Reactome Biological Pathways Scraper

Scrape curated biological pathways, reactions and their participants from Reactome — the open, peer-reviewed pathway knowledgebase — for 15+ species. Powered by the free, key-less Reactome 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

{
  "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	Protein sequence & annotation	What is this protein
ChEMBL	Bioactivity / chemistry	What compounds hit this target
Ensembl	Genes & genomes	Where is this gene on the genome
RCSB PDB / AlphaFold	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 · chembl-scraper · alphafold-structures-scraper · 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.