uniprot-database

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24.4k23993 months ago

Direct REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For Python workflows with multiple databases, prefer bioservices (unified interface to 40+ services). Use this for direct HTTP/REST work or UniProt-specific control.

Quick Install

npxskills add davila7/claude-code-templates--skill uniprot-database

Instructions

UniProt Database

Overview

UniProt is the world's leading comprehensive protein sequence and functional information resource. Search proteins by name, gene, or accession, retrieve sequences in FASTA format, perform ID mapping across databases, access Swiss-Prot/TrEMBL annotations via REST API for protein analysis.

When to Use This Skill

This skill should be used when:

Searching for protein entries by name, gene symbol, accession, or organism
Retrieving protein sequences in FASTA or other formats
Mapping identifiers between UniProt and external databases (Ensembl, RefSeq, PDB, etc.)
Accessing protein annotations including GO terms, domains, and functional descriptions
Batch retrieving multiple protein entries efficiently
Querying reviewed (Swiss-Prot) vs. unreviewed (TrEMBL) protein data
Streaming large protein datasets
Building custom queries with field-specific search syntax

Core Capabilities

1. Searching for Proteins

Search UniProt using natural language queries or structured search syntax.

Common search patterns:

# Search by protein name
query = "insulin AND organism_name:\"Homo sapiens\""

# Search by gene name
query = "gene:BRCA1 AND reviewed:true"

# Search by accession
query = "accession:P12345"

# Search by sequence length
query = "length:[100 TO 500]"

# Search by taxonomy
query = "taxonomy_id:9606"  # Human proteins

# Search by GO term
query = "go:0005515"  # Protein binding

Use the API search endpoint: https://rest.uniprot.org/uniprotkb/search?query={query}&format={format}

Supported formats: JSON, TSV, Excel, XML, FASTA, RDF, TXT

2. Retrieving Individual Protein Entries

Retrieve specific protein entries by accession number.

Accession number formats:

Classic: P12345, Q1AAA9, O15530 (6 characters: letter + 5 alphanumeric)
Extended: A0A022YWF9 (10 characters for newer entries)

Retrieve endpoint: https://rest.uniprot.org/uniprotkb/{accession}.{format}

Example: https://rest.uniprot.org/uniprotkb/P12345.fasta

3. Batch Retrieval and ID Mapping

Map protein identifiers between different database systems and retrieve multiple entries efficiently.

ID Mapping workflow:

Submit mapping job to: https://rest.uniprot.org/idmapping/run
Check job status: https://rest.uniprot.org/idmapping/status/{jobId}
Retrieve results: https://rest.uniprot.org/idmapping/results/{jobId}

Supported databases for mapping:

UniProtKB AC/ID
Gene names
Ensembl, RefSeq, EMBL
PDB, AlphaFoldDB
KEGG, GO terms
And many more (see /references/id_mapping_databases.md)

Limitations:

Maximum 100,000 IDs per job
Results stored for 7 days

4. Streaming Large Result Sets

For large queries that exceed pagination limits, use the stream endpoint:

https://rest.uniprot.org/uniprotkb/stream?query={query}&format={format}

The stream endpoint returns all results without pagination, suitable for downloading complete datasets.

5. Customizing Retrieved Fields

Specify exactly which fields to retrieve for efficient data transfer.

Common fields:

accession - UniProt accession number
id - Entry name
gene_names - Gene name(s)
organism_name - Organism
protein_name - Protein names
sequence - Amino acid sequence
length - Sequence length
go_* - Gene Ontology annotations
cc_* - Comment fields (function, interaction, etc.)
ft_* - Feature annotations (domains, sites, etc.)

Example: https://rest.uniprot.org/uniprotkb/search?query=insulin&fields=accession,gene_names,organism_name,length,sequence&format=tsv

See /references/api_fields.md for complete field list.

Python Implementation

For programmatic access, use the provided helper script scripts/uniprot_client.py which implements:

search_proteins(query, format) - Search UniProt with any query
get_protein(accession, format) - Retrieve single protein entry
map_ids(ids, from_db, to_db) - Map between identifier types
batch_retrieve(accessions, format) - Retrieve multiple entries
stream_results(query, format) - Stream large result sets

Alternative Python packages:

Unipressed: Modern, typed Python client for UniProt REST API
bioservices: Comprehensive bioinformatics web services client

Query Syntax Examples

Boolean operators:

kinase AND organism_name:human
(diabetes OR insulin) AND reviewed:true
cancer NOT lung

Field-specific searches:

gene:BRCA1
accession:P12345
organism_id:9606
taxonomy_name:"Homo sapiens"
annotation:(type:signal)

Range queries:

length:[100 TO 500]
mass:[50000 TO 100000]

Wildcards:

gene:BRCA*
protein_name:kinase*

See /references/query_syntax.md for comprehensive syntax documentation.

Best Practices

Use reviewed entries when possible: Filter with reviewed:true for Swiss-Prot (manually curated) entries
Specify format explicitly: Choose the most appropriate format (FASTA for sequences, TSV for tabular data, JSON for programmatic parsing)
Use field selection: Only request fields you need to reduce bandwidth and processing time
Handle pagination: For large result sets, implement proper pagination or use the stream endpoint
Cache results: Store frequently accessed data locally to minimize API calls
Rate limiting: Be respectful of API resources; implement delays for large batch operations
Check data quality: TrEMBL entries are computational predictions; Swiss-Prot entries are manually reviewed

Resources

scripts/

uniprot_client.py - Python client with helper functions for common UniProt operations including search, retrieval, ID mapping, and streaming.

references/

api_fields.md - Complete list of available fields for customizing queries
id_mapping_databases.md - Supported databases for ID mapping operations
query_syntax.md - Comprehensive query syntax with advanced examples
api_examples.md - Code examples in multiple languages (Python, curl, R)

Additional Resources

API Documentation: https://www.uniprot.org/help/api
Interactive API Explorer: https://www.uniprot.org/api-documentation
REST Tutorial: https://www.uniprot.org/help/uniprot_rest_tutorial
Query Syntax Help: https://www.uniprot.org/help/query-fields
SPARQL Endpoint: https://sparql.uniprot.org/ (for advanced graph queries)

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