ChlamBase: a curated model organism database for the Chlamydia research community.

Tim Putman,Derek Jow,Sebastien Lelong,Kevin Hybiske,Gregory S Stupp,Cyrus Afrasiabi,Andra Waagmeester,Andrew I Su,Chunlei Wu,Marco Alvarado Cano,Benjamin M Good

doi:10.1093/database/baz041

Abstract

The accelerating growth of genomic and proteomic information for Chlamydia species, coupled with unique biological aspects of these pathogens, necessitates bioinformatic tools and features that are not provided by major public databases. To meet these growing needs, we developed ChlamBase, a model organism database for Chlamydia that is built upon the WikiGenomes application framework, and Wikidata, a community-curated database. ChlamBase was designed to serve as a central access point for genomic and proteomic information for the Chlamydia research community. ChlamBase integrates information from numerous external databases, as well as important data extracted from the literature that are otherwise not available in structured formats that are easy to use. In addition, a key feature of ChlamBase is that it empowers users in the field to contribute new annotations and data as the field advances with continued discoveries. ChlamBase is freely and publicly available at chlambase.org.

Highlights

Chlamydiae are major human and veterinary pathogens; Chlamydia trachomatis is the most common bacterial sexually transmitted infection, responsible for millions of new infections every year [1,2,3]
To build ChlamBase, we leveraged the basic architecture of WikiGenomes.org [11], the genomic data web application for viewing and crowdsourcing bacterial genomic annotations in Wikidata [12,13,14,15,16]
ChlamBase was built with AngularJS, a web framework for dynamic web applications, and Django, an open-source Python framework for running web servers

Summary

Introduction

Chlamydiae are major human and veterinary pathogens; Chlamydia trachomatis is the most common bacterial sexually transmitted infection, responsible for millions of new infections every year [1,2,3]. ChlamBase was designed as a user-friendly platform that integrates data uniquely valued by the Chlamydia research community and allows for reference-based curation and annotation of knowledge not accessible in other public databases. We will work toward adding more plasmids and whole genome sequences as the data become more available in NCBI, and the needs of the ChlamBase user community grow.

Results

Conclusion