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gene-ontology.md

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1# Gene Ontology (GO) API Reference

Gene Ontology (GO) API Reference

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3## Base URLs

4- **QuickGO (EBI, recommended)**: `https://www.ebi.ac.uk/QuickGO/services` — most reliable endpoint

5- **GO API**: `https://api.geneontology.org/api` — current OpenAPI schema: `https://api.geneontology.org/openapi.json`

6- **AmiGO / GOlr (Solr-based)**: `https://golr.geneontology.org/solr`

Base URLs

QuickGO (EBI, recommended): https://www.ebi.ac.uk/QuickGO/services — most reliable endpoint
GO API: https://api.geneontology.org/api — current OpenAPI schema: https://api.geneontology.org/openapi.json
AmiGO / GOlr (Solr-based): https://golr.geneontology.org/solr

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8## Authentication

9None required. All endpoints are public.

Authentication

None required. All endpoints are public.

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11## Rate Limits

12No published hard limits. QuickGO recommends reasonable usage.

14---

Rate Limits

No published hard limits. QuickGO recommends reasonable usage.

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16## GO API (api.geneontology.org)

GO API (api.geneontology.org)

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18### 1. GO Term Lookup

19```

20GET https://api.geneontology.org/api/ontology/term/{go_id}

21```

22Example:

23```

24GET https://api.geneontology.org/api/ontology/term/GO%3A0008150

25```

26Returns JSON with term name, definition, namespace (biological_process / molecular_function / cellular_component), synonyms.

1. GO Term Lookup

GET https://api.geneontology.org/api/ontology/term/{go_id}

Example:

GET https://api.geneontology.org/api/ontology/term/GO%3A0008150

Returns JSON with term name, definition, namespace (biological_process / molecular_function / cellular_component), synonyms.

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28### 2. Gene/Protein Annotations (Bioentity)

29```

30GET https://api.geneontology.org/api/bioentity/gene/{gene_id}/function

31```

32Example — GO annotations for a UniProt protein:

33```

34GET https://api.geneontology.org/api/bioentity/gene/UniProtKB%3AP04637/function

35```

36Returns GO annotations with evidence codes, qualifiers, references.

2. Gene/Protein Annotations (Bioentity)

GET https://api.geneontology.org/api/bioentity/gene/{gene_id}/function

Example — GO annotations for a UniProt protein:

GET https://api.geneontology.org/api/bioentity/gene/UniProtKB%3AP04637/function

Returns GO annotations with evidence codes, qualifiers, references.

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38### 3. Genes Annotated to a GO Term

39```

40GET https://api.geneontology.org/api/bioentity/function/{go_id}/genes

41```

42Example:

43```

44GET https://api.geneontology.org/api/bioentity/function/GO%3A0006915/genes?rows=20

45```

46Returns genes/proteins annotated with that GO term.

3. Genes Annotated to a GO Term

GET https://api.geneontology.org/api/bioentity/function/{go_id}/genes

Example:

GET https://api.geneontology.org/api/bioentity/function/GO%3A0006915/genes?rows=20

Returns genes/proteins annotated with that GO term.

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48### 4. Search Entities

49```

50GET https://api.geneontology.org/api/search/entity/autocomplete/{query}

51```

52Example:

53```

54GET https://api.geneontology.org/api/search/entity/autocomplete/apoptosis

55```

4. Search Entities

GET https://api.geneontology.org/api/search/entity/autocomplete/{query}

Example:

GET https://api.geneontology.org/api/search/entity/autocomplete/apoptosis

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57### 5. Ontology Ancestors / Descendants

58```

59GET https://api.geneontology.org/api/ontology/term/{go_id}/graph

60```

62---

5. Ontology Ancestors / Descendants

GET https://api.geneontology.org/api/ontology/term/{go_id}/graph

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64## QuickGO API (EBI — recommended for robust annotation queries)

QuickGO API (EBI — recommended for robust annotation queries)

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66### 1. GO Term Details

67```

68GET https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/{go_ids}

69```

70Example:

71```

72GET https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO:0008150

73```

74Accepts comma-separated IDs (up to 25).

1. GO Term Details

GET https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/{go_ids}

Example:

GET https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO:0008150

Accepts comma-separated IDs (up to 25).

