Disease Portals A Platform for Genetic and Genomic Research

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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 Database Human and
Molecular Genetics Center Medical College of
Wisconsin
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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
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Disease PortalsA Platform for Genetic and
Genomic Research
Disease and Phenotype Data in the Context of the
Genome
Goals
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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
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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
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Disease PortalsA Platform for Genetic and
Genomic Research
Disease and Phenotype Data in the Context of the
Genome
Building the portals
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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)
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Disease PortalsA Platform for Genetic and
Genomic Research
Disease and Phenotype Data in the Context of the
Genome
Results
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Search options
Scorecard
GViewer
Lists of annotated objects genes, QTL strains
GO-slim charts
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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.
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Top-level nodes for the disease ontology the
default ontology
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Top- and second-level nodes for the disease
ontology the default ontology
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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.
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Top-level nodes for the phenotype ontology
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Top- and second-level nodes for the phenotype
ontology
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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.
Note that if there are many objects in the list,
it is possible to scroll, also note the arrows
for the GO-slim charts.
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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.
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Rat Genome V3.1 Genome Browser Showing 1 Mbp
from Chr10, positions 95,000,000 to 96,000,000
around Ace gene
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Search options
Scorecard
GViewer
Lists of annotated objects genes, QTL strains
GO-slim charts
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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

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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 Database Human and
Molecular Genetics Center Medical College of
Wisconsin