximum, from 1 up to 1,000,000 models per run. The Actor stops when it reaches your limit or when no more results match.
Does this Actor download the model files themselves?	No, it collects the metadata records. Each record includes the model's URL, which you can use to download the SBML or other format file separately.
Can I search by model ID instead of keyword?	Yes. Enter the model ID as your query string and the Actor will return that model's record if it exists.
Is this Actor affiliated with BioModels or EMBL-EBI?	No. This is an independent scraper that reads publicly available data from the BioModels website.
How do I run this on a schedule?	After publishing the Actor, you can set up a scheduled run in Apify to collect new or updated models at a regular interval.

Related actors

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 EMBL-EBI. 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.