Disease Portals A Platform for Genetic and Genomic Research Disease and Phenotype Data in the Context of the Genome Victoria Petri, Mary Shimoyama, Andrew Patzer, Jennifer Smith, Dorothy Reilly, Weihong Jin, Jiali Chen, Simon Twigger, Anne Kwitek, Howard J. Jacob Rat Genome Database Human and Molecular Genetics Center Medical College of Wisconsin

Disease Portals A Platform for Genetic and Genomic Research Disease and Phenotype Data in the Context of the Genome Goals Building the portals Results Future directions

Disease Portals A Platform for Genetic and Genomic Research Disease and Phenotype Data in the Context of the Genome Goals

Disease Portals A Platform for Genetic and Genomic Research Disease and Phenotype Data in the Context of the Genome Goals - better addressing the needs of the audience - capturing more complex, diverse, stratified information - addressing the issues of genes and diseases - providing a map for the road leading from the ‘normal’ to the ‘transformed’ phenotype

Disease Portals A Platform for Genetic and Genomic Research Disease and Phenotype Data in the Context of the Genome Goals - target particular broad disease categories – neurological, cardiovascular, cancer types, etc - annotate genes associated with conditions within the broad category, also QTL, strains - use several ontologies to capture various aspects describing the above objects - provide all information within a single web site equipped with tools and links - provide a one-stop resource for researchers interested in particular diseases

Disease Portals A Platform for Genetic and Genomic Research Disease and Phenotype Data in the Context of the Genome Building the portals

Disease Portals A Platform for Genetic and Genomic Research Disease and Phenotype Data in the Context of the Genome Building the portals - various databases are used to compile master lists of genes targeting a particular portal - gene curation using four ontologies – gene, disease, phenotype and pathway ontologies - gene curation across three species for disease, phenotype and pathway (Rn, Mm, Hs) - QTL and strain curation to disease and phenotype ontology, QTL for rat and human - tools for dynamic analyses, viewing, browsing data, navigate between data types - tools and technologies – AJAX, Adobe Flash, 3rd-party Flash (Fusion Charts)

Disease Portals A Platform for Genetic and Genomic Research Disease and Phenotype Data in the Context of the Genome Results

Search options Scorecard GViewer Lists of annotated objects – genes, QTL strains GO-slim charts

Within a given ontology annotations are categorized in top- or second- level nodes - general versus more specific terms – that a user can choose from a drop-down menu. A scorecard displays total annotations at-a-glance for a chosen category; if no selection is made the scoreboard displays annotations to all terms in the term lists for one of the four ontologies. The default ontology is disease ontology. The other choices are phenotype, GO process and pathway ontology.

Top-level nodes for the disease ontology – the default ontology

Top- and second-level nodes for the disease ontology – the default ontology

In addition to the scoreboard - lists of genes split by species, along with qtl, strain for the selected category are provided. The genes in the selected category are ‘rolled-up’ using GO-Slim and displayed as charts.

Top-level nodes for the phenotype ontology

Top- and second-level nodes for the phenotype ontology

The genes in the selected category are ‘rolled-up’ using GO-Slim and displayed as charts. Note that if there are many objects in the list, it is possible to scroll, also note the arrows for the GO-slim charts. In addition to the scoreboard - lists of genes split by species, along with qtl, strain for the selected category are provided.

Partial gene report page and partial list of annotations for Ace linked to from the list of genes in the portal. Note that Ace is a candidate gene for several blood pressure QTL; homolog information can be accessed from the links in the portal for the respective genes, or from the individual report page.

Rat Genome V3.1 – Genome Browser Showing 1 Mbp from Chr10, positions 95,000,000 to 96,000,000 around Ace gene

Search options Scorecard GViewer Lists of annotated objects – genes, QTL strains GO-slim charts

Disease Portals A Platform for Genetic and Genomic Research Disease and Phenotype Data in the Context of the Genome Future directions - continue to target new categories of diseases to add to the portals - update the existing portals as more data become available -improve on the policies and guidelines for curation and annotations - continue to expand the tools/applications capabilities of the portals

Disease Portals A Platform for Genetic and Genomic Research Disease and Phenotype Data in the Context of the Genome Victoria Petri, Mary Shimoyama, Andrew Patzer, Jennifer Smith, Dorothy Reilly, Weihong Jin, Jiali Chen, Simon Twigger, Anne Kwitek, Howard J. Jacob Rat Genome Database Human and Molecular Genetics Center Medical College of Wisconsin