uniprot-protein-database
Query UniProt REST API: search by gene/protein name, fetch FASTA, map IDs (Ensembl, PDB, RefSeq), access Swiss-Prot annotations. Use bioservices for multi-DB access; alphafold-database for structures.
npx skills add BioTender-max/awesome-bio-agent-skills --skill uniprot-protein-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.
# UniProt — Protein Database ## Overview UniProt is the most comprehensive protein sequence and functional annotation database, containing 250M+ entries. This skill covers programmatic access via the UniProt REST API for protein search, sequence retrieval, ID mapping, and annotation queries. Swiss-Prot entries are manually curated; TrEMBL entries are computationally predicted. ## When to Use - Searching for proteins by gene name, accession, organism, or function keywords - Retrieving protein sequences in FASTA format for downstream analysis - Mapping identifiers between databases (UniProt ↔ Ensembl, PDB, RefSeq, KEGG) - Accessing protein annotations: GO terms, domains, post-translational modifications - Batch retrieving multiple protein entries for comparative analysis - Downloading reviewed (Swiss-Prot) protein datasets for a specific organism - For **unified access to 40+ databases**, use bioservices instead - For **protein 3D structures**, use alphafold-database or pdb-database ## Prerequisites ```bash pip install requests pandas ``` **API Rate Limits**: UniProt REST API has no strict rate limit but recommends adding `time.sleep(0.5)` between batch requests. For large queries (>
- Overview
- When to Use
- Prerequisites
- Quick Start
- Core API
- 1. Protein Search
- 2. Protein Entry Retrieval
- 3. ID Mapping
- 4. Batch Retrieval and Streaming
- 5. Pagination and Cursor-Based Iteration
- 6. Field Selection and Annotations
- Key Parameters
- Best Practices
- Common Recipes
pip install requests pandas
What does the uniprot-protein-database skill do?
Query UniProt REST API: search by gene/protein name, fetch FASTA, map IDs (Ensembl, PDB, RefSeq), access Swiss-Prot annotations. Use bioservices for multi-DB access; alphafold-database for structures.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill uniprot-protein-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.