--- name: api_examples description: api_examples skill metadata: short-description: api_examples skill category: utilities source: claude-code-templates --- # Api_Examples # UniProt API Examples Practical code examples for interacting with the UniProt REST API in multiple languages. ## Python Examples ### Example 1: Basic Search ```python import requests # Search for human insulin proteins url = "https:\/\/rest.uniprot.org\/uniprotkb\/search" params = { "query": "insulin AND organism_id:9606 AND reviewed:true", "format": "json", "size": 10 } response = requests.get(url, params=params) data = response.json() for result in data['results']: print(f"{result['primaryAccession']}: {result['proteinDescription']['recommendedName']['fullName']['value']}") ``` ### Example 2: Retrieve Protein Sequence ```python import requests # Get human insulin sequence in FASTA format accession = "P01308" url = f"https:\/\/rest.uniprot.org\/uniprotkb\/{accession}.fasta" response = requests.get(url) print(response.text) ``` ### Example 3: Custom Fields ```python import requests # Get specific fields only url = "https:\/\/rest.uniprot.org\/uniprotkb\/search" params = { "query": "gene:BRCA1 AND reviewed:true", "format": "tsv", "fields": "accession,gene_names,organism_name,length,cc_function" } response = requests.get(url, params=params) print(response.text) ``` ### Example 4: ID Mapping ```python import requests import time def map_uniprot_ids(ids, from_db, to_db): # Submit job submit_url = "https:\/\/rest.uniprot.org\/idmapping\/run" data = { "from": from_db, "to": to_db, "ids": ",".join(ids) } response = requests.post(submit_url, data=data) job_id = response.json()["jobId"] # Poll for completion status_url = f"https:\/\/rest.uniprot.org\/idmapping\/status\/{job_id}" while True: response = requests.get(status_url) status = response.json() if "results" in status or "failedIds" in status: break time.sleep(3) # Get results results_url = f"https:\/\/rest.uniprot.org\/idmapping\/results\/{job_id}" response = requests.get(results_url) return response.json() # Map UniProt IDs to PDB ids = ["P01308", "P04637"] mapping = map_uniprot_ids(ids, "UniProtKB_AC-ID", "PDB") print(mapping) ``` ### Example 5: Stream Large Results ```python import requests # Stream all reviewed human proteins url = "https:\/\/rest.uniprot.org\/uniprotkb\/stream" params = { "query": "organism_id:9606 AND reviewed:true", "format": "fasta" } response = requests.get(url, params=params, stream=True) # Process in chunks with open("human_proteins.fasta", "w") as f: for chunk in response.iter_content(chunk_size=8192, decode_unicode=True): if chunk: f.write(chunk) ``` ### Example 6: Pagination ```python import requests def get_all_results(query, fields=None): """Get all results with pagination""" url = "https:\/\/rest.uniprot.org\/uniprotkb\/search" all_results = [] params = { "query": query, "format": "json", "size": 500 # Max size per page } if fields: params["fields"] = ",".join(fields) while True: response = requests.get(url, params=params) data = response.json() all_results.extend(data['results']) # Check for next page if 'next' in data: url = data['next'] else: break return all_results # Get all human kinases results = get_all_results( "protein_name:kinase AND organism_id:9606 AND reviewed:true", fields=["accession", "gene_names", "protein_name"] ) print(f"Found {len(results)} proteins") ``` ## cURL Examples ### Example 1: Simple Search ```bash # Search for insulin proteins curl "https:\/\/rest.uniprot.org\/uniprotkb\/search?query=insulin&format=json&size=5" ``` ### Example 2: Get Protein Entry ```bash # Get human insulin in FASTA format curl "https:\/\/rest.uniprot.org\/uniprotkb\/P01308.fasta" ``` ### Example 3: Custom Fields ```bash # Get specific fields in TSV format curl "https:\/\/rest.uniprot.org\/uniprotkb\/search?query=gene:BRCA1&format=tsv&fields=accession,gene_names,length" ``` ### Example 4: ID Mapping - Submit Job ```bash # Submit mapping job curl -X POST "https:\/\/rest.uniprot.org\/idmapping\/run" \ -H "Content-Type: application\/x-www-form-urlencoded" \ -d "from=UniProtKB_AC-ID&to=PDB&ids=P01308,P04637" ``` ### Example 5: ID Mapping - Get Results ```bash # Get mapping results (replace JOB_ID) curl "https:\/\/rest.uniprot.org\/idmapping\/results\/JOB_ID" ``` ### Example 6: Download All Results ```bash # Download all human reviewed proteins curl "https:\/\/rest.uniprot.org\/uniprotkb\/stream?query=organism_id:9606+AND+reviewed:true&format=fasta" \ -o human_proteins.fasta ``` ## R Examples ### Example 1: Basic Search ```r library(httr) library(jsonlite) # Search for insulin proteins url <- "https:\/\/rest.uniprot.org\/uniprotkb\/search" query_params <- list( query = "insulin AND organism_id:9606", format = "json", size = 10 ) response <- GET(url, query = query_params) data <- fromJSON(content(response, "text")) # Extract accessions and names