drug-discovery-prompts/upstream/K-Dense-AI-scientific-agent-skills/skills/database-lookup/references/reactome.md

title, task, lineage_type, upstream_source, upstream_sha, imported_at, prompt_class, upstream_changes, author, validated

title	task	lineage_type	upstream_source	upstream_sha	imported_at	prompt_class	upstream_changes	author	validated
Reactome Content Service REST API		import	https://github.com/K-Dense-AI/scientific-agent-skills/blob/9c9bd2e9/skills/database-lookup/references/reactome.md	9c9bd2e9	2026-06-26	prompt	accepted	upstream	false

Reactome Content Service REST API

Base URL

https://reactome.org/ContentService

No authentication required. JSON by default.

Key Endpoints

Search (full-text across pathways, reactions, proteins)

GET /search/query?query={term}

Parameters:

• query (required) — search term (e.g. "apoptosis", "TP53", "R-HSA-109581")
• species — filter by species (e.g. "Homo sapiens")
• types — filter by type: Pathway, Reaction, Protein, Complex, SmallMolecule
• cluster — boolean, cluster results (default true)
• rows — page size
• Start row — offset for pagination

Example:

/search/query?query=apoptosis&species=Homo+sapiens&types=Pathway

Response:

{
  "results": [
    {
      "typeName": "Pathway",
      "rows": [
        {
          "dbId": 109581,
          "stId": "R-HSA-109581",
          "name": "Apoptosis",
          "species": ["Homo sapiens"],
          "summation": ["..."]
        }
      ]
    }
  ],
  "found": 42
}

Autocomplete

GET /search/suggest?query={partial_term}

Top-level pathways for a species

GET /data/pathways/top/{species}

Example: /data/pathways/top/Homo+sapiens

Pathway details

GET /data/query/{id}

Where {id} is a stable ID like R-HSA-109581 or a numeric dbId.

Events contained in a pathway

GET /data/pathway/{id}/containedEvents

Participants of a reaction

GET /data/event/{id}/participants

Ancestors of an event

GET /data/event/{id}/ancestors

Map external ID to pathways (e.g. UniProt to Reactome pathways)

GET /data/mapping/{resource}/{id}/pathways

Example — find pathways for TP53 (UniProt P04637):

/data/mapping/UniProt/P04637/pathways

Map external ID to reactions

GET /data/mapping/{resource}/{id}/reactions

Generic entity lookup

GET /data/query/{id}

Reference entities for an event

GET /data/participants/{id}/referenceEntities

All species

GET /data/species/all

Event hierarchy for a species (large response)

GET /data/eventsHierarchy/{species}

Stable ID Format

R-{species_code}-{number}

Code	Species
HSA	Homo sapiens
MMU	Mus musculus
RNO	Rattus norvegicus
DME	Drosophila melanogaster
CEL	C. elegans
SCE	S. cerevisiae

External Resource Names for Mapping

UniProt, ChEBI, ENSEMBL, miRBase, GeneCards, NCBI

Multiple values for same parameter: repeat the parameter (e.g. types=Pathway&types=Reaction).

Rate Limits

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).