[Treebase-devel] remedying mismatched OTU names

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

Dear all--

A common problem with data sharing in phylogenetics is that OTU names  
do not match between files, e.g., between the alignment and the tree  
from the same study.  I think I heard it from Bill that this is a  
common problem in TreeBASE submissions.  I have encountered it many  
times and have thought about how to design software to deal with the  
problem.

After discussing this with Vivek, I decided to make a more formal  
description of the problem which is available here (sorry about the  
pptx format):

   http://dl.dropbox.com/u/7727158/name_matching.pptx

This includes real examples of mismatched names collected in the wild,  
an explanation of why the problem occurs, mock-ups of  interactive  
user sessions, and implementation notes.  Vivek already started  
playing with some of the concepts and put an app on appspot (the link  
is in the presentation).

Comments are welcome.   If implemented as described, how well would  
this tool serve the community need for name-matching?  What would make  
it better?

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