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uniprot-database

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.

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@K-Dense-AI

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UniProt Database - Protein Sequence and Functional Information Query Tool

Skill Overview


The UniProt Database skill provides direct REST API access to the world-leading database of protein sequences and functional information, supporting protein search, FASTA sequence retrieval, ID mapping, and Swiss-Prot/TrEMBL annotation queries.

Applicable Scenarios

  • Basic protein research: Search detailed annotations for specific proteins, obtain amino acid sequences, find protein entries corresponding to gene names, and retrieve proteome data for particular species.

  • Cross-database identifier conversion: Map UniProt IDs to other databases such as Ensembl, RefSeq, PDB, AlphaFoldDB, etc., supporting batch processing of up to 100,000 identifiers.

  • Large-scale data download and streaming processing: Download complete protein datasets via a streaming interface, supporting formats such as JSON, TSV, FASTA, etc., suitable for genomics analyses and machine learning data preparation.

    • Core Features

  • Flexible protein search: Support multi-dimensional searches by protein name, gene symbol, accession, species, sequence length, GO terms, and more, with advanced query syntax including Boolean operators and wildcards.

  • Multi-format data retrieval: Support output formats including JSON, TSV, Excel, XML, FASTA, RDF, etc., and allow custom field selection to optimize transfer efficiency.

  • ID mapping and bulk operations: Provide an asynchronous ID mapping service, supporting identifier conversion between UniProt and 40+ external databases, with results retained for 7 days.

    • Frequently Asked Questions

    What is the UniProt Database skill?


    This is a skill that provides direct access to the UniProt protein database REST API, supporting searching protein entries, downloading FASTA sequences, performing identifier mapping, and accessing Swiss-Prot (manually reviewed) and TrEMBL (automatically annotated) protein annotation information.

    What is the difference between Swiss-Prot and TrEMBL?


    Swiss-Prot contains high-quality protein entries that have been manually reviewed and annotated, and is recommended for research requiring accuracy; TrEMBL contains computationally predicted entries, has broader coverage but is not manually verified. Use the filter reviewed:true to limit searches to Swiss-Prot entries only.

    When should I use bioservices instead of this skill?


    If you need unified access to 40+ bioinformatics services (including UniProt, NCBI, PDB, etc.), it is recommended to use bioservices for a consistent interface experience. If you are focused on UniProt-specific features, need finer-grained API control, or are making direct HTTP/REST calls, using this skill is more appropriate.