{credit}Screenshot/Jeffrey Perkel{/credit}
For decades, the research communities surrounding the major model organisms have each had an online place to call home. There’s the SGD, MGD, and RGD — the Saccharomyces, mouse, and rat genome databases, respectively; FlyBase and WormBase for Drosophila and C. elegans; and ZFIN, the Zebrafish Information Network.
Each of these resources, called ‘model organism databases‘, or MODs, provides a one-stop shop for all things related to their chosen organisms: an annotated genome sequence, gene expression data, phenotype and mutant information, curated literature references, access to strain and stock repositories, and more. But what they don’t provide is an easy way to search across organisms. In this age of comparative genomics, the MODs focus mostly on their namesakes.
Now, a new web site aims to change that. Earlier this month, the six major MOD teams, plus the team behind the controlled life sciences vocabulary called the Gene Ontology, announced the launch of an integrated search portal called alliancegenome.org, the official web site of the Alliance of Genome Resources.
The portal allows users to perform “faceted queries” across all the databases at once, says Judith Blake of the Jackson Laboratory in Bar Harbor, Maine, who is a PI for both the Gene Ontology Consortium and Mouse Genome Database. “You can search on a gene, you can search on a disease, you can search on a biological function. And so you have a lot of different ways of accessing this data. And we’re providing extensive links back into the resources.”
Gene pages include basic information on the gene, functional annotations, orthologous genes in other organisms, and human disease associations if available. An integrated genome browser displays the gene structure in its chromosomal context.
The portal reflects a plan to reduce MOD funding by the US National Institutes of Health. As Nature reported last year, “Officials with the National Human Genome Research Institute (NHGRI) told researchers in May [2016] that the agency plans to gradually cut support for the databases by 30–40% beginning next year. For the current fiscal year, the agency has dedicated US$17.6 million to support the 5 databases, each of which is run independently.” The report added, “NHGRI officials asked principal investigators in charge of the five databases [supported by the institute: SGD, MGD, WormBase, FlyBase and ZFIN] to submit a proposal within several months for integrating some of their features. The agency would like to merge administration of the databases completely over the next few years.”
According to a ZFIN blog post announcing the launch of the new web site, “The Alliance aims to provide a synergistic integration of expertly-curated information about the functioning of cellular systems from model organisms, including zebrafish, and humans to facilitate better understanding of human biology and disease. Other MODs and related resources will be added to the Alliance going forward.”
Carol Bult of the Jackson Laboratory, who also is PI of the MGD, says the new site allows users to access key information from the different MODs without having to learn to navigate the different MOD interfaces. “That’s one of the motivating factors of this initiative, so users don’t have to learn the idiosyncrasies of the different model organism databases.”
That’s not to say the new site won’t change. Per ZFIN, the Alliance team plans to incorporate “other model organism information resources and bioinformatic tools within a common data platform, facilitating data access, comparative analyses, and cross-species data integration.”
But the underlying MODs also will evolve, Blake says. With 20-plus years of development work behind them in some cases, these sites continue to serve their communities, and not all their data has been migrated to the new web site. Strain and reagent data, for instance, currently is available only on the MODs. “There’s large components of the databases that still reflect community needs,” she says.
Jeffrey Perkel is Technology Editor, Nature
13 Nov 2017: This post has been updated to include the level of NHGRI support for MODs, and the scale of the proposed budget cuts.
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