Sunday, May 15, 2016

Monarch's Phenogrid widget provides similarity visualizations for the International Mouse Phenotyping Consortium.


Monarch's Phenogrid phenotype comparison tool is now available for phenotype profile comparisons on the International Mouse Phenotype Consortium (mousephenotype.org) site.

Visitors to the IMPC site can find Phenogrid comparisons on disease pages such as the entry for Pfeiffer Syndrome.  Under the mouse models, you will see a plus ("+") symbol at the end of each row:
Accessing Phenogrid from the IMPC mouse model listing.

Clicking on that plus sign will reveal the Phenogrid widget showing mouse strains  with phenotype profiles similar to those of the gene in question. For Pfeiffer, the grid will reveal multiple variants of Fgfr1, illustrating differences in phenotypes seen across these strains.  Mousing over the cells will show the details of the match between the given phenotype and the model:
Monarch phenogrid comparison detail view

Mousing over the model label will lead to the display of a dialog box with listings of the specific genotype of the model and relevant phenotypes, all of which can be clicked to access  pages with additional detail.
Monarch Phenogrid model detail view

As with other phenotype comparisons on the Monarch site, these views are driven by Monarch's ontological similarity comparison algorithms.

This integration of Phenogrid on the IMPC represents the application of  Monarch's ontologies and algorithms to IMPC data.  We've developed Phenogrid with this sort of third-party integration in mind - adding Phenogrid to other data sites simply involves downloading the widget from the github repository and following the installation and configuration instructions.

Building tools that bring phenotype similarity comparisons to a broad range of biomedical tools and problems is central to Monarch's mission. If you're interested in adopting our tools, please contact us.