Re: [Treebase-devel] [CDAO-discuss] interoperability of resources using CDAO -- telecon Tuesday Aug 17

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

As noted last week, a teleconference is scheduled for Tuesday at 11:00  
am EST (GMT -5).  The agenda is to discuss steps to improve  
interoperability among tools that use CDAO (see message below for  
details).

To connect,
1. call 1-213-289-0500  (this is a long-distance call to Los Angeles),  
then
2. when prompted, enter 375259

After the telecon is over, I will post a summary somewhere accessible.

Arlin

On Aug 13, 2010, at 12:35 PM, Arlin Stoltzfus wrote:

> 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
>
>
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-------
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