ParseForge
Reactome Pathways Scraper
parseforge/reactome-pathways-scraper
Developer toolsAIOther
Scrapes Reactome pathway records by search term, stable ID, or species, and returns each record as a flat row with stable ID, name, type, and species.
- Total users
- 2
- Monthly active
- 1
- Total runs
- 86
- Bookmarked
- 0
- Rating
- Not rated yet
- Last modified
- 12 days ago
Overview
Reactome Pathways Scraper
Scrape Reactome pathways, reactions, proteins, and complexes by search term, stable ID, or species. Every record comes with its stable identifier, name, type, and species, ready for CSV, JSON, Excel, or XML export. No API key or login required.
Reactome's official API requires you to learn their content service and handle pagination yourself. This Actor reads the public pathway database directly, so you can search for a term like 'apoptosis', look up a single stable ID like R-HSA-109581, or list top-level pathways for a species such as human or mouse, and get each match as one flat row.
| Who uses it | What they scrape Reactome for |
|---|---|
| Bioinformaticians | Pull pathway lists for enrichment analysis or network building |
| Computational biologists | Gather reaction and protein data for modeling biological processes |
| Pharma researchers | Map drug targets to pathways and complexes |
| Data journalists | Collect pathway data for stories on disease mechanisms |
| Educators | Download pathway examples for teaching molecular biology |
What it does
This Actor collects Reactome pathway records by search term, stable identifier, or species, and returns each one as a flat row with its stable ID, name, type, and species.
- 🔍 Search by term: find pathways, reactions, proteins, and complexes matching a keyword like 'glucose' or 'TP53'.
- 🆔 Look up by stable ID: retrieve a single entity by its Reactome stId, such as R-HSA-109581 for Apoptosis.
- 🧬 List by species: get top-level pathways for human, mouse, rat, zebrafish, fly, worm, yeast, plant, cow, or chicken.
- 📊 Structured output: every record is returned as a flat row with stable ID, name, type, and species, ready for export.
Results export to CSV, JSON, Excel, or XML, or straight from the API.
What you can do with Reactome data
🧪 Build pathway enrichment inputs.
A bioinformatician searches Reactome for 'apoptosis' and exports the matching pathway IDs to feed an enrichment analysis tool.
🎯 Map drug targets to pathways.
A pharma researcher looks up a protein by stable ID and collects the pathways and complexes it participates in to prioritize targets.
📚 Download species pathway lists.
An educator lists top-level pathways for Homo sapiens and downloads the CSV to create a teaching dataset on human metabolism.
🔬 Compare model organisms.
A computational biologist runs the Actor for mouse and rat, then compares pathway names and IDs across species for a comparative study.
📰 Gather disease pathway data.
A data journalist searches for 'cancer' and collects pathway records to support a story on signaling networks.
Why choose this scraper
| What you get | |
|---|---|
| No API key | Reads the public Reactome database directly, no registration or authentication needed. |
| Three input modes | Search by keyword, look up a single stable ID, or list top-level pathways for a species. |
| Flat row output | Each pathway, reaction, protein, or complex is returned as one row with consistent fields. |
| Flexible limits | Set the maximum number of records per run, from 1 to 1,000,000. |
How it compares
This Actor offers the same core Reactome data collection as the competitor, with the same export formats and no API key requirement.
| Feature | ParseForge | Reactome Pathways Scraper |
|---|---|---|
| Search by term | Yes | Not listed |
| Look up by stable ID | Yes | Not listed |
| List top-level pathways by species | Yes | Not listed |
| Export to CSV, JSON, Excel, XML | Yes | Yes |
| No API key required | Yes | Not listed |
Configure the run
Drive the Actor from a search term, a stable ID, or a species, and cap the number of records returned per run. The Input tab lists every parameter.
A first run with the defaults:
{
"maxItems": 10
}
A larger pull:
{
"maxItems": 200
}
Pricing
Pay-per-result: $0.003 per result collected. You pay only for the results written to your dataset.
| Results collected | Approximate cost |
|---|---|
| 100 results | $0.30 |
| 1,000 results | $3.00 |
| 10,000 results | $30.00 |
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 Reactome Pathways 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 Reactome 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/reactome-pathways-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 search term for typos or try a broader keyword. If you set a stable ID, make sure it is correct. Also verify that the species is set correctly when listing top-level pathways.
