EBI OLS Ontologies List Scraper

EBI OLS Ontologies List Scraper

Scrape the complete list of ontologies from the EMBL-EBI Ontology Lookup Service, up to a million per run. Every ontology comes with its ID, title, description, and namespace. No API key or registration. Export to CSV, JSON, Excel, or XML.

The EMBL-EBI Ontology Lookup Service (OLS) hosts hundreds of biomedical ontologies, but browsing them manually or querying the API for a full inventory is slow and rate-limited. This Actor reads the public ontology list directly and returns every entry in one flat dataset. It is built for bioinformaticians and data curators who need a current, machine-readable index of all available OLS ontologies.

Who uses it	What they scrape EBI OLS for
Bioinformaticians	Build a local registry of all public biomedical ontologies for tool integration.
Data curators	Audit which ontologies are currently available in OLS for a metadata mapping project.
Semantic web developers	Fetch the latest ontology namespace and prefix list for an RDF application.
Research data managers	Monitor the OLS catalog for new or deprecated ontologies relevant to their domain.

What it does

This Actor collects the list of all ontologies available in the EBI OLS and returns each one as a flat row.

• 📋 Full catalog dump: Collect every ontology listed on the OLS front page in a single run.
• 🔢 Configurable limit: Set a maximum number of ontologies to fetch, from one to a million.
• 📄 Flat, structured output: Each ontology is returned as a clean row with its ID, title, description, and namespace, ready for analysis.

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

What you can do with EBI OLS data

🧬 Build a local ontology registry.

A bioinformatics platform ingests the full OLS ontology list weekly to keep its internal lookup service synchronized with the latest public ontologies.

📊 Audit ontology coverage for a project.

A data curator runs the scraper before a metadata harmonization sprint to confirm which relevant ontologies are present and note any gaps.

🔗 Populate an RDF namespace map.

A semantic web developer fetches the ontology list to auto-generate prefix-to-namespace mappings for a SPARQL endpoint configuration.

📈 Monitor the OLS catalog over time.

A research data manager schedules a monthly scrape to detect newly added ontologies in a specific biomedical domain and update downstream documentation.

Why choose this scraper

	What you get
No API key needed	Reads the public ontology listing without registration or authentication.
Always current	Each run fetches the live list from OLS, so your data reflects the latest catalog.
Fixed schema	Every ontology is returned with the same fields, making it easy to parse and import.
Bulk export	Save the full list to CSV, JSON, Excel, or XML for offline use or pipeline ingestion.

How it compares

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

	EBI OLS Ontologies List Scraper	Build it in-house	By hand
Setup	Run it now, zero config	Days of engineering	None, but hours per pull
When EBI OLS 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 by setting a maximum number of ontologies to collect, and it will return the most current list from the EBI OLS. The Input tab lists every parameter.

A first run with the defaults:

{
 "maxItems": 10
}

A larger pull:

{
 "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 EBI OLS Ontologies List 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 EBI OLS 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/ebi-ols-ontologies-list-scraper"

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

Troubleshooting

Why am I getting fewer results than expected?

Check the 'Maximum ontologies' input setting. If it is set lower than the total number of ontologies on OLS, the Actor stops after reaching that limit. Increase the number to collect the full list.

The run failed with a timeout error.

The EBI OLS website may have been slow to respond. Try increasing the run timeout in the Actor's advanced settings, or retry the run during a less busy period.

Some fields are empty in the output.

Not every ontology in OLS has a description or a namespace filled in. Empty fields reflect missing metadata on the OLS page itself, not a scraping error.

The scraper returns an empty dataset.

Ensure the 'Maximum ontologies' is set to at least 1. If the OLS website layout has changed, the scraper may need an update; check the Actor's page for a newer version or report the issue.

FAQ

Question	Answer
Does this scraper require an API key or login?	No. It reads the public ontology listing from the EBI OLS website, so no registration or authentication is needed.
What fields does each ontology row contain?	Each row includes the ontology ID, title, description, and namespace as displayed on the OLS ontologies page. The exact field list is shown in the sample output on the Actor's page.
Can I scrape only a specific subset of ontologies?	This Actor collects the full list in the order it appears on OLS. You can limit the total number of ontologies returned, but it does not filter by domain or keyword. Use the exported dataset to filter after the run.
How often is the OLS ontology list updated?	The EBI OLS catalog is updated as new ontologies are added or existing ones are modified. Run this Actor on a schedule to capture changes as they happen.
What is the maximum number of ontologies I can collect?	You can set the limit up to 1,000,000 ontologies per run, which is far more than the current total number of ontologies in OLS.
Can I get the ontology file itself, not the metadata?	No, this Actor scrapes the ontology list metadata from the OLS directory. To download the full ontology files, you would need a different tool that follows the individual ontology links.
Is this an official EMBL-EBI tool?	No, this is a third-party scraper built on Apify. It is not developed or endorsed by EMBL-EBI.
What output formats are supported?	You can export the dataset to CSV, JSON, Excel, or XML from the Apify platform.
Can I run this scraper on a schedule?	Yes, Apify supports scheduled runs. You can configure it to scrape the OLS ontology list daily, weekly, or at any custom 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.