Saccharomyces genome database update: server architecture, pan-genome nomenclature, and external resources

Abstract

As one of the first model organism knowledgebases, Saccharomyces Genome Database (SGD) has been supporting the scientific research community since 1993. As technologies and research evolve, so does SGD: from updates in software architecture, to curation of novel data types, to incorporation of data from, and collaboration with, other knowledgebases. We are continuing to make steps toward providing the community with an S. cerevisiae pan-genome. Here, we describe software upgrades, a new nomenclature system for genes not found in the reference strain, and additions to gene pages. With these improvements, we aim to remain a leading resource for students, researchers, and the broader scientific community.

Keywords: Saccharomyces cerevisiae; MOD; SGD; budding yeast; knowledgebase; model organism database.

Fig. 1.

Streamlining SGD's backend with Fargate and Docker. AWS managed services are above the horizontal line, SGD managed services are below. a) Previous architecture of SGD. AWS managed services are limited to load balancer and elasticsearch; all other services are SGD managed. b) Current architecture, with SGD managed services reduced to the curation web server.

Fig. 2.

Secondary structures from RNAcentral are now available on SGD RNA gene pages. a) Thumbnail view of SNR42/YNCK0020C secondary structure on Locus Summary page and (b) detailed view of secondary structure of SNR42/YNCK0020C on Sequence page.