[Tdwg-phylo] Publishing a trees in RDF

Roderic Page r.page at bio.gla.ac.uk
Fri Oct 22 17:00:14 CEST 2010

There are other issues here as well. Technology advances rapidly, and  
what once seemed a good choice may rapidly become dated. Without  
wishing to start a flame war, I think Java applets are dead (sorry  
Phylowidget), Flash is fading away (thank you Steve), and increasingly  
we will see lightweight SVG and Canvas-based browsers, non-web based  
browsers that exploit specific hardware (iPad anyone), and Google- 
Earth based browsers.

I doubt one-size-fits all will work. Standards themselves won't  
address this issue, and I personally doubt RDF is where we want to be  
focussing efforts anyway. A decent JSON format for trees and  
associated metadata would be much more palatable for developers. It's  
worth remembering that the great success of Newick (and Nexus) was  
largely due to the ease of parsing.



On 22 Oct 2010, at 15:29, Arlin Stoltzfus wrote:

> 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.
> Arlin
> 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
> http://lists.tdwg.org/mailman/listinfo/tdwg-phylo

Roderic Page
Professor of Taxonomy
Institute of Biodiversity, Animal Health and Comparative Medicine
College of Medical, Veterinary and Life Sciences
Graham Kerr Building
University of Glasgow
Glasgow G12 8QQ, UK

Email: r.page at bio.gla.ac.uk
Tel: +44 141 330 4778
Fax: +44 141 330 2792
AIM: rodpage1962 at aim.com
Facebook: http://www.facebook.com/profile.php?id=1112517192
Twitter: http://twitter.com/rdmpage
Blog: http://iphylo.blogspot.com
Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html

More information about the tdwg-phylo mailing list