[Treebase-devel] current best practices for publishing trees electronically

[Arlin S. <ar...@um...>]

Dear treebase developers--

Hello.  As you know, in the next few years, we can expect thousands or  
tens of thousands of trees to be archived or published electronically  
in share-able ways (as opposed to the current situation in which most  
trees are just graphic images of trees, or they can't be linked to  
anything because the information in the tree consists only of  
arbitrary labels for things).  So, now is a good time to think about  
best practices for publishing trees electronically, and to identify  
strengths and weaknesses so as to help the phylogenetic community move  
toward greater re-use, sharing, and integration of data.

Last week, at the TDWG (Biodiversity Information Standards) meeting,  
the TDWG Phylogenetic Standards working group started a project to  
assess current best practices for publishing trees electronically. The  
work we have done so far is described here:

http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/LinkingTrees2010

Dan Rosauer, Torsten Ericksson and I are going to finish up a  
preliminary report for TDWG, and then we would like to move on to  
develop a manuscript for publication in the next 6 to 8 weeks.

We'd appreciate your help in making sure that we are making the best  
use of TreeBase and any other technologies that you might recommend  
for making trees available electronically.   At the TDWG meeting,  
several of us experimented with the TreeBase submission process.  We  
were impressed with the support for representing the 3 kinds of  
linkable quantities that we targeted in our assessment: species names  
(or LSIDs or other taxonomic identifiers), accession numbers, and  
geographic coordinates.  The only weakness we have noticed so far is  
the lack of access to all of these data though treebase interfaces.

Arlin
-------
Arlin Stoltzfus (ar...@um...)
Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
IBBR, 9600 Gudelsky Drive, Rockville, MD
tel: 240 314 6208; web: www.molevol.org