Visualizing Biological Data Using the SVGmap Browser by Casey Bergman.
From the post:
Early in 2012, Nuria Lopez-Bigas‘ Biomedical Genomics Group published a paper in Bioinformatics describing a very interesting tool for visualizing biological data in a spatial context called SVGmap. The basic idea behind SVGMap is (like most good ideas) quite straightforward – to plot numerical data on a pre-defined image to give biological context to the data in an easy-to-interpret visual form.
To do this, SVGmap takes as input an image in Scalable Vector Graphics (SVG) format where elements of the image are tagged with an identifier, plus a table of numerical data with values assigned to the same identifier as in the elements of the image. SVGMap then integrates these files using either a graphical user interface that runs in standard web browser or a command line interface application that runs in your terminal, allowing the user to display color-coded numerical data on the original image. The overall framework of SVGMap is shown below in an image taken from a post on the Biomedical Genomics Group blog.
We’ve been using SVGMap over the last year to visualize tissue-specific gene expression data in Drosophila melanogaster from the FlyAtlas project, which comes as one of the pre-configured “experiments” in the SVGMap web application.
More recently, we’ve been also using the source distribution of SVGMap to display information about the insertion preferences of transposable elements in a tissue-specific context, which as required installing and configuring a local instance of SVGMap and run it via the browser. The documentation for SVGMap is good enough to do this on your own, but it took a while for us to get a working instance the first time around. We ran into the same issues again the second time, so I thought I write up my notes for future reference and to help others get SVGMap up and running as fast as possible.
Topic map interfaces aren’t required to take a particular form.
A drawing of a fly could be topic map interface.
Useful for people studying flies, less useful (maybe) if you are mapping Lady Gaga discography.
What interface do you want to create for a topic map?
