# Reactome Biological Pathways Scraper (`ninhothedev/reactome-pathways-scraper`) Actor

$0.5/1K 🔥 Reactome Pathways! Pull biological pathways, reactions & participants by species or query. No key. JSON, CSV, Excel or API in seconds. Power bioinformatics and drug-target research ⚡

- **URL**: https://apify.com/ninhothedev/reactome-pathways-scraper.md
- **Developed by:** [ninhothedev](https://apify.com/ninhothedev) (community)
- **Categories:** Developer tools
- **Stats:** 2 total users, 1 monthly users, 100.0% runs succeeded, 0 bookmarks
- **User rating**: No ratings yet

## Pricing

from $0.50 / 1,000 results

This Actor is paid per event. You are not charged for the Apify platform usage, but only a fixed price for specific events.

Learn more: https://docs.apify.com/platform/actors/running/actors-in-store#pay-per-event

## What's an Apify Actor?

Actors are web data automations that power AI and operations. They run on the Apify platform to scrape websites, process data, connect APIs, and automate workflows.
In Batch mode, an Actor accepts a well-defined JSON input, performs an action which can take anything from a few seconds to a few hours,
and optionally produces a well-defined JSON output, datasets with results, or files in key-value store.
In Standby mode, an Actor provides a web server which can be used as a website, API, or an MCP server.
Actors are written with capital "A".

## How to integrate an Actor?

If asked about integration, you help developers integrate Actors into their projects.
You adapt to their stack and deliver integrations that are safe, well-documented, and production-ready.
The best way to integrate Actors is as follows.

- **AI agents and MCP clients** — the [Apify MCP server](https://docs.apify.com/integrations/mcp.md) at `https://mcp.apify.com` (remote, streamable HTTP, OAuth on first use).
- **Agentic workflows and local Actor development** — [Agent Skills](https://apify.com/.well-known/agent-skills/index.json) with the [Apify CLI](https://docs.apify.com/cli/docs.md): `npm install -g apify-cli`, then `apify login`.
- **JavaScript/TypeScript projects** — the official [JS/TS client](https://docs.apify.com/api/client/js/docs.md): `npm install apify-client`.
- **Python projects** — the official [Python client](https://docs.apify.com/api/client/python/docs.md): `pip install apify-client`.
- **Any other language** — the [REST API](https://docs.apify.com/api/v2.md).

For usage examples, see the [API](#api) section below.

For more details, see Apify documentation as [Markdown index](https://docs.apify.com/llms.txt) and [Markdown full-text](https://docs.apify.com/llms-full.txt).

# README

## Reactome Biological Pathways Scraper

Scrape **curated biological pathways, reactions and their participants** from
[Reactome](https://reactome.org) — the open, peer-reviewed pathway
knowledgebase — for **15+ species**. Powered by the free, key-less
[Reactome ContentService](https://reactome.org/ContentService). **No API key,
no account, no scraping tricks.** Clean JSON in, clean JSON out.

From roughly **~$0.50 per 1,000 pathways**, this actor turns Reactome's
manually-curated systems-biology graph into flat, pipeline-ready records.

### What you get

Each record is a normalised pathway *or* reaction:

| field | meaning |
|-------|---------|
| `st_id` | Reactome stable ID (e.g. `R-HSA-70171`) |
| `db_id` | internal Reactome dbId |
| `name` | display name |
| `species` / `tax_id` | species name + NCBI taxonomy id |
| `is_in_disease` | boolean disease flag |
| `has_diagram` | boolean — a process diagram exists |
| `summary` | human-readable summation (capped 4,000 chars) |
| `sub_event_count` | number of child events |
| `sub_events` | compact `[{stId, name}]` list (capped 30) |
| `literature_count` | number of literature references |
| `is_reaction` | `true` = reaction (ReactionLikeEvent), `false` = pathway |
| `url` | Reactome detail page |
| `diagram_url` | pathway diagram PNG (ContentService exporter) |
| `source`, `scraped_at` | provenance |

> Note on `diagram_url`: standard process diagrams and reactions export
> reliably as PNG. A handful of very high-level "EHLD" landing pathways
> (e.g. *Autophagy*, *Cell Cycle*) use illustrated overviews and may not
> render through the diagram exporter — the URL is still emitted for
> completeness.

### Modes

| mode | does | key inputs |
|------|------|-----------|
| `toplevel` *(default)* | Top-level pathways for a species | `species` |
| `search` | Find pathways/reactions by keyword | `queries`, `species` |
| `pathways` | Rich detail for explicit stable IDs | `stIds` |

#### Input

```json
{
  "mode": "toplevel",
  "species": "9606",
  "queries": ["glycolysis", "apoptosis"],
  "stIds": ["R-HSA-70171"],
  "maxItems": 200
}
```

- **species** accepts an NCBI tax id (`9606` human, `10090` mouse, `10116`
  rat, …) *or* a display name (`Homo sapiens`).
- Human currently exposes **29 top-level pathways**; a keyword search like
  `glycolysis` returns the *Glycolysis* pathway (`R-HSA-70171`) with its 16
  sub-events.

### Use cases

- **Systems biology** — pull the full curated pathway hierarchy per organism.
- **Pathway enrichment pipelines** — feed gene/reaction sets into over-
  representation or GSEA workflows with clean stable IDs.
- **Drug-target research** — flag disease pathways (`is_in_disease`) and drill
  into reactions around a target.
- **Teaching & courses** — ready-made, referenced pathway summaries and
  diagrams for lectures and notebooks.

