154 lines
3.0 KiB
Markdown
154 lines
3.0 KiB
Markdown
---
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title: "Reactome Content Service REST API"
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task: ""
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lineage_type: import
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upstream_source: https://github.com/K-Dense-AI/scientific-agent-skills/blob/9c9bd2e9/skills/database-lookup/references/reactome.md
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upstream_sha: 9c9bd2e9
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imported_at: 2026-06-26
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prompt_class: prompt
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upstream_changes: accepted
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author: upstream
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validated: false
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---
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# Reactome Content Service REST API
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## Base URL
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```
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https://reactome.org/ContentService
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```
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No authentication required. JSON by default.
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## Key Endpoints
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### Search (full-text across pathways, reactions, proteins)
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```
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GET /search/query?query={term}
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```
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Parameters:
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- `query` (required) — search term (e.g. "apoptosis", "TP53", "R-HSA-109581")
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- `species` — filter by species (e.g. "Homo sapiens")
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- `types` — filter by type: `Pathway`, `Reaction`, `Protein`, `Complex`, `SmallMolecule`
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- `cluster` — boolean, cluster results (default true)
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- `rows` — page size
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- `Start row` — offset for pagination
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Example:
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```
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/search/query?query=apoptosis&species=Homo+sapiens&types=Pathway
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```
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Response:
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```json
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{
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"results": [
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{
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"typeName": "Pathway",
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"rows": [
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{
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"dbId": 109581,
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"stId": "R-HSA-109581",
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"name": "Apoptosis",
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"species": ["Homo sapiens"],
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"summation": ["..."]
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}
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]
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}
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],
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"found": 42
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}
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```
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### Autocomplete
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```
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GET /search/suggest?query={partial_term}
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```
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### Top-level pathways for a species
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```
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GET /data/pathways/top/{species}
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```
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Example: `/data/pathways/top/Homo+sapiens`
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### Pathway details
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```
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GET /data/query/{id}
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```
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Where `{id}` is a stable ID like `R-HSA-109581` or a numeric dbId.
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### Events contained in a pathway
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```
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GET /data/pathway/{id}/containedEvents
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```
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### Participants of a reaction
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```
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GET /data/event/{id}/participants
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```
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### Ancestors of an event
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```
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GET /data/event/{id}/ancestors
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```
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### Map external ID to pathways (e.g. UniProt to Reactome pathways)
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```
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GET /data/mapping/{resource}/{id}/pathways
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```
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Example — find pathways for TP53 (UniProt P04637):
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```
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/data/mapping/UniProt/P04637/pathways
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```
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### Map external ID to reactions
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```
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GET /data/mapping/{resource}/{id}/reactions
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```
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### Generic entity lookup
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```
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GET /data/query/{id}
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```
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### Reference entities for an event
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```
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GET /data/participants/{id}/referenceEntities
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```
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### All species
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```
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GET /data/species/all
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```
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### Event hierarchy for a species (large response)
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```
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GET /data/eventsHierarchy/{species}
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```
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## Stable ID Format
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`R-{species_code}-{number}`
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| Code | Species |
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|---|---|
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| HSA | Homo sapiens |
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| MMU | Mus musculus |
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| RNO | Rattus norvegicus |
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| DME | Drosophila melanogaster |
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| CEL | C. elegans |
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| SCE | S. cerevisiae |
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## External Resource Names for Mapping
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`UniProt`, `ChEBI`, `ENSEMBL`, `miRBase`, `GeneCards`, `NCBI`
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Multiple values for same parameter: repeat the parameter (e.g. `types=Pathway&types=Reaction`).
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## Rate Limits
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No API key required. No formal rate limit published, but be reasonable — avoid hundreds of concurrent requests. For bulk data, use Reactome's downloadable dumps (MySQL, Neo4j, BioPAX, SBML).
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