quickgo-database
Query EBI QuickGO REST API for GO terms and protein annotations. Fetch term metadata by ID, search by keyword, walk ancestor/descendant hierarchies, download annotations filtered by taxon, evidence code, aspect. Use for GO resolution, ontology traversal, annotation retrieval before enrichment. Use gseapy-gene-enrichment for enrichment; uniprot-protein-database for proteins.
npx skills add BioTender-max/awesome-bio-agent-skills --skill quickgo-database --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
What it does
Fetches GO term metadata by ID, searches GO terms by keyword, retrieves annotations for proteins (with filters by taxon and evidence codes), and traverses GO term hierarchies (ancestors/descendants). It also supports batch GO term resolution and term lookup in a single API call.
How it works
- Uses the QuickGO REST base URL https://www.ebi.ac.uk/QuickGO/services for all endpoints.
- Query GO term metadata via endpoints like /ontology/go/terms/{go_id} and /ontology/go/terms/{ids_param} for batch resolution.
- Retrieve protein annotations through /annotation/search with parameters such as geneProductId (UniProtKB:...), limit, page, and optional evidenceCode filters.
- Obtain ancestors/descendants with /ontology/go/terms/{go_id}/ancestors and /descendants, supplying relation filters.
- Perform ontology searches with /ontology/go/search by keyword, limiting results.
- Obtain annotation statistics via /annotation/search and summarize by evidence code or GO aspect.
- Support batch resolution of multiple GO IDs in one call and provide results including id, name, aspect, and optional definition.
When to use it
- Resolve GO IDs to names, definitions, and aspects.
- Retrieve all GO annotations for a UniProt protein filtered by evidence codes and taxon.
- Search GO terms by keyword to identify relevant IDs for enrichment.
- Walk GO DAG upward (ancestors) or downward (descendants) from a term.
- Get annotation counts by evidence code or GO aspect for analysis or enrichment workflows.
- Use batch GO term resolution to fetch multiple IDs in a single request.
What it can touch
- Endpoints under https://www.ebi.ac.uk/QuickGO/services
- Tools: claude-code
Caveats
- API is free and returns JSON; no authentication required.
- No explicit hard rate limit published; the examples suggest polite batching with time.sleep between requests.
- Data model includes fields like id, name, aspect, synonyms, definition, isObsolete, goName, goAspect, evidenceCode, and numberOfHits for pagination.
# QuickGO Database ## Overview QuickGO is the EBI's Gene Ontology annotation browser and REST API. It provides programmatic access to the GO ontology (terms, synonyms, hierarchies) and to the manually curated and electronic GO annotations for proteins across all species. The API is free, requires no authentication, and returns JSON responses. All endpoints live under `https://www.ebi.ac.uk/QuickGO/services/`. ## When to Use - Resolving a GO term ID (e.g., `GO:0006915`) to its name, definition, and aspect (biological_process, molecular_function, cellular_component) - Retrieving all GO annotations for a UniProt protein, filtered by evidence code and taxon - Searching GO terms by keyword (e.g., "apoptosis") to find relevant term IDs before enrichment analysis - Walking the GO DAG upward (ancestors) or downward (descendants) from a specific term - Getting annotation counts stratified by evidence code or GO aspect for a set of proteins - Resolving multiple GO IDs in one batch request to avoid looping over individual term lookups - For enrichment analysis (ORA/GSEA) on a gene list use `gseapy-gene-enrichment`; QuickGO provides the raw annotation data - For comprehensive protein function
- Overview
- When to Use
- Prerequisites
- Quick Start
- Core API
- Query 1: GO Term Lookup
- Query 2: Annotation Search
- Query 3: Term Hierarchy
- Query 4: Ontology Search
- Query 5: Annotation Statistics
- Query 6: Batch GO Term Query
- Key Concepts
- GO Ontology Structure
- Evidence Code Categories
pip install requests pandas matplotlib
What does the quickgo-database skill do?
Query EBI QuickGO REST API for GO terms and protein annotations. Fetch term metadata by ID, search by keyword, walk ancestor/descendant hierarchies, download annotations filtered by taxon, evidence code, aspect. Use for GO resolution, ontology traversal, annotation retrieval before enrichment. Use gseapy-gene-enrichment for enrichment; uniprot-protein-database for proteins.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill quickgo-database --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.