KEGGAPI.jl is a Julia package for accesing the Kyoto Encyclopedia of Genes and Genomes, striving to take advantage of the speed and flexibility that Julia offers and make it accessible to the bioinformatics and functional annotation communities.

Installation

pkg> add KEGGAPI

Usage

The package wraps the KEGG REST API operations:

Function	KEGG operation	Purpose
kegg_info	info	Database release information and statistics
kegg_list	list	Entry identifiers and associated names
kegg_find	find	Search entries by keyword or chemical data
kegg_get	get	Retrieve entries, sequences, images, KGML, JSON
kegg_conv	conv	Convert between KEGG and outside identifiers
kegg_link	link	Find related entries via cross-references
kegg_ddi	ddi	Adverse drug-drug interactions

using KEGGAPI

result = kegg_find("compound", "glucose")
result.colnames    # column names
result.data        # retrieved data

Documentation

• Getting started
• Examples
• API reference

Worked end-to-end use cases:

• Case 1: From a UniProt ID to KEGG information
• Case 2: EC reaction information in KEGG
• Case 3: Identifying a compound in KEGG
• Case 4: Target molecule information at KEGG

Speed Tests

See benchmarking/ for how to reproduce these numbers.

Citation

publication pending