Overview

Chewie-NS is a Nomenclature Server based on the TypOn ontology that integrates with chewBBACA to provide a centralized service to share and update gene-by-gene schemas, allowing the easy sharing of results, while ensuring the reproducibility and consistency of these steps.

A diagram of the implementation of Chewie-NS is displayed below:

Figure 1.1: Chewie-NS implementation.

Motivation

Current typing methods suffer from standardization issues that become clear when trying to compare results from distinct tools but, most importantly, when a meaningful comparison is needed between results obtained with the same tool.

We have previously proposed a suite, chewBBACA, that allows the creation of gene-by-gene schemas and the determination of allelic profiles from genome assemblies. The results obtained using this suite may not be immediatly comparable due to the use of different argument values that hinder the comparison and shareability of the results.

To tackle these issues we developed Chewie-NS, which provides a centralized service to manage gene-by-gene typing schemas and a common nomenclature for allele calling, ensuring the reproducibility of the analyses and the privacy of the data.

Implementation

Chewie-NS provides a public and centralized web service, separated into a backend component that handles command line and server requests and a frontend component that allows a user-friendly interaction with the service.

Backend

The backend of the service uses Virtuoso, a triple store database management system, based on the TypOn ontology.

Figure 2.1: TypOn ontology. Adapted from Vaz et al, 2014.

A REST API, built with Flask, a Python web development microframework, is available to allow users to interact with the Virtuoso database. It also facilitates the integration with chewBBACA to support the development of modules that will handle schema upload, download and synchronization from the command line.

Frontend

A user-friendly interface, built using the ReactJS web framework, simplifies access for all types of users, providing a listing of available schemas per species and displaying relevant schema and loci statistics. Access to compressed versions of the available schemas is available, allowing their direct download for local use.

The main instance of Chewie-NS is available at chewbbaca.online.

Data Privacy

Chewie-NS provides a distinct approach when compared with other publicly available web services due to its’ integration with chewBBACA, which enables local analyses and has the potential to considerably expedite the generation of results, while also providing the option to share newly identified alleles still respecting data privacy and ownership concerns.