🧬 Reactome Pathways Scraper

🚀 Export curated biology pathways in seconds. Pull the full set of top-level human pathways (29 entries), search 10+ result types per keyword, or look up any entity by stable ID with its summary and sub-event count.

🕒 Last updated: 2026-06-04 · 📊 Up to 13 fields per record · 10 species supported · Reactome ContentService (open, keyless)

Reactome is a free, open-source, peer-reviewed knowledgebase of biological pathways. This Actor turns its public ContentService into clean, structured records you can drop straight into a notebook, a spreadsheet, or a downstream pipeline. Point it at a species to list every top-level pathway, search by a gene or process keyword, or resolve a single stable identifier such as R-HSA-109581.

Coverage spans curated pathways, reactions, proteins, complexes, and sets. Each record carries the Reactome stable identifier, display name, species, schema class, disease flag, diagram availability, and a direct Pathway Browser link, so you always know exactly which entity you are looking at and where to view it.

🎯 Target Audience	💡 Primary Use Cases
Bioinformaticians and computational biologists	Building pathway reference tables for enrichment analysis
Data scientists in life sciences and pharma	Mapping genes and proteins to curated pathways
Researchers and graduate students	Pulling pathway summaries and sub-event counts for review
Knowledge engineers and database builders	Seeding internal catalogs with stable Reactome identifiers

📋 What the Reactome Pathways Scraper does

• Lists every top-level pathway for a chosen species (Homo sapiens returns 29 entries).
• Searches Reactome by keyword and returns matching pathways, reactions, proteins, complexes, and sets.
• Looks up a single entity by stable identifier and adds a plain-text summary plus a sub-event count.
• Strips embedded HTML from names and summaries so values are ready to use.
• Builds a direct Pathway Browser link for every record.

🎬 Full Demo (🚧 Coming soon)

⚙️ Input

Provide one of three modes. A stable identifier takes priority, then a search term, otherwise the Actor lists top-level pathways for the selected species.

Field	Type	Description
searchTerm	string	Keyword to search across Reactome, for example apoptosis, glucose, or TP53.
stId	string	Reactome stable identifier to look up a single entity, for example R-HSA-109581.
species	select	Species for the top-level listing. Defaults to Homo sapiens (9606). Ten species supported.
maxItems	integer	Free users limited to 10 items. Paid users up to 1,000,000.

Example 1, list top-level human pathways:

{
  "species": "9606",
  "maxItems": 10
}

Example 2, search by keyword:

{
  "searchTerm": "apoptosis",
  "maxItems": 25
}

⚠️ Good to Know: Reactome search names and summaries arrive wrapped in HTML highlight tags. This Actor removes those tags for you, so the values you receive are clean text. Stable identifiers are species-specific, for example R-HSA for human and R-MMU for mouse.

📊 Output

Each record is one pathway, reaction, or entity. Conditional fields appear only when the source provides them: name on listing and lookup records, summary when a description exists, subEventCount in lookup mode, and searchType in search mode.

Field	Description
🆔 stId	Reactome stable identifier
🔢 dbId	Internal Reactome database identifier
📌 displayName	Human readable name
🏷 name	All known names, joined
🧬 speciesName	Species the entity belongs to
🗂 schemaClass	Reactome class, such as Pathway or TopLevelPathway
🩺 isInDisease	Whether the entity is associated with disease
🖼 hasDiagram	Whether a pathway diagram exists
✨ hasEHLD	Whether an enhanced high level diagram exists
🔗 url	Direct Pathway Browser link
📝 summary	Plain text description, when available
🔁 subEventCount	Number of contained sub-events, lookup mode
🔎 searchType	Result type label, search mode
🕒 scrapedAt	Timestamp of collection
❌ error	Error message, null on success

Three real records from a live run:

{
  "stId": "R-HSA-9612973",
  "dbId": 9612973,
  "displayName": "Autophagy",
  "name": "Autophagy",
  "speciesName": "Homo sapiens",
  "schemaClass": "TopLevelPathway",
  "isInDisease": false,
  "hasDiagram": true,
  "hasEHLD": true,
  "url": "https://reactome.org/PathwayBrowser/#/R-HSA-9612973",
  "scrapedAt": "2026-06-04T19:42:28.000Z",
  "error": null
}

{
  "stId": "R-HSA-1640170",
  "dbId": 1640170,
  "displayName": "Cell Cycle",
  "name": "Cell Cycle",
  "speciesName": "Homo sapiens",
  "schemaClass": "TopLevelPathway",
  "isInDisease": false,
  "hasDiagram": true,
  "hasEHLD": true,
  "url": "https://reactome.org/PathwayBrowser/#/R-HSA-1640170",
  "scrapedAt": "2026-06-04T19:42:28.000Z",
  "error": null
}