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76### 2. Search Annotations

77```

78GET https://www.ebi.ac.uk/QuickGO/services/annotation/search?geneProductId={uniprot_id}

79```

80Example — annotations for TP53:

81```

82GET https://www.ebi.ac.uk/QuickGO/services/annotation/search?geneProductId=P04637&limit=25

83```

2. Search Annotations

GET https://www.ebi.ac.uk/QuickGO/services/annotation/search?geneProductId={uniprot_id}

Example — annotations for TP53:

GET https://www.ebi.ac.uk/QuickGO/services/annotation/search?geneProductId=P04637&limit=25

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85### 3. Annotations by GO Term

86```

87GET https://www.ebi.ac.uk/QuickGO/services/annotation/search?goId=GO:0006915&taxonId=9606&limit=25

88```

3. Annotations by GO Term

GET https://www.ebi.ac.uk/QuickGO/services/annotation/search?goId=GO:0006915&taxonId=9606&limit=25

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90### 4. Filter Annotations by Evidence

91```

92GET https://www.ebi.ac.uk/QuickGO/services/annotation/search?geneProductId=P04637&goUsage=descendants&evidenceCode=ECO:0000269&limit=25

93```

4. Filter Annotations by Evidence

GET https://www.ebi.ac.uk/QuickGO/services/annotation/search?geneProductId=P04637&goUsage=descendants&evidenceCode=ECO:0000269&limit=25

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95### 5. GO Term Children

96```

97GET https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO:0008150/children

98```

5. GO Term Children

GET https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO:0008150/children

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100### 6. GO Term Ancestors (Chart)

101```

102GET https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO:0006915/ancestors?relations=is_a,part_of

103```

104

6. GO Term Ancestors (Chart)

GET https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO:0006915/ancestors?relations=is_a,part_of

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105### 7. Search GO Terms by Name

106```

107GET https://www.ebi.ac.uk/QuickGO/services/ontology/go/search?query=apoptosis&limit=10

108```

109

7. Search GO Terms by Name

GET https://www.ebi.ac.uk/QuickGO/services/ontology/go/search?query=apoptosis&limit=10

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110## QuickGO Annotation Search Parameters

111| Parameter | Description |

112|-----------|-------------|

113| `geneProductId` | UniProt accession (e.g., P04637) |

114| `goId` | GO term (e.g., GO:0006915) |

115| `goUsage` | `exact` or `descendants` (include child terms) |

116| `taxonId` | NCBI taxonomy ID (9606 = human) |

117| `evidenceCode` | ECO code (e.g., ECO:0000269 = experimental) |

118| `aspect` | `biological_process`, `molecular_function`, `cellular_component` |

119| `limit` | Results per page (max 200) |

120| `page` | Page number (1-based) |

121

QuickGO Annotation Search Parameters

Parameter	Description
`geneProductId`	UniProt accession (e.g., P04637)
`goId`	GO term (e.g., GO:0006915)
`goUsage`	`exact` or `descendants` (include child terms)
`taxonId`	NCBI taxonomy ID (9606 = human)
`evidenceCode`	ECO code (e.g., ECO:0000269 = experimental)
`aspect`	`biological_process`, `molecular_function`, `cellular_component`
`limit`	Results per page (max 200)
`page`	Page number (1-based)

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122## QuickGO Response Format

123```json

124{

125 "numberOfHits": 1234,

126 "results": [

127 {

128 "geneProductId": "P04637",

129 "symbol": "TP53",

130 "goId": "GO:0006915",

131 "goName": "apoptotic process",

132 "evidenceCode": "ECO:0000269",

133 "goAspect": "biological_process",

134 "taxonId": 9606,

135 "reference": "PMID:12345678",

136 "assignedBy": "UniProt"

137 }

138 ]

139}

140```

141

QuickGO Response Format

{
  "numberOfHits": 1234,
  "results": [
    {
      "geneProductId": "P04637",
      "symbol": "TP53",
      "goId": "GO:0006915",
      "goName": "apoptotic process",
      "evidenceCode": "ECO:0000269",
      "goAspect": "biological_process",
      "taxonId": 9606,
      "reference": "PMID:12345678",
      "assignedBy": "UniProt"
    }
  ]
}

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142## Notes

143- QuickGO (EBI) is generally more robust and better documented for annotation queries.

144- GO API pagination uses `start`/`rows` on supported bioentity routes. Inspect the current OpenAPI schema for per-route parameters; the autocomplete route replaces the former general entity-search route.

145- URL-encode GO IDs when constructing paths (e.g., `GO%3A0008150` for `GO:0008150`).

146- Three GO namespaces: biological_process (BP), molecular_function (MF), cellular_component (CC).

147- Evidence codes: IDA (direct assay), IMP (mutant phenotype), IGI (genetic interaction), IEA (electronic annotation), etc.

Notes

QuickGO (EBI) is generally more robust and better documented for annotation queries.
GO API pagination uses start/rows on supported bioentity routes. Inspect the current OpenAPI schema for per-route parameters; the autocomplete route replaces the former general entity-search route.
URL-encode GO IDs when constructing paths (e.g., GO%3A0008150 for GO:0008150).
Three GO namespaces: biological_process (BP), molecular_function (MF), cellular_component (CC).
Evidence codes: IDA (direct assay), IMP (mutant phenotype), IGI (genetic interaction), IEA (electronic annotation), etc.

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