uniprot

# UniProt Protein Database ## Overview UniProt is the comprehensive resource for protein sequence and functional annotation. UniProtKB has two sections: Swiss-Prot (reviewed, curated) and TrEMBL (unreviewed, automated). ## REST API Access ```python import requests # Fetch a single entry r = requests.get("https://rest.uniprot.org/uniprotkb/P04637.json") entry = r.json() print(entry["proteinDescription"]["recommendedName"]["fullName"]["value"]) ``` ## Search Queries ```python params = { "query": "(gene:TP53) AND (organism_id:9606) AND (reviewed:true)", "format": "json", "size": 10, "fields": "accession,gene_names,protein_name,organism_name,length" } r = requests.get("https://rest.uniprot.org/uniprotkb/search", params=params) results = r.json()["results"] ``` ## Key Fields - **accession**: Primary identifier (e.g., P04637 for human TP53). - **gene_names**: Associated gene symbols. - **features**: Domains, active sites, variants, PTMs. - **cross-references**: Links to PDB, Pfam, GO, ChEMBL, etc. - **sequence**: Full amino acid sequence. ## Common Query Syntax - `gene:BRCA1` -- by gene name. - `organism_id:9606` -- human. - `reviewed:true` -- Swiss-Prot only. - `ec:3.4.21.*` -- by enzyme classification. - `keyword:kinase` -- by keyword annotation. ## Key Details - Accession format: [OPQ][0-9][A-Z0-9]{3}[0-9] (e.g., P04637). - Batch retrieval: POST to `/uniprotkb/accessions` with list of IDs. - ID mapping: `https://rest.uniprot.org/idmapping/run` for cross-da...