Automatization and self-maintenance of the O-GlcNAcome catalog: a smart scientific database

Post-translational modifications (PTMs) are ubiquitous and essential for protein function and signaling, motivating the need for sustainable benefit and open models of web databases. Highly conserved O-GlcNAcylation is a case example of one of the most recently discovered PTMs, investigated by a growing community. Historically, details about O-GlcNAcylated proteins and sites were dispersed across literature and in non-O-GlcNAc-focused, rapidly outdated or now defunct web databases. In a first effort to fill the gap, we recently published a human O-GlcNAcome catalog with a basic web interface. Based on the enthusiasm generated by this first resource, we extended our O-GlcNAcome catalog to include data from 42 distinct organisms and released the O-GlcNAc Database v1.2. In this version, more than 14 500 O-GlcNAcylated proteins and 11 000 O-GlcNAcylation sites are referenced from the curation of 2200 publications. In this article, we also present the extensive features of the O-GlcNAc Database, including the user-friendly interface, back-end and client-server interactions. We particularly emphasized our workflow, involving a mostly automatized and self-maintained database, including machine learning approaches for text mining. We hope that this software model will be useful beyond the O-GlcNAc community, to set up new smart, scientific online databases, in a short period of time. Indeed, this database system can be administrated with little to no programming skills and is meant to be an example of a useful, sustainable and cost-efficient resource, which exclusively relies on free open-source software elements (www.oglcnac.mcw.edu).

Automated summary

Post-translational modifications are crucial for protein function and signaling, with O-GlcNAcylation being a highly conserved case in point. The development of the O-GlcNAc Database v1.2, with data from 42 organisms and over 14,500 O-GlcNAcylated proteins, marks a significant advancement in consolidating information on O-GlcNAcylation. The database system, emphasizing user-friendliness and automation, showcases a sustainable and cost-efficient model for creating scientific online databases beyond the O-GlcNAc research community.