### How this differs from our other life-science scrapers

This account also publishes **sequence** and **structure** scrapers. They
answer *different* questions:

| Actor | Layer | Answers |
|-------|-------|---------|
| **Reactome (this)** | **Pathways & reactions** | *How do molecules interact — the curated biological process* |
| [UniProt](https://apify.com/ninhothedev/uniprot-scraper) | Protein sequence & annotation | *What is this protein* |
| [ChEMBL](https://apify.com/ninhothedev/chembl-scraper) | Bioactivity / chemistry | *What compounds hit this target* |
| [Ensembl](https://apify.com/ninhothedev/ensembl-scraper) | Genes & genomes | *Where is this gene on the genome* |
| [RCSB PDB](https://reactome.org) / [AlphaFold](https://apify.com/ninhothedev/alphafold-structures-scraper) | 3D structure | *What does the molecule look like* |

**Reactome is the pathway/network layer** — curated, reviewed reactions and
the pathways that contain them — not sequences, genes or 3D coordinates. Use
it when you need *biological process context*, then join on `st_id` /
cross-references to the actors above.

Related actors:
[uniprot-scraper](https://apify.com/ninhothedev/uniprot-scraper) ·
[chembl-scraper](https://apify.com/ninhothedev/chembl-scraper) ·
[alphafold-structures-scraper](https://apify.com/ninhothedev/alphafold-structures-scraper) ·
[ensembl-scraper](https://apify.com/ninhothedev/ensembl-scraper)

### Data & licence

Reactome data is released under **CC-BY-4.0** — free to use with attribution
to Reactome. This actor only reads the public ContentService; please cite
Reactome in derived work.

# Actor input Schema

## `mode` (type: `string`):

What to scrape. 'toplevel' = top-level pathways for a species. 'search' = query pathways/reactions by keyword. 'pathways' = fetch rich detail for an explicit list of Reactome stable IDs.

## `species` (type: `string`):

NCBI taxonomy id (e.g. '9606' for human, '10090' mouse, '10116' rat) or a species display name (e.g. 'Homo sapiens'). Used by 'toplevel' and as a filter for 'search'. Reactome covers 15+ species.

## `queries` (type: `array`):

Keywords to search when mode = 'search', e.g. glycolysis or apoptosis. Each query is searched independently and results are de-duplicated by stId.

## `stIds` (type: `array`):

Explicit Reactome stable IDs to fetch when mode = 'pathways', e.g. R-HSA-70171 (Glycolysis). Accepts both pathway and reaction IDs.

## `maxItems` (type: `integer`):

Maximum number of records to output across the run.

## Actor input object example

```json
{
  "mode": "toplevel",
  "species": "9606",
  "queries": [
    "glycolysis",
    "apoptosis"
  ],
  "stIds": [
    "R-HSA-70171"
  ],
  "maxItems": 200
}
```

# Actor output Schema

## `results` (type: `string`):

No description

# API

You can run this Actor programmatically using our API. Below are code examples in JavaScript, Python, and CLI, as well as the OpenAPI specification and MCP server setup.

## JavaScript example

```javascript
import { ApifyClient } from 'apify-client';

// Initialize the ApifyClient with your Apify API token
// Replace the '<YOUR_API_TOKEN>' with your token
const client = new ApifyClient({
    token: '<YOUR_API_TOKEN>',
});

// Prepare Actor input
const input = {
    "queries": [
        "glycolysis",
        "apoptosis"
    ],
    "stIds": [
        "R-HSA-70171"
    ]
};

// Run the Actor and wait for it to finish
const run = await client.actor("ninhothedev/reactome-pathways-scraper").call(input);

// Fetch and print Actor results from the run's dataset (if any)
console.log('Results from dataset');
console.log(`💾 Check your data here: https://console.apify.com/storage/datasets/${run.defaultDatasetId}`);
const { items } = await client.dataset(run.defaultDatasetId).listItems();
items.forEach((item) => {
    console.dir(item);
});

// 📚 Want to learn more 📖? Go to → https://docs.apify.com/api/client/js/docs

```

## Python example

```python
from apify_client import ApifyClient

# Initialize the ApifyClient with your Apify API token
# Replace '<YOUR_API_TOKEN>' with your token.
client = ApifyClient("<YOUR_API_TOKEN>")

# Prepare the Actor input
run_input = {
    "queries": [
        "glycolysis",
        "apoptosis",
    ],
    "stIds": ["R-HSA-70171"],
}

# Run the Actor and wait for it to finish
run = client.actor("ninhothedev/reactome-pathways-scraper").call(run_input=run_input)

# Fetch and print Actor results from the run's dataset (if there are any)
print(f"💾 Check your data here: https://console.apify.com/storage/datasets/{run.default_dataset_id}")
for item in client.dataset(run.default_dataset_id).iterate_items():
    print(item)

# 📚 Want to learn more 📖? Go to → https://docs.apify.com/api/client/python/docs/quick-start

```

## CLI example

```bash
echo '{
  "queries": [
    "glycolysis",
    "apoptosis"
  ],
  "stIds": [
    "R-HSA-70171"
  ]
}' |
apify call ninhothedev/reactome-pathways-scraper --silent --output-dataset

```

## MCP server setup

```json
{
    "mcpServers": {
        "apify": {
            "type": "http",
            "url": "https://mcp.apify.com/?tools=fetch-actor-details,ninhothedev/reactome-pathways-scraper"
        }
    }
}

```

The hosted server signs you in with OAuth on first connect, so no API token belongs in this config. Clients without OAuth support can send an `Authorization: Bearer <APIFY_API_TOKEN>` header instead, using a token from API & Integrations in Apify Console (https://console.apify.com/settings/integrations).

## OpenAPI specification

Download the OpenAPI definition: https://api.apify.com/v2/actors/qUoxlcGcVHnaBcIC5/builds/3nbDLNhScfAxMdZ6P/openapi.json