Model organism databases: essential resources that need the support of both funders and users

Abstract

Modern biomedical research depends critically on access to databases that house and disseminate genetic, genomic, molecular, and cell biological knowledge. Even as the explosion of available genome sequences and associated genome-scale data continues apace, the sustainability of professionally maintained biological databases is under threat due to policy changes by major funding agencies. Here, we focus on model organism databases to demonstrate the myriad ways in which biological databases not only act as repositories but actively facilitate advances in research. We present data that show that reducing financial support to model organism databases could prove to be not just scientifically, but also economically, unsound.

Fig. 1.

Mean number of manually curated annotations (bars) and genes annotated (line) in PomBase per peer-reviewed paper in 5-year intervals. Counts exclude high-throughput experiments and use the same criteria for all years

Fig. 2.

Sequenced fungal genomes and their functional annotation. a Phylogenetic tree showing selected fungal taxa in which one or more species has a genome sequence available. For subphyla (e.g., Pezizomycotina), the number of publications on species within the subphylum and the number of available genome sequences are shown. Red text denotes classes that include species for which a MOD exists. b Information flow in Gene Ontology annotation. Curators at MODs and UniProtKB create manual annotations based on published experiments; the number of such annotations is shown for each database. Some UniProtKB annotations are incorporated into MOD datasets and all are submitted to the GO repository. Annotations are then transferred to orthologous genes