proteins <- data$results[, c("primaryAccession", "proteinDescription")] print(proteins) ``` ### Example 2: Get Sequences ```r library(httr) # Get protein sequence accession <- "P01308" url <- paste0("https:\/\/rest.uniprot.org\/uniprotkb\/", accession, ".fasta") response <- GET(url) sequence <- content(response, "text") cat(sequence) ``` ### Example 3: Download to Data Frame ```r library(httr) library(readr) # Get data as TSV url <- "https:\/\/rest.uniprot.org\/uniprotkb\/search" query_params <- list( query = "gene:BRCA1 AND reviewed:true", format = "tsv", fields = "accession,gene_names,organism_name,length" ) response <- GET(url, query = query_params) data <- read_tsv(content(response, "text")) print(data) ``` ## JavaScript Examples ### Example 1: Fetch API ```javascript \/\/ Search for proteins async function searchUniProt(query) { const url = `https:\/\/rest.uniprot.org\/uniprotkb\/search?query=${encodeURIComponent(query)}&format=json&size=10`; const response = await fetch(url); const data = await response.json(); return data.results; } \/\/ Usage searchUniProt("insulin AND organism_id:9606") .then(results => console.log(results)); ``` ### Example 2: Get Protein Entry ```javascript async function getProtein(accession, format = "json") { const url = `https:\/\/rest.uniprot.org\/uniprotkb\/${accession}.${format}`; const response = await fetch(url); if (format === "json") { return await response.json(); } else { return await response.text(); } } \/\/ Usage getProtein("P01308", "fasta") .then(sequence => console.log(sequence)); ``` ### Example 3: ID Mapping ```javascript async function mapIds(ids, fromDb, toDb) { \/\/ Submit job const submitUrl = "https:\/\/rest.uniprot.org\/idmapping\/run"; const formData = new URLSearchParams({ from: fromDb, to: toDb, ids: ids.join(",") }); const submitResponse = await fetch(submitUrl, { method: "POST", body: formData }); const { jobId } = await submitResponse.json(); \/\/ Poll for completion const statusUrl = `https:\/\/rest.uniprot.org\/idmapping\/status\/${jobId}`; while (true) { const statusResponse = await fetch(statusUrl); const status = await statusResponse.json(); if ("results" in status || "failedIds" in status) { break; } await new Promise(resolve => setTimeout(resolve, 3000)); } \/\/ Get results const resultsUrl = `https:\/\/rest.uniprot.org\/idmapping\/results\/${jobId}`; const resultsResponse = await fetch(resultsUrl); return await resultsResponse.json(); } \/\/ Usage mapIds(["P01308", "P04637"], "UniProtKB_AC-ID", "PDB") .then(mapping => console.log(mapping)); ``` ## Advanced Examples ### Example: Batch Processing with Rate Limiting ```python import requests import time from typing import List, Dict class UniProtClient: def __init__(self, rate_limit=1.0): self.base_url = "https:\/\/rest.uniprot.org" self.rate_limit = rate_limit self.last_request = 0 def _rate_limit(self): """Enforce rate limiting""" elapsed = time.time() - self.last_request if elapsed < self.rate_limit: time.sleep(self.rate_limit - elapsed) self.last_request = time.time() def batch_get_proteins(self, accessions: List[str], batch_size: int = 100) -> List[Dict]: """Get proteins in batches""" results = [] for i in range(0, len(accessions), batch_size): batch = accessions[i:i + batch_size] query = " OR ".join([f"accession:{acc}" for acc in batch]) self._rate_limit() response = requests.get( f"{self.base_url}\/uniprotkb\/search", params={ "query": query, "format": "json", "size": batch_size } ) if response.ok: data = response.json() results.extend(data.get('results', [])) else: print(f"Error in batch {i\/\/batch_size}: {response.status_code}") return results # Usage client = UniProtClient(rate_limit=0.5) accessions = ["P01308", "P04637", "P12345", "Q9Y6K9"] proteins = client.batch_get_proteins(accessions) ``` ### Example: Download with Progress Bar ```python import requests from tqdm import tqdm def download_with_progress(query, output_file, format="fasta"): """Download results with progress bar""" url = "https:\/\/rest.uniprot.org\/uniprotkb\/stream" params = { "query": query, "format": format } response = requests.get(url, params=params, stream=True) total_size = int(response.headers.get('content-length', 0)) with open(output_file, 'wb') as f, \ tqdm(total=total_size, unit='B', unit_scale=True) as pbar: for chunk in response.iter_content(chunk_size=8192): f.write(chunk) pbar.update(len(chunk)) # Usage download_with_progress( "organism_id:9606 AND reviewed:true", "human_proteome.fasta" ) ``` ## Resources - API Documentation: https:\/\/www.uniprot.org\/help\/api - Interactive API Explorer: https:\/\/www.uniprot.org\/api-documentation - Python client (Unipressed): https:\/\/github.com\/multimeric\/Unipressed - Bioservices package: https:\/\/bioservices.readthedocs.io\/ ## Usage Invoke this skill with: ``` $api_examples [arguments] ``` Or let Codex auto-select based on your prompt.