QuickGO API

Overview

QuickGO is the EBI's fast browser and API for Gene Ontology (GO) annotations — the standard framework for describing gene/protein functions across all organisms. It provides access to 800M+ GO annotations covering biological processes, molecular functions, and cellular components. Essential for functional genomics, pathway analysis, and gene set enrichment. Free, no authentication.

API Endpoints

Base URL

https://www.ebi.ac.uk/QuickGO/services

Search GO Terms

# Search terms by keyword
curl "https://www.ebi.ac.uk/QuickGO/services/ontology/go/search?query=apoptosis&limit=20"

# Get term details
curl "https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO:0006915"

# Get term ancestors/descendants
curl "https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO:0006915/ancestors"
curl "https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO:0006915/descendants"

Query Annotations

# Get annotations for a protein (UniProt ID)
curl "https://www.ebi.ac.uk/QuickGO/services/annotation/search?geneProductId=P04637&limit=50"

# Annotations for a GO term
curl "https://www.ebi.ac.uk/QuickGO/services/annotation/search?goId=GO:0006915&taxonId=9606&limit=50"

# Filter by evidence code
curl "https://www.ebi.ac.uk/QuickGO/services/annotation/search?\
goId=GO:0006915&taxonId=9606&evidence=EXP,IDA,IMP&limit=50"

# Filter by aspect (ontology branch)
curl "https://www.ebi.ac.uk/QuickGO/services/annotation/search?\
geneProductId=P04637&aspect=biological_process"

Download Annotations

# Download as TSV
curl "https://www.ebi.ac.uk/QuickGO/services/annotation/downloadSearch?\
goId=GO:0006915&taxonId=9606&downloadLimit=10000" -o annotations.tsv

GO Aspects

Aspect	Code	Description
Biological Process	biological_process	What the gene does
Molecular Function	molecular_function	Biochemical activity
Cellular Component	cellular_component	Where in the cell

Evidence Codes

Code	Meaning	Reliability
EXP	Inferred from Experiment	High
IDA	Inferred from Direct Assay	High
IMP	Inferred from Mutant Phenotype	High
IPI	Inferred from Physical Interaction	Medium
ISS	Inferred from Sequence Similarity	Medium
IEA	Inferred from Electronic Annotation	Lower

Python Usage

import requests

BASE_URL = "https://www.ebi.ac.uk/QuickGO/services"


def search_go_terms(query: str, limit: int = 20) -> list:
    """Search Gene Ontology terms."""
    resp = requests.get(
        f"{BASE_URL}/ontology/go/search",
        params={"query": query, "limit": limit},
    )
    resp.raise_for_status()
    data = resp.json()

    results = []
    for term in data.get("results", []):
        results.append({
            "id": term.get("id"),
            "name": term.get("name"),
            "aspect": term.get("aspect"),
            "definition": term.get("definition", {}).get("text", ""),
        })
    return results


def get_protein_annotations(uniprot_id: str,
                            aspect: str = None,
                            experimental_only: bool = False) -> list:
    """Get GO annotations for a protein."""
    params = {"geneProductId": uniprot_id, "limit": 100}
    if aspect:
        params["aspect"] = aspect
    if experimental_only:
        params["evidence"] = "EXP,IDA,IMP,IPI,IGI,IEP"

    resp = requests.get(
        f"{BASE_URL}/annotation/search",
        params=params,
    )
    resp.raise_for_status()
    data = resp.json()

    annotations = []
    for ann in data.get("results", []):
        annotations.append({
            "go_id": ann.get("goId"),
            "go_name": ann.get("goName"),
            "aspect": ann.get("goAspect"),
            "evidence": ann.get("goEvidence"),
            "reference": ann.get("reference"),
        })
    return annotations


def get_term_genes(go_id: str, taxon_id: int = 9606,
                   limit: int = 100) -> list:
    """Get genes annotated with a GO term."""
    params = {
        "goId": go_id,
        "taxonId": taxon_id,
        "limit": limit,
    }
    resp = requests.get(
        f"{BASE_URL}/annotation/search",
        params=params,
    )
    resp.raise_for_status()
    data = resp.json()

    genes = set()
    for ann in data.get("results", []):
        genes.add(ann.get("geneProductId", ""))
    return sorted(genes)


# Example: search for apoptosis-related GO terms
terms = search_go_terms("programmed cell death")
for t in terms[:5]:
    print(f"{t['id']}: {t['name']} ({t['aspect']})")

# Example: get p53 protein annotations
annotations = get_protein_annotations("P04637",
                                      experimental_only=True)
for a in annotations[:10]:
    print(f"  {a['go_id']} {a['go_name']} [{a['evidence']}]")

References

• QuickGO
• QuickGO API Docs
• Gene Ontology
• Binns, D. et al. (2009). "QuickGO: a web-based tool for Gene Ontology searching." Bioinformatics 25(22).