Harmonizing model organism data in the Alliance of Genome Resources

Abstract

The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein-protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides.

Keywords: biocuration; data mining; gene expression; gene function; gene interaction; genome; knowledgebase; phenotype; variants.

Fig. 1.

The Alliance Portal provides a harmonized view of research organism information. Left, current MOD pages; Right, current Alliance release 4.0 gene pages.

Fig. 2.

Example of Alliance JBrowse. The top is the standard control bar. Next are curated variants, often with known phenotypic consequences. The gene structure models (introns and exons) for each gene are shown, with the high throughput variants shown in the next track. The reference sequence in all reading frames is followed by a conservation track from University of California, Santa Cruz. Two alleles are highlighted in this figure: the blue box shows the e1417 allele to be in a conserved intron region, while the gold box shows the n378 allele to be in a coding exon.

Fig. 3.

Conceptual map of gene-centered information. Perturbations of gene activity include alleles, variants, RNAi, knockdown, and transgenic overexpression.

Fig. 4.

The expression widget. This example is for the Drosophila gene per. The links to primary sources are customized and the number varies among species depending on data.

Fig. 5.

Montage of types of variant information and displays. The variant page has a summary, snapshot of Genomic Location, and then tables of Phenotypes, Molecular Consequences, and Disease Associations.

Fig. 6.

Automatically generated gene summaries from structured data. Example of a gene summary for C. elegans gene tra-1 showing different data categories highlighted in different colors.

Fig. 7.

Views of pathways. GO-CAM model with simplified view for pmk-1.

Fig. 8.

AllianceMine. Screen shots of AllianceMine output. Using a template query of disease ontology (DO) to all genes with the term “autism” a) returns 1088 genes b). Mousing over petena pops up a brief description of that gene c).