Chris--
It sounds like you have the skills and interest to do this. Our first goal is very modest: just assess what's possible given currently available tools. I only know about one so far, which will translate a file into CDAO with the option to add it to a triple store. A web server interface is here:
If you know about other tools, that would be great.
The next step (weeks from now) would be to look ahead to the future and identify gaps. If you are interested, all you need to do is to sign up for TDWG twiki access (if you don't have it already) and start working.
Arlin
On Oct 19, 2010, at 12:33 PM, Chris Baron wrote:
Hi,
My name is Chris Baron - a software developer, computer science graduate student interested in linked data, working in BioSync at the Field Museum on tree visualization. I have a few ideas on how to publish trees in RDF (have even created a tool to do so) and would like to speak to Biologists about how their data exists at publication so I can form a proper solution.
On Tue, Oct 19, 2010 at 5:00 AM,
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Today's Topics:
1. publishing trees in CDAO as linked open data? (Arlin Stoltzfus)
----------------------------------------------------------------------
Message: 1
Date: Mon, 18 Oct 2010 12:32:39 -0400
From: Arlin Stoltzfus <arlin@umd.edu>
Subject: [Tdwg-phylo] publishing trees in CDAO as linked open data?
To: CDAO list <cdao-discuss@lists.sourceforge.net>, Phylogenetics
Standards Interest Group <tdwg-phylo@lists.tdwg.org>
Message-ID: <BAAFA68C-2622-409A-B530-1CABADC36016@umd.edu>
Content-Type: text/plain; charset="US-ASCII"; format=flowed; delsp=yes
Dear all--
At the Biodiversity Information Standards (TDWG) meeting last month, a
sub-group of the phylogenetic standards working group started a
project to assess "current best practices for publishing trees
electronically". At present, probably the best way to publish a tree
is to use the TreeBASE submission process, which makes it possible to
upload a NEXUS file and create associations of OTUs with taxon IDs,
and of data rows with accessions, and so on. But there are also some
other possibilities. The preliminary report is being assembled here:
http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/LinkingTrees2010
Our plan is (over the next 6 weeks) to get feedback on this
preliminary report, then analyze the results and prepare a more
extensive report for publication.
One possibility that we haven't examined yet is to publish a tree
electronically by rendering it in RDF in the language of CDAO
(Comparative Data Analysis Ontology) and then contributing it to the
Linked-Open-Data cloud in some way.
Does anyone out there want to explore this idea and contribute the
results to the TDWG project? If so, please let me know.
Arlin
-------
Arlin Stoltzfus (arlin@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
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--
Chris Baron
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Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
IBBR, 9600 Gudelsky Drive, Rockville, MD