Why does the Actor return fewer records than my maximum?
The Actor returns only the records that match your input. If you searched for a term, there may be fewer matches than your maximum. If you listed top-level pathways, the number depends on the species.
Why does my stable ID lookup return nothing?
Make sure the stable ID is in the correct format, such as R-HSA-109581. If the ID is valid but no record is returned, the entity may not be available in the current Reactome release.
Can I search for multiple terms at once?
No, the Actor accepts one search term per run. To search for multiple terms, run the Actor multiple times or use a separate run for each term.
Why does the Actor time out?
If you set a very high maximum and the search returns many results, the run may take a long time. Try reducing the maximum or narrowing your search.
FAQ
| Question | Answer |
|---|---|
| What is Reactome? | Reactome is a free, open-source, curated database of biological pathways, reactions, proteins, and complexes. It covers many species, including human, mouse, rat, and others. |
| Do I need an API key to use this Actor? | No. The Actor reads the public Reactome database directly, so no API key, registration, or authentication is required. |
| What can I search for? | You can search for any keyword, such as a gene name, protein, pathway, or biological process. The Actor returns matching pathways, reactions, proteins, and complexes. |
| What is a stable ID (stId)? | A stable ID is a unique identifier for a Reactome entity, such as R-HSA-109581 for Apoptosis. You can use it to look up a single record. |
| Which species are supported? | The Actor supports ten species: Homo sapiens, Mus musculus, Rattus norvegicus, Danio rerio, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, Arabidopsis thaliana, Bos taurus, and Gallus gallus. |
| What fields are returned for each record? | Each record includes the stable ID, name, type, and species. The exact fields are shown in the sample output from a real run. |
| Can I limit the number of results? | Yes. Set the 'Maximum pathways' input to any number from 1 to 1,000,000. The Actor will stop after collecting that many records. |
| What export formats are supported? | You can export the results as CSV, JSON, Excel, or XML from the Apify dataset. |
| Is the data from Reactome free to use? | Reactome data is freely available under a Creative Commons license. Check the Reactome website for the current license terms. |
| How do I list all top-level pathways for a species? | Leave both the search term and stId empty, and select the species from the dropdown. The Actor will return the top-level pathways for that species. |
Related actors
- reactome-pathways-scraper: Use this Actor to scrape Reactome pathways, reactions, proteins, and complexes by search term, stable ID, or species.
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 Reactome. 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.
Input
| Field | Type | What it does | Default |
|---|---|---|---|
| searchTerm | string | Keyword to search across Reactome (for example 'apoptosis', 'glucose', 'TP53'). Returns matching pathways, reactions, proteins, and complexes. Leave empty to list top-level pathways for the chosen species. | not set |
| stId | string | Reactome stable identifier to look up a single entity, for example R-HSA-109581 (Apoptosis). When set, this takes priority over the search term. | not set |
| species | string (10 options) | Species for the top-level pathway listing. Used only when no search term and no stId are provided. | 9606 |
| maxItems | integer | How many pathways to collect per run. | 10 |
Pricing
from $2.00 per 1,000 results
| Charged for | What it is | Price each |
|---|---|---|
| result | Single result in the default dataset. | $0.002 to $0.003 |
Tiered: the lower figure is the price on a higher Apify plan. Billing and the free credit live on Apify.
API
One POST returns the dataset directly. Same shape for every scraper in the library, so swapping the slug is the only change.
curl -X POST "https://api.apify.com/v2/acts/parseforge~reactome-pathways-scraper/run-sync-get-dataset-items?token=$APIFY_TOKEN" \
-H "Content-Type: application/json" \
-d '{
"helloWorld": 123
}' Examples
Input that runs as-is.
{
"helloWorld": 123
} Reviews
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Issues
We build and maintain this scraper, so a problem with it comes to us. Report it on the Apify listing and the thread stays attached to the scraper where the next person can find it: open an issue.
Broken and urgent, or you would rather not post in public? Write to parseforge@protonmail.com and it reaches the people who wrote it.