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QuickGO

Access Gene Ontology data via the QuickGO API.

Overview

QuickGO provides fast access to Gene Ontology (GO) data:

  • GO Terms - Term definitions and relationships
  • Annotations - Gene-GO associations
  • Hierarchy - Parent/child relationships

Quick Start

from biodbs.fetch import (
    quickgo_search_terms,
    quickgo_get_terms,
    quickgo_search_annotations,
)

# Search GO terms
terms = quickgo_search_terms("apoptosis")

GO Terms

Search Terms

from biodbs.fetch import quickgo_search_terms

terms = quickgo_search_terms("apoptosis")
terms = quickgo_search_terms("kinase activity")

Get Terms

from biodbs.fetch import quickgo_get_terms

terms = quickgo_get_terms(["GO:0006915", "GO:0008150"])

Term Hierarchy

from biodbs.fetch import quickgo_get_term_children, quickgo_get_term_ancestors

children = quickgo_get_term_children("GO:0008150")
ancestors = quickgo_get_term_ancestors("GO:0006915")

Annotations

Search Annotations

from biodbs.fetch import quickgo_search_annotations

# By gene product
annotations = quickgo_search_annotations(
    gene_product_id="UniProtKB:P04637"
)

# By GO term
annotations = quickgo_search_annotations(
    go_id="GO:0006915"
)

Download Annotations

from biodbs.fetch import quickgo_download_annotations, quickgo_search_annotations_all

# Download in different formats
annotations = quickgo_download_annotations(
    gene_product_id="UniProtKB:P04637",
    format="tsv"
)

# Get all annotations (paginated)
all_annotations = quickgo_search_annotations_all(
    taxon_id=9606,
    aspect="biological_process"
)

Gene Product Info

from biodbs.fetch import quickgo_get_gene_product

product = quickgo_get_gene_product("UniProtKB:P04637")

Using the Fetcher Class

from biodbs.fetch.QuickGO import QuickGO_Fetcher

fetcher = QuickGO_Fetcher()
terms = fetcher.search_terms("apoptosis")
  • UniProt - Get detailed protein information for GO-annotated gene products. QuickGO uses UniProt accessions for queries.
  • Over-Representation Analysis - Perform GO term enrichment analysis with ora_go().
  • Knowledge Graphs - Build knowledge graphs from GO data with build_go_graph().
  • ID Translation - Translate gene identifiers to UniProt format for QuickGO annotation lookups.