[Treebase-devel] interoperability of resources using CDAO -- telecon notes, FYI

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

Notes from the teleconference are here (should be visible to everyone):

    http://groups.google.com/group/feas2ls/web/cdao-3-way-interop-challenge

Synopsis:
* Vivek will identify and (ideally) solve problems to view TreeBase2  
RDFs in Nexplorer3
* Arlin will start developing a set of CDAO instance test files using  
the NEXUS test files in Bio::NEXUS
* we will have another teleconference in early to mid-September

We still need someone to work on the problem of reconciling different  
versions of the nexml-to-CDAO translator (XSLT).  Let me know if  
anyone wants to do that.

Arlin

On Aug 16, 2010, at 5:56 PM, Arlin Stoltzfus wrote:

> 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
>
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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