[Tdwg-phylo] Publishing a trees in RDF

Kidd, David M d.kidd at imperial.ac.uk
Fri Oct 22 16:55:35 CEST 2010

Thank you Rutger, Christian, Cindy, Hilmar and Arlin,

Whatever the technological maturity of tools, there remains the hurdle of finding the viewers, assessing their functionality and assessing whether a task can be completed with the available tools given a time-scale and skill set. I have just started to put together a comparison site describing functionality and where the same trees can be viewed in the different viewers.

Sorry for interrupting the RDF flow - it has been very interesting to follow.

 - 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 Arlin Stoltzfus
Sent: 22 October 2010 15:30
To: tdwg-phylo at lists.tdwg.org Interest Group
Subject: Re: [Tdwg-phylo] Publishing a trees in RDF

QED.  The technology is out there.  IMHO, the continual propagation of new tree-viewers by developers, and the sense of users that there is no tree viewer that satisfies their needs, is (in the medium-term and
long-term) a cultural-organizational-educational problem and not at all a technical problem.

If this is true, then in order to solve the real problem, we need to think about  things like changes in funding structure, standards development, and modes of user engagement, not new graphics libraries that do just the right thing with only a few commands.


On Oct 21, 2010, at 12:57 PM, Christian M Zmasek wrote:

> Hi, Dave and Rutger:
> My own tree viewer "Archaeopteryx" provides such an overview when  
> zoomed
> in, plus some other features described as "missing" in most current  
> tools.
> See: http://www.phylosoft.org/archaeopteryx/
> Example: http://www.phylosoft.org/archaeopteryx/examples/mollusca.html
> Archaeopteryx also provides other useful features (at least for
> comparative genomics use cases). For example, the ability to infer
> internal taxonomies (if all external nodes have _some_ taxonomic
> information associated with them; standalone version only; via uniprot
> taxonomy database).
> Please let me know if you'd like to know more or have suggestions for
> improvement (although keep in mind that this Archaeopteryx is just a
> peculiar hobby of mine).
> Christian
> On 10/21/2010 3:39 AM, Rutger Vos wrote:
>> Hi Dave,
>>> 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.
>> Rod Page has coded a web widget (I believe all javascript) that has a
>> small preview window for the whole tree and a larger "zoomed in"  
>> view.
>> "TreeJuxtaposer" is a java app(let?) that allows you to contract and
>> expand selections of nodes/clades. I think these come closest to what
>> you are talking about, though neither operates on networks.
>> Cheers,
>> Rutger
> _______________________________________________
> tdwg-phylo mailing list
> tdwg-phylo at lists.tdwg.org
> http://lists.tdwg.org/mailman/listinfo/tdwg-phylo

Arlin Stoltzfus (arlin at umd.edu)
Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
IBBR, 9600 Gudelsky Drive, Rockville, MD
tel: 240 314 6208; web: www.molevol.org

tdwg-phylo mailing list
tdwg-phylo at lists.tdwg.org

More information about the tdwg-phylo mailing list