{
  "stId": "R-HSA-1500931",
  "dbId": 1500931,
  "displayName": "Cell-Cell communication",
  "name": "Cell-Cell communication",
  "speciesName": "Homo sapiens",
  "schemaClass": "TopLevelPathway",
  "isInDisease": false,
  "hasDiagram": true,
  "hasEHLD": true,
  "url": "https://reactome.org/PathwayBrowser/#/R-HSA-1500931",
  "scrapedAt": "2026-06-04T19:42:28.000Z",
  "error": null
}

✨ Why choose this Actor

• Three modes in one tool, listing, search, and single lookup.
• Keyless and stable, built on the official Reactome ContentService.
• Clean values, HTML highlight tags removed before you receive them.
• Conditional fields only when real, so you never ship always-null columns.
• Direct Pathway Browser links on every record for instant context.

📈 How it compares to alternatives

Approach	Setup	Clean output	Multi-mode	Maintenance
This Actor	None, run and go	Yes	Listing, search, lookup	Managed
Manual API calls	Write and host code	You parse HTML yourself	You build each call	Yours
Copy from the website	Slow and manual	No	No	High effort

🚀 How to use

1. Create a free Apify account using this sign-up link.
2. Open the Reactome Pathways Scraper in the Apify Console.
3. Choose a mode, set a species, type a search term, or paste a stable identifier.
4. Set how many records you want with the items limit.
5. Run the Actor and collect your structured pathway records.

💼 Business use cases

Pharma and biotech research

Need	How this helps
Target discovery context	Map proteins and genes to curated pathways
Disease association review	Filter records by the disease flag

Bioinformatics pipelines

Need	How this helps
Reference tables	Seed enrichment analysis with stable identifiers
Reproducibility	Pin records to versioned Reactome entries

Academic and teaching

Need	How this helps
Course materials	Pull pathway names and summaries for slides
Literature reviews	Resolve identifiers to readable descriptions

Knowledge base and catalog building

Need	How this helps
Internal catalogs	Populate tables with names, species, and links
Cross referencing	Use stable identifiers as join keys

🔌 Automating Reactome Pathways Scraper

Connect the Actor to the tools your team already uses. Trigger runs and route results through Make, Zapier, Slack, Airbyte, GitHub Actions, or Google Drive using the Apify API and integrations. Schedule recurring runs to keep a local pathway catalog fresh, or post new lookups to a Slack channel for your research group.

🌟 Beyond business use cases

• Research: assemble pathway datasets for a thesis or a paper.
• Personal: explore the biology behind a gene or a condition you care about.
• Non-profit: build open educational resources around cell biology.
• Experimentation: prototype a pathway browser or a graph of biological events.

🤖 Ask an AI assistant

Pair the structured output with ChatGPT, Claude, Perplexity, or Microsoft Copilot to summarize pathway descriptions, group results by schema class, or draft an enrichment report from your collected records.

❓ Frequently Asked Questions

Is this Actor affiliated with Reactome? No. It is an independent tool that reads the public Reactome ContentService. Only publicly available data is collected.

Do I need an API key? No. The Reactome ContentService is open and keyless.

Which species are supported? Ten, including Homo sapiens, Mus musculus, Rattus norvegicus, Danio rerio, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, Arabidopsis thaliana, Bos taurus, and Gallus gallus.

How many top-level pathways does human return? Twenty-nine at the time of writing. Mouse returns twenty-eight.

What is a stable identifier? A persistent Reactome ID such as R-HSA-109581. The R-HSA prefix marks human entities, R-MMU marks mouse.

What gets returned in search mode? Matching pathways, reactions, proteins, complexes, and sets, each with a result type label.

Why are some fields missing on some records? Fields appear only when the source provides them. Search entries, for example, do not carry diagram flags, so those fields are omitted rather than shipped as null.

Does it return pathway descriptions? Yes, when available. Lookup mode and search results include a plain text summary with HTML tags removed.

How many records can I collect? Free users get up to 10 items per run. Paid users can collect up to 1,000,000.

Can I see the pathway diagram? Each record includes a direct Pathway Browser link where you can open the diagram.

How fresh is the data? Records reflect the live Reactome ContentService at the moment of the run.

Can I automate recurring runs? Yes. Use Apify schedules and integrations to run the Actor on a cadence and route results to your tools.

🔌 Integrate with any app

Use the Apify API, webhooks, and the integrations catalog to push records into your database, data warehouse, or workflow automation tool. Every run produces a structured dataset you can fetch programmatically.

🔗 Recommended Actors

• KEGG Pathways Scraper
• UniProt Scraper
• ChEMBL Molecules Scraper
• Ensembl Genomics Scraper
• Open Targets Platform Scraper

💡 Pro Tip: browse the complete ParseForge collection.

🆘 Need Help? Open our contact form

⚠️ Disclaimer: independent tool, not affiliated with Reactome. Only publicly available data collected.