Visualizing RDFa semantic annotations using SVG and NeXML/JSON

TreeBASE emits richly RDFa-annotated NeXML. An example of this is the annotation of taxa/OTUs, whose names TreeBASE tries to match to the NCBI taxonomy. The annotations that indicate such a match use skos:closeMatch as predicate and the URIs as provided by UniProt as the object. Below is a tree that uses the same logic and code, more or less, as a previous post, but embeds these UniProt URIs as xlink:href clickable links (in bold face) in the generated SVG.


  1. Nice. Another feature of SVG is the ability to have "layers" that you can toggle on and off using Javascript. For example, you could have different sets of taxon labels, such as OTUs (e.g., "Leptodactylus ocellatus AY843688"), taxon names (e.g., "Leptodactylus ocellatus"), accession numbers (AY843688), and so on.

    1. Absolutely, once we have richly annotated data (tip links and labels are probably the trivial case) there should be different, switchable, views for different annotations. Ideally each view should be somehow consistent between visualizers (e.g. speciations, extinctions, gene duplications each would have the same "look" across tools) so that we build up a visual language beyond just nodes and branches.