Mouse Genome Informatics (MGI): reflecting on 25 years

Abstract

From its inception in 1989, the mission of the Mouse Genome Informatics (MGI) resource remains to integrate genetic, genomic, and biological data about the laboratory mouse to facilitate the study of human health and disease. This mission is ever more feasible as the revolution in genetics knowledge, the ability to sequence genomes, and the ability to specifically manipulate mammalian genomes are now at our fingertips. Through major paradigm shifts in biological research and computer technologies, MGI has adapted and evolved to become an integral part of the larger global bioinformatics infrastructure and honed its ability to provide authoritative reference datasets used and incorporated by many other established bioinformatics resources. Here, we review some of the major changes in research approaches over that last quarter century, how these changes are reflected in the MGI resource you use today, and what may be around the next corner.

Fig. 1

Data visualization using the Encyclopedia of the Mouse Genome software. This view displays data for the Pgd1 gene on Chromosome 4. The left panel shows mammalian species with published homologs. The center panel displays Chromosome 4, with the region around Pgd1 expanded. Note that not all loci are visible in the whole chromosome view due to gene density. The right panel displays the syntenic loci for Chromosome 4. Options buttons to view additional panels include gene lists (all or selected subsets) and references

Fig. 2

The first worldwide web homepage of the future MGI, 1994. Links to MGD release 1.2 and to the Encyclopedia of the Mouse Genome for Unix and Mac can be seen

Fig. 3

Timeline 1985–2015. Above the timeline are projects and activities in the mouse community. Below the timeline are biotechnology changes and punctuated advances. The bottom section (blue) shows how the MGI resource was developed over time. The time ranges are approximate and not drawn strictly to scale

Fig. 4

Human–Mouse Disease Connection (HMDC), www.diseasemodel.org. The top panel shows the upper portion of the HMDC homepage with 3 distinct search boxes to allow searching by mouse or human genes, genome locations, or disease or phenotype terms. Note that options are provided to upload a gene file or a VCF file to use as search parameters as well. In this example, Paget Disease of Bone 2, Early-Onset was entered in the disease/phenotype term box. The lower panel shows the resulting grid display where human and mouse orthologs are shown in rows and phenotypes and diseases are shown in columns. Blue indicates mouse data; orange indicates human data. The highlighted Paget Disease of Bone column shows both human SQSTM1 and mouse Sqstm1, respectively, are associated to the disease. Mouse gene Inpp5d and human gene TNFRSF11A are associated to this human disease as well, but not coincidentally. These data suggest that mice with mutations in Tnfrsf11a should be examined for phenotypes correlated to human Paget Disease of Bone 2 and that human patients with Paget Disease of Bone 2 phenotypes might be checked for mutations in the INPP5D gene

Fig. 5

The MGI 25th celebration. Photo of participants and attendees at the celebration of MGI’s 25th year, October 30, 2014, Bar Harbor, Maine

Fig. 6

Staff of MGI over its first 25 years. The 168 members of the MGI team, 1989–2015