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. 2020 Jan 8;48(D1):D650-D658.
doi: 10.1093/nar/gkz813.

Alliance of Genome Resources Portal: unified model organism research platform

Alliance of Genome Resources Consortium
Collaborators

Alliance of Genome Resources Portal: unified model organism research platform

Alliance of Genome Resources Consortium. Nucleic Acids Res. .

Abstract

The Alliance of Genome Resources (Alliance) is a consortium of the major model organism databases and the Gene Ontology that is guided by the vision of facilitating exploration of related genes in human and well-studied model organisms by providing a highly integrated and comprehensive platform that enables researchers to leverage the extensive body of genetic and genomic studies in these organisms. Initiated in 2016, the Alliance is building a central portal (www.alliancegenome.org) for access to data for the primary model organisms along with gene ontology data and human data. All data types represented in the Alliance portal (e.g. genomic data and phenotype descriptions) have common data models and workflows for curation. All data are open and freely available via a variety of mechanisms. Long-term plans for the Alliance project include a focus on coverage of additional model organisms including those without dedicated curation communities, and the inclusion of new data types with a particular focus on providing data and tools for the non-model-organism researcher that support enhanced discovery about human health and disease. Here we review current progress and present immediate plans for this new bioinformatics resource.

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Figures

Figure 1.
Figure 1.
Alliance gene detail page. Here, a quick search box at top right permits search by Gene symbol, GO term, Allele Symbol or Disease term. A drop-down box facilitates term selection. In this example of a search return for Bmp4, as noted in the Category listed on the left side, there are 335 results from the search resulting in links to data from 9 Genes, 34 Diseases, 21 Alleles and 271 Gene Ontology terms. Linking to any category extends access to all the underlying data. The page, here presented in List form, can also be viewed as a Table.
Figure 2.
Figure 2.
Automated gene description example of mouse gene Bmp4.
Figure 3.
Figure 3.
Ribbon summary display for GO biological function, disease associations and expression data. (A) Overview of the biological functions of the Trp53 gene, as currently annotated in the Alliance using the Gene Ontology. There are 3 sections informing on the annotated functions, processes and cellular components of Trp53. (B) Another high-level view of the mouse Trp53 gene highlighting the currently annotated disease associations using the Disease Ontology. In addition to (A), several orthologs are shown to emphasize interspecies variability. Subsections of the ribbon group related diseases (e.g. ‘All disease of anatomical entity’), with the first column of the group summarizing all annotations for that group. (C) A high-level view of expression data of the mouse Trp53 gene and orthologs. The expression ribbon has subsections for anatomical location, developmental stage, and subcellular location. Each ribbon cell represents a high-level anatomical system, tissue, developmental stage, or subcellular component. For each ribbon, the gradient color of each ribbon cell represents the number of currently available annotations for each type of biological data (GO, disease, expression). White cells indicate no data available while color gradient indicate the relative number of annotations available for each cell. Clicking on any colored cell produces a data table with details for the annotations to that section.
Figure 4.
Figure 4.
Orthology section in the gene report. Mouse Ihh gene report shown. Data are presented in a table based on an integrated representation of orthology inferences by multiple algorithms, listed in ‘Method’ columns. The ‘Count’ indicates the number of methods that call a specific ortholog pair; ‘Best’ and ‘Best reverse’ are based on the counts. Multiple filtering options are offered, including several precomputed options labelled ‘Stringent’ and ‘Moderate’. The ‘Stringent’ option includes all orthologs called by three or more methods that are also a best count OR a best reverse count; an ortholog called by two methods is included if it is both a best count AND a best reverse count; an ortholog predicted by ZFIN or HGNC is always included, regardless of count. Additional information about filtering can be found in the help button pop-up. At the top of the Orthology section is a link to a customized Panther ‘Gene tree’, which incorporates a phylogenetic view and options such as multiple sequence alignments.
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