disease portals a platform for genetic and genomic research disease and phenotype data in the...
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Disease PortalsA 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 DatabaseHuman and Molecular Genetics Center
Medical College of Wisconsin
Disease PortalsA Platform for Genetic and Genomic Research
Disease and Phenotype Data in the Context of the Genome
Goals
Building the portals
Results
Future directions
Disease PortalsA Platform for Genetic and Genomic Research
Disease and Phenotype Data in the Context of the Genome
Goals
Disease PortalsA 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 PortalsA 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 PortalsA Platform for Genetic and Genomic Research
Disease and Phenotype Data in the Context of the Genome
Building the portals
Disease PortalsA 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 PortalsA 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; ifno 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 withqtl, strain for the selected category are provided.
The genes in the selectedcategory are ‘rolled-up’using GO-Slim and displayedas charts.
Top-level nodes for the phenotype ontology
Top- and second-level nodes for the phenotype ontology
The genes in the selectedcategory are ‘rolled-up’using GO-Slim and displayedas 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 withqtl, strain for the selected category are provided.
Partial gene report page andpartial list of annotations for Acelinked to from the list of genesin the portal.
Note that Ace is a candidate gene for several blood pressure QTL;homolog information can be accessedfrom the links in the portal for the respective genes, or from theindividual 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 PortalsA 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 PortalsA 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 DatabaseHuman and Molecular Genetics Center
Medical College of Wisconsin
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