[Tdwg-phylo] Publishing a trees in RDF

Karen Cranston karen.cranston at gmail.com
Thu Oct 21 17:56:27 CEST 2010

> The problem of visualizing large trees, e.g., hundreds of thousands or  
> millions of nodes, has been solved again and again by computer  
> scientists.  We've all seen some visualizations of the internet done  
> with such tools.  There is no fundamental technology barrier.  The  
> technology exists to visualize large trees and zoom around and  
> navigate and so on.
There is a distinction between a generic solution for visualizing very large graphs / networks and a solution tailed for phylogenetic trees / acyclic graphs. The visualizations of the internet (for example) are trying to convey a different type of information - clusters of connectivity, hubs - rather than the specific branching pattern of a phylogeny. We've invited smart comp sci & visual folks to workshops on treeviz, and they haven't told us the problem is already solved. That's not to say that isn't anything of value to learn from these generic projects, but the reality is that we don't have a user-friendly, widely accepted solution for visualizing large (>100K leaves) phylogenetic trees.  

The iPlant project that I've been working with has an interactive solution that works for trees of ~500K leaves (it was 1M with the standalone version, but we lost some performance when we moved to a web-based solution). We've been focused on the topology up to this point, but now it is time to start developing an interface for attaching metadata and annotations. Wiki pages for the project:
prototype implementation (no ability to upload trees here yet): 

> The problem has to do with how to develop stable and adaptable  
> software for a community that is poor, dispersed, fractious (unable to  
> agree on standards), and constantly changing in its needs.
This is definitely part of the problem with treeviz. We're starting (finally) to talk about this in the iPlant project.  Having a key resource like TreeBASE to point to is going to be helpful in this process. 

> The second issue that I don't understand is: what is the proper  
> netiquette when a list message is cc'ed to half a dozen people?  If we  
> all keep repeating the cc pattern, recipients may be getting lots of  
> messages that they don't want.  If we stick to the list only, they  
> could miss out.
Problem here seems to be determining who is on the list and who isn't. I am, so I don't need to be copied separately. 


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