uniprot-database

You can retrieve protein sequences in FASTA format by querying the UniProt REST API endpoint /uniprotkb/{accession}.{format}. The Skill executes this request programmatically to fetch sequence data directly without manual web interactions, supporting JSON, TSV, and XML formats as well.

Mapping protein IDs between UniProt and databases like Ensembl, RefSeq, or PDB is accomplished using the /idmapping/run endpoint. The Skill automates submitting identifiers, polling for status, and retrieving cross-database mapping results to integrate protein data across platforms.

Yes, you can batch retrieve and stream large protein datasets from UniProt using the /uniprotkb/stream endpoint. The Skill supports streaming retrieval to handle high-volume datasets efficiently, returning large result sets in formats like JSON, TSV, FASTA, or XML.

You search UniProt by protein name, gene, accession, or organism using the /uniprotkb/search endpoint. The Skill constructs and executes these queries programmatically, enabling precise filtering to locate target proteins across the UniProtKB database.

No, this UniProt data retrieval approach requires only the standard Python requests library as a dependency. The Skill provides a Python client script to simplify usage, wrapping REST API endpoints for straightforward integration into bioinformatics pipelines.

Cross-database ID mapping is needed for protein analysis when integrating UniProt data with structural or genomic databases like PDB or Ensembl. It enables real-world scenarios such as fetching target proteins and mapping to PDB IDs for downstream structural modeling.