--- name: quickgo-api-d92b5fe317e3 description: "Browse and search Gene Ontology annotations via the QuickGO API" metadata: openclaw: emoji: "🧬" category: "domains" subcategory: "biomedical" keywords: ["Gene Ontology", "GO annotations", "protein function", "QuickGO", "EBI", "functional genomics"] source: "https://www.ebi.ac.uk/QuickGO/" --- # 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 ```bash # 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 ```bash # 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 ```bash # 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 ```python 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](https://www.ebi.ac.uk/QuickGO/) - [QuickGO API Docs](https://www.ebi.ac.uk/QuickGO/api) - [Gene Ontology](http://geneontology.org/) - Binns, D. et al. (2009). 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