interoperability of resources using CDAO -- planned telecon Tuesday Aug 17

[Arlin Stoltzfus]

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...@umd.edu)
Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
IBBR, 9600 Gudelsky Drive, Rockville, MD
tel: 240 314 6208; web: www.molevol.org

[Arlin Stoltzfus]

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

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[Rutger Vos]

I am sorry I won't be able to call in. I'm looking forward to see the
summary, though.

Best wishes,

Rutger

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--
Dr. Rutger A. Vos
School of Biological Sciences
Philip Lyle Building, Level 4
University of Reading
Reading
RG6 6BX
United Kingdom
Tel: +44 (0) 118 378 7535
http://www.nexml.org
http://rutgervos.blogspot.com

[Arlin Stoltzfus]

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

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-------

[Rutger Vos]

> 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.

A functioning nexml-to-CDAO translator is vital for the TreeBASE RDF
output, so I will be involved in this, but perhaps not on my own?
Anyway, one thing that needs to happen is that the RDFa extraction
needs to be folded into the core translator so that the whole thing
becomes a one step process. On TreeBASE, for example, I now fold the
outputs of the two translations into one in java code. I'd hate to see
others having to replicate that, and it's not very performant either.

Rutger