KEGGAPI.jl is a Julia client for the Kyoto Encyclopedia of Genes and Genomes REST API.

KEGG usage terms

KEGG makes its REST service at rest.kegg.jp available only for academic use by academic users. Read KEGG's REST restriction notice and legal terms, including its licensing requirements for non-academic use.

KEGGAPI.jl's MIT license covers only the Julia client code. It does not grant any rights to KEGG data or services.

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

The vector forms of kegg_conv, kegg_get, kegg_link, and kegg_list send at most 10 entries per request. Set request_delay to control the pause between requests:

entries = ["hsa:$id" for id in 10458:10468]
result = kegg_get(entries; request_delay = 0.5)

The deprecated timeout keyword remains available as an alias for request_delay.

Documentation

• Getting started
• Examples
• API reference

Worked 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

Benchmarks

See benchmarking/ for how to reproduce these numbers.

Citation

publication pending