医学公开数据库查询与登记

references/reactome.md

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 — zero-based offset (URL-encode the space as %20)
• Force filters=true — keep requested filters even when no records match; the default can relax filters to obtain results. Encode this name as Force%20filters.

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%20sapiens

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/participants/{id}

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).