[Treebase-devel] interoperability of resources using CDAO -- planned telecon Tuesday Aug 17

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

Dear CDAO developers and users--

For the past 2 years, CDAO has been an experimental project done in  
our spare time.  Last summer, we reached our first big milestones with  
an initial ontology version and a publication.     This summer, we are  
poised for another milestone where CDAO mediates interoperability  
between real tools developed for use  by researchers.  TreeBase2  
(phylo database used by systematists), CDAOstore (experimental  
triplestore by CDAO developers), and Nexplorer3 (phylogenetic data  
viewer developed and used at NIAID) are open-source projects that have  
made recent efforts to support CDAO encodings for import or export or  
internal representation.  They were presented at the 2010 "iEvoBio"  
satellite meeting at Evolution 2010 in Portland this summer.

* TreeBase2 claims to deliver CDAO instance files (RDF-XML) in  
response to phylows URLs
* Both CDAOstore  and Nexplorer3 claim to be able to consume CDAO  
instance files via a URL.
* CDAOstore also has a translator, so that a user can upload a NEXUS  
or phylip file, and translate it into CDAO

Thus, in principle, CDAOstore can be used as a query interface to a  
TreeBase2 data entry by giving it a phyloWS URL like this:

   http://purl.org/phylo/treebase/phylows/study/TB2:S1787?format=RDF

and loading the result into the triplestore.  Likewise, in principle,  
Nexplorer3 can be used as an interface to visualize a TreeBase2 data  
entry via its phyloWS URL.  Or we could translate a NEXUS file (e.g.,  
from TreeBase2) using CDAO-store's online translator, then view the  
result in Nexplorer3.  To achieve this kind of interoperability would  
fulfill the hopes of the NESCent evolutionary informatics working  
group (2006-2009), from whose members sprang the CDAO, phyloWS and  
nexml projects.

But we aren't there yet.  Having tried all of the pairwise  
interoperations listed above, I found that none of them actually  
works.  But I'm not discouraged by that, and neither are the TreeBase,  
CDAO-store and Nexplorer3 developers.  Now that we have actual  
concrete targets for interoperability, we can focus on finding  
problems and solving them.

We have planned an initial teleconference on this issue Tuesday, the  
17th at 11:00 am Eastern (GMT -5).  Details will be provided later.

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