[Tdwg-phylo] Publishing a trees in RDF

Kidd, David M d.kidd at imperial.ac.uk
Thu Oct 21 11:20:34 CEST 2010

I am yet to consider the visualizing RDF trees, however, I have am interest in visualizing and interacting with trees and networks in a web context.

I've been looking at the various web tree visualizers, as well as more generic visualization libraries, for the last week or so. Understanding the functionality, maturity, user community and inter-browser compatability is time consuming, and not always simple to determine.

Specifically, I am looking for a tool that supports, or can extended to support;

1. Both both trees and networks,
2. The selection of multiple nodes, e.g. subtrees
3. The browsing of large trees/networks - I get some weird effects with large trees in jsPhyloSVG. 
4. (Readable) Labels at all nodes.
5. Alternate layouts (circular, hyperbolic, etc.)
6. Works in as many browsers as possible.
7. A variety of I/O formats - I store my trees in PhyloDB, which I am thinking of generalizing for networks.

The ability to browse large trees seems to be a particular limitation of existing tools (I'd love to be corrected if I am wrong). Having a tree larger than the widget, as in Phylowidget, is one approach, however, an overview window would be nice to orientate your view in relation to the entire tree. I have also been considering displaying only a subset of nodes and then having 'expand', 'contract' and 'pan' (by expanding and contracting) functions for navagation. The ability to display node subsets is probably more important for networks than trees as reticulation will often result in visual occlusion.

I would be very interested in any comments regarding existing tools and the above issues (an others I have not thought about). I would be happy to compile all comments and perhaps some comparative demos somewhere.

 - Dave

David M. Kidd

Research Associate
Center for Population Biology
Silwood Park Campus
Imperial College London
0207 594 2470

-----Original Message-----
From: tdwg-phylo-bounces at lists.tdwg.org [mailto:tdwg-phylo-bounces at lists.tdwg.org] On Behalf Of Richard Ree
Sent: 20 October 2010 21:47
To: Hilmar Lapp
Cc: tdwg-phylo at lists.tdwg.org Interest Group; Chris Baron
Subject: Re: [Tdwg-phylo] Publishing a tree in RDF

The purposes of tree visualization are many and varied, so it seems natural to me that tool development reflects that diversity.  One distinction of tred is that it exposes server-side and client-side functionality.


On Wed, Oct 20, 2010 at 3:17 PM, Hilmar Lapp <hlapp at nescent.org> wrote:
> On Oct 20, 2010, at 2:43 PM, Chris Baron wrote:
> Also, I've been working on a phylogentic tree editor called tred.  
> http://code.google.com/p/tred/
> Interesting. How does your editor compare to the dozens of tree 
> editors and visualizers already available. For example PhyloWidget, or jsPhyloSVG?
> I may sound like a broken record here, and I don't want to discourage 
> you at all from developing tools for phylogenetics. We certainly need 
> more developers. I also do think though that as a community we make 
> the most progress if we aren't sprouting new tools for the same purpose all the time.
> -hilmar
> --
> ===========================================================
> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
> ===========================================================
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