EBI Ontology Lookup Service Scraper
Pricing
from $7.50 / 1,000 results
EBI Ontology Lookup Service Scraper
Scrapes ontology terms from the EBI Ontology Lookup Service and returns each term as a flat row with its IRI, label, ontology name, description, and synonyms.
Pricing
from $7.50 / 1,000 results
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ParseForge
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EBI Ontology Lookup Service Scraper
Scrape ontology terms from the EBI Ontology Lookup Service, up to a million per run. Every term comes with its IRI, label, synonyms, and ontology source. No login or API key. Export to CSV, JSON, Excel, or XML.
The EBI Ontology Lookup Service (OLS) is the central place to search hundreds of biomedical ontologies, but its web interface and API are built for browsing one term at a time. This Actor reads the public OLS search endpoint directly and returns every matching ontology term in one flat, consistent schema. No registration, no OAuth, no rate-limit headaches.
| Who uses it | What they scrape EBI Ontology Lookup Service for |
|---|---|
| Bioinformaticians | Building a local dictionary of terms from a specific ontology for annotation pipelines |
| Data curators | Checking which ontologies already define a concept before creating a duplicate term |
| Semantic web developers | Harvesting IRIs and labels to populate a knowledge graph or triple store |
| Clinical researchers | Extracting standardized disease or phenotype terms for cohort definitions |
What it does
This Actor collects ontology terms from the EBI Ontology Lookup Service and returns each one as a flat row with its IRI, label, synonyms, and source ontology.
- 🔎 Search-driven collection: the Actor queries the OLS search endpoint and returns every term that matches, not the first page.
- 📦 Flat row output: each term is one record with its IRI, label, synonyms, and ontology, ready for spreadsheets or databases.
- ⚙️ Simple input: set a maximum number of terms and the Actor handles pagination and rate limits for you.
- 🌐 Public endpoint only: no API key or authentication, so you can start a run immediately.
Results export to CSV, JSON, Excel, or XML, or straight from the API.
What you can do with EBI Ontology Lookup Service data
🧬 Build a local ontology dictionary.
A bioinformatician runs the Actor with a high maxItems value to download all terms from a specific ontology, then loads the CSV into a local database for fast annotation lookups.
🔍 Check for existing terms before curation.
A data curator runs the Actor to list terms matching a concept, then compares labels and synonyms to decide whether a new term is really needed.
📊 Populate a knowledge graph.
A semantic web developer collects IRIs and labels from several ontologies and uses the JSON export to seed a triple store or graph database.
🏥 Standardize clinical variables.
A clinical researcher extracts disease terms from a disease ontology and maps free-text patient records to those standardized IRIs for analysis.
Why choose this scraper
| What you get | |
|---|---|
| No API key | The OLS public search endpoint needs no registration, so you can run this Actor right away. |
| One flat schema | Every term is returned with the same fields, so you can merge results from different ontologies without cleaning. |
| Up to a million terms | The maxItems input lets you collect a small sample or a full ontology dump in one run. |
| Standard export formats | Download as CSV, JSON, Excel, or XML and load directly into your analysis tools. |
How it compares
No other Store actor targets EBI Ontology Lookup Service the same way, so the honest comparison is with the alternatives teams actually weigh.
| EBI Ontology Lookup Service Scraper | Build it in-house | By hand | |
|---|---|---|---|
| Setup | Run it now, zero config | Days of engineering | None, but hours per pull |
| When EBI Ontology Lookup Service 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 with a maximum term count, and it will collect that many ontology terms from the EBI Ontology Lookup Service search results. The Input tab lists every parameter.
A first run with the defaults:
A larger pull:
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
- Create a free Apify account with $5 in credit.
- Open the EBI Ontology Lookup Service Scraper.
- Set your inputs and any filters, then click Start.
- 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 Ontology Lookup Service through the Model Context Protocol. Add the Actor to Claude, Cursor, or any MCP client:
Then prompt it in plain language to run the scraper and read back the results.
Troubleshooting
Why am I getting no results?
The OLS search endpoint may have returned an empty result set for the current query. Try running the Actor again later, or check the OLS website directly to confirm that terms exist for your area of interest.
Why did the run stop before reaching my maxItems?
The Actor stops when there are no more results from the OLS search, even if maxItems is higher. This is expected behavior when the total number of matching terms is smaller than your limit.
Why are some fields empty in the output?
Not every ontology term has synonyms or a description. Empty fields mean the OLS record did not include that information.
Why did I get a timeout error?
The OLS endpoint can be slow during peak hours. Increase the Actor's timeout setting in the run options, or retry the run at a different time.
Can I get results for a specific ontology only?
The Actor currently collects from the general OLS search. After the run, filter the dataset by the ontology field to keep only the terms you need.
FAQ
| Question | Answer |
|---|---|
| Do I need an API key for the EBI Ontology Lookup Service? | No. This Actor uses the public OLS search endpoint, which does not require authentication or registration. |
| Which ontologies does this Actor cover? | It queries the OLS search across all ontologies hosted by the EBI. The results include the source ontology for each term, so you can filter afterwards. |
| What fields are returned for each ontology term? | Each row includes the term IRI, label, synonyms, and the ontology it belongs to. The exact field list is shown in the sample output below. |
| Can I limit the number of terms collected? | Yes. Set the maxItems input to any number from 1 to 1,000,000. The Actor stops after collecting that many terms. |
| How does the Actor handle pagination? | It automatically follows the OLS search result pages until it reaches your maxItems limit or there are no more results. |
| Is there a rate limit on the OLS endpoint? | The public endpoint has reasonable usage limits. The Actor includes polite delays between requests to avoid being blocked. |
| Can I search for a specific term or ontology? | This Actor collects terms from the general OLS search. To narrow results, you can filter the exported dataset by ontology or label after the run. |
| What output formats are supported? | You can export the results as CSV, JSON, Excel, or XML from the Apify dataset. |
| Is this Actor affiliated with the EBI? | No. This is an independent scraper that reads the public OLS interface. It is not endorsed by or connected to the European Bioinformatics Institute. |
| Can I run this Actor on a schedule? | Yes. You can set up an Apify schedule to run it daily, weekly, or at any interval to keep your ontology term list up to date. |
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 European Bioinformatics 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.
