uniprot-database
GitHub提供UniProt数据库的REST API直接访问能力，支持按名称、基因或ID搜索蛋白质、获取FASTA序列、跨库ID映射及注释查询。适用于需要精细控制HTTP请求或处理批量数据流的Python工作流。
Trigger Scenarios
Install
npx skills add synthetic-sciences/openscience --skill uniprot-database -g -y
SKILL.md
Frontmatter
{
"name": "uniprot-database",
"license": "Unknown",
"category": "databases",
"metadata": {
"skill-author": "Synthetic Sciences"
},
"description": "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."
}
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 numberid- Entry namegene_names- Gene name(s)organism_name- Organismprotein_name- Protein namessequence- Amino acid sequencelength- Sequence lengthgo_*- Gene Ontology annotationscc_*- 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 queryget_protein(accession, format)- Retrieve single protein entrymap_ids(ids, from_db, to_db)- Map between identifier typesbatch_retrieve(accessions, format)- Retrieve multiple entriesstream_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:truefor 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 queriesid_mapping_databases.md- Supported databases for ID mapping operationsquery_syntax.md- Comprehensive query syntax with advanced examplesapi_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)
Version History
- e9844a4 Current 2026-07-11 17:25
