Skills › Scientific Agent Skills › database-lookup › reactome.md

reactome.md

141 lines · skills/database-lookup/references/reactome.md at 5f2bc03

Open on GitHub

1# Reactome Content Service REST API

Reactome Content Service REST API

Raw lines 1 to 2

3## Base URL

5```

6https://reactome.org/ContentService

7```

9No authentication required. JSON by default.

Base URL

https://reactome.org/ContentService

No authentication required. JSON by default.

Raw lines 3 to 10

11## Key Endpoints

Key Endpoints

Raw lines 11 to 12

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

15```

16GET /search/query?query={term}

17```

19Parameters:

20- `query` (required) — search term (e.g. "apoptosis", "TP53", "R-HSA-109581")

21- `species` — filter by species (e.g. "Homo sapiens")

22- `types` — filter by type: `Pathway`, `Reaction`, `Protein`, `Complex`, `SmallMolecule`

23- `cluster` — boolean, cluster results (default true)

24- `rows` — page size

25- `Start row` — zero-based offset (URL-encode the space as `%20`)

26- `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`.

28Example:

29```

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

31```

33Response:

34```json

35{

36 "results": [

37 {

38 "typeName": "Pathway",

39 "rows": [

40 {

41 "dbId": 109581,

42 "stId": "R-HSA-109581",

43 "name": "Apoptosis",

44 "species": ["Homo sapiens"],

45 "summation": ["..."]

46 }

47 ]

48 }

49 ],

50 "found": 42

51}

52```

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
}

Raw lines 13 to 53

54### Autocomplete

55```

56GET /search/suggest?query={partial_term}

57```

Autocomplete

GET /search/suggest?query={partial_term}

Raw lines 54 to 58

59### Top-level pathways for a species

60```

61GET /data/pathways/top/{species}

62```

63Example: `/data/pathways/top/Homo%20sapiens`

Top-level pathways for a species

GET /data/pathways/top/{species}

Example: /data/pathways/top/Homo%20sapiens

Raw lines 59 to 64

65### Pathway details

66```

67GET /data/query/{id}

68```

69Where `{id}` is a stable ID like `R-HSA-109581` or a numeric dbId.

Pathway details

GET /data/query/{id}

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

Raw lines 65 to 70

71### Events contained in a pathway

72```

73GET /data/pathway/{id}/containedEvents

74```

Events contained in a pathway

GET /data/pathway/{id}/containedEvents

Raw lines 71 to 75

76### Participants of a reaction

77```

78GET /data/participants/{id}

79```

Participants of a reaction

GET /data/participants/{id}

Raw lines 76 to 80

81### Ancestors of an event

82```

83GET /data/event/{id}/ancestors

84```

Ancestors of an event

GET /data/event/{id}/ancestors

Raw lines 81 to 85

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

87```

88GET /data/mapping/{resource}/{id}/pathways

89```

90Example — find pathways for TP53 (UniProt P04637):

91```

92/data/mapping/UniProt/P04637/pathways

93```

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

Raw lines 86 to 94

95### Map external ID to reactions

96```

97GET /data/mapping/{resource}/{id}/reactions

98```

Map external ID to reactions

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

Raw lines 95 to 99

100### Generic entity lookup

101```

102GET /data/query/{id}

103```

104

Generic entity lookup

GET /data/query/{id}

Raw lines 100 to 104

105### Reference entities for an event

106```

107GET /data/participants/{id}/referenceEntities

108```

109

Reference entities for an event

GET /data/participants/{id}/referenceEntities

Raw lines 105 to 109

110### All species

111```

112GET /data/species/all

113```

114

All species

GET /data/species/all

Raw lines 110 to 114

115### Event hierarchy for a species (large response)

116```

117GET /data/eventsHierarchy/{species}

118```

119

Event hierarchy for a species (large response)

GET /data/eventsHierarchy/{species}

Raw lines 115 to 119

120## Stable ID Format

121

122`R-{species_code}-{number}`

123

124| Code | Species |

125|---|---|

126| HSA | Homo sapiens |

127| MMU | Mus musculus |

128| RNO | Rattus norvegicus |

129| DME | Drosophila melanogaster |

130| CEL | C. elegans |

131| SCE | S. cerevisiae |

132

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

Raw lines 120 to 132

133## External Resource Names for Mapping

134

135`UniProt`, `ChEBI`, `ENSEMBL`, `miRBase`, `GeneCards`, `NCBI`

136

137Multiple values for same parameter: repeat the parameter (e.g. `types=Pathway&types=Reaction`).

138

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).

Raw lines 133 to 138

139## Rate Limits

140

141No 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).

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).

Raw lines 139 to 141