kegg_pull

kegg_pull retrieves and saves entries from the Kyoto Encyclopedia of Genes and Genomes (KEGG) via its RESTful API to support incorporation of genomic, biomolecular, and metabolic data into bioinformatics analyses.

Key Features:

• KEGG RESTful API access: Interfaces with the KEGG RESTful API to request and obtain database entries from the Kyoto Encyclopedia of Genes and Genomes.
• Python API: Provides a Python application programming interface for programmatic retrieval and handling of KEGG entries.
• Bulk retrieval: Allows downloading and saving an arbitrary number of KEGG database entries, including retrieval of entire databases with a single method call.
• Parallel retrieval: Leverages multiple CPU cores to perform parallel data retrieval for improved throughput.
• Fault-tolerant operations: Offers options to optimize fault tolerance across single-process and multi-process retrieval operations.

Scientific Applications:

• Genomic and biomolecular data acquisition: Enables retrieval of gene, protein, and pathway entries from KEGG for downstream genomic and biomolecular analyses.
• Metabolic and pathway modeling: Supports collection of metabolic and pathway information from KEGG for modeling and systems biology studies.

Methodology:

kegg_pull issues requests to the KEGG RESTful API to download and save entries, supports retrieval of entire databases via single method calls, and performs parallelized, multi-process fetching across multiple CPU cores with configurable fault-tolerance options.