医学公开数据库查询与登记

references/gene-ontology.md

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

Authentication

None required. All endpoints are public.

Rate Limits

No published hard limits. QuickGO recommends reasonable usage.

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GO API (api.geneontology.org)

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.

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.

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.

4. Search Entities

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

Example:

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

5. Ontology Ancestors / Descendants

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

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QuickGO API (EBI — recommended for robust annotation queries)

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).

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

3. Annotations by GO Term

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

4. Filter Annotations by Evidence

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

5. GO Term Children

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

6. GO Term Ancestors (Chart)

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

7. Search GO Terms by Name

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

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)

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"
    }
  ]
}

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.