KEGGRESTpy

KEGGRESTpy is a Python package providing a simple interface to access the KEGG (Kyoto Encyclopedia of Genes and Genomes) REST API. This package allows users to fetch and interact with data from KEGG databases, enabling bioinformatics research on genomic and pathway data.

Note: This package was modified based on the KEGGREST package from Bioconductor.

Installation

Clone the repository and install with:

pip install KEGGRESTpy

Overview KEGGRESTpy offers several key functions for querying the KEGG REST API:

kegg_info(): Retrieve information about KEGG databases. kegg_list(): List entries in a KEGG database. kegg_get(): Retrieve specific entries from KEGG databases. kegg_find(): Search by keywords within KEGG databases. kegg_conv(): Convert identifiers between KEGG and external databases. kegg_link(): Link entries across KEGG databases. Each of these functions interacts directly with the KEGG API, handling data parsing and returning structured results.

Usage

1. Exploring KEGG Resources with kegg_list()

To list all available databases:

from KEGGRESTpy import list_databases

print(list_databases())

To list all organisms in KEGG:

from KEGGRESTpy import kegg_list

pathway = kegg_list("pathway")
print(pathway)

2. Retrieving Specific Entries with kegg_get()

To retrieve detailed information about specific entries in KEGG, such as genes:

from KEGGRESTpy import kegg_get

data = kegg_get(["hsa:10458", "ece:Z5100"])
print(data)

You can also retrieve amino acid or nucleotide sequences:

sequences = kegg_get(["hsa:10458", "ece:Z5100"], option="aaseq")
print(sequences)

3. Searching by Keywords with kegg_find()

To search for entries related to a keyword:

from KEGGRESTpy import kegg_find

results = kegg_find("genes", "shiga toxin")
print(results)

4. Converting Identifiers with kegg_conv()

To convert identifiers between KEGG and other databases:

from KEGGRESTpy import kegg_conv

conversion = kegg_conv("ncbi-proteinid", ["hsa:10458", "ece:Z5100"])
print(conversion)

5. Linking Across Databases with kegg_link()

To find relationships between different entities in KEGG:

from KEGGRESTpy import kegg_link

pathways = kegg_link("pathway", "hsa")
print(pathways)

Contributing

Contributions to KEGGRESTpy are welcome! Please submit pull requests or open issues to discuss features, bugs, or improvements.

License

This project is licensed under the MIT License - see the LICENSE file for details.

Citation and Restrictions

The KEGG API is provided for academic use by researchers affiliated with academic institutions. Please refer to the official KEGG REST API documentation for more information.