bio-uniprot-access
Query UniProt's REST API (post-2022 endpoint at rest.uniprot.org) for protein sequences, annotations, GO terms, cross-references, ID mappings, and proteomes. Use when fetching UniProtKB entries, navigating the JSON schema, choosing between UniProtKB/UniRef/UniParc/Proteomes resources, deciding stream vs search endpoint for batch retrieval, running ID-mapping jobs with the async pattern, handling isoform suffixes, or filtering reviewed Swiss-Prot vs auto-annotated TrEMBL. Encodes the legacy URL migration (2022), the new JSON schema layout, and bulk-pull patterns.
npx skills add BioTender-max/awesome-bio-agent-skills --skill uniprot-access --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.
## Version Compatibility Reference examples tested with: requests 2.31+, pandas 2.2+; UniProt REST API as of 2024_06 release Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show requests pandas` - API surface: confirm endpoint URLs match https://www.uniprot.org/help/api The REST API JSON schema is stable within a release; major schema changes are documented at https://www.uniprot.org/release-notes. The 2022 migration broke the legacy `https://www.uniprot.org/uniprot/...` endpoints. # UniProt Access **"Get protein information from UniProt"** -> Two facts dominate every UniProt workflow in 2026: (1) **the API endpoint migrated in 2022** from `https://www.uniprot.org/uniprot/...` to `https://rest.uniprot.org/uniprotkb/...` with a substantially different JSON schema; pre-2022 code does not work as-is. (2) **`?fields=`** is essential — default JSON returns the full entry (~20-30 KB each); for bulk pulls, request only the fields actually needed. The major databases under the UniProt umbrella have different scopes: - **UniProtKB**: the curated knowledgebase — Swiss-Prot (manually reviewed, ~570K entries as of 2024) + TrEMBL (auto-annotated,
- Version Compatibility
- Required Setup
- Endpoint reference
- Search query syntax
- ?fields= for bulk pulls
- Stream vs search vs accessions
- JSON schema navigation (the post-2022 layout)
- Isoform handling
- ID Mapping API (async)
- Code patterns
- Single entry with defensive JSON parsing
- Search via TSV with fields= (bulk-friendly)
- Stream endpoint for >500 results
- ID mapping with proper async polling
What does the bio-uniprot-access skill do?
Query UniProt's REST API (post-2022 endpoint at rest.uniprot.org) for protein sequences, annotations, GO terms, cross-references, ID mappings, and proteomes. Use when fetching UniProtKB entries, navigating the JSON schema, choosing between UniProtKB/UniRef/UniParc/Proteomes resources, deciding stream vs search endpoint for batch retrieval, running ID-mapping jobs with the async pattern, handling isoform suffixes, or filtering reviewed Swiss-Prot vs auto-annotated TrEMBL. Encodes the legacy URL migration (2022), the new JSON schema layout, and bulk-pull patterns.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill uniprot-access --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.