Hi,<br><br>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.<br>
<br><br><br><div class="gmail_quote">On Tue, Oct 19, 2010 at 5:00 AM, <span dir="ltr"><<a href="mailto:tdwg-phylo-request@lists.tdwg.org">tdwg-phylo-request@lists.tdwg.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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Today's Topics:<br>
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1. publishing trees in CDAO as linked open data? (Arlin Stoltzfus)<br>
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Message: 1<br>
Date: Mon, 18 Oct 2010 12:32:39 -0400<br>
From: Arlin Stoltzfus <<a href="mailto:arlin@umd.edu">arlin@umd.edu</a>><br>
Subject: [Tdwg-phylo] publishing trees in CDAO as linked open data?<br>
To: CDAO list <<a href="mailto:cdao-discuss@lists.sourceforge.net">cdao-discuss@lists.sourceforge.net</a>>, Phylogenetics<br>
Standards Interest Group <<a href="mailto:tdwg-phylo@lists.tdwg.org">tdwg-phylo@lists.tdwg.org</a>><br>
Message-ID: <<a href="mailto:BAAFA68C-2622-409A-B530-1CABADC36016@umd.edu">BAAFA68C-2622-409A-B530-1CABADC36016@umd.edu</a>><br>
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Dear all--<br>
<br>
At the Biodiversity Information Standards (TDWG) meeting last month, a<br>
sub-group of the phylogenetic standards working group started a<br>
project to assess "current best practices for publishing trees<br>
electronically". At present, probably the best way to publish a tree<br>
is to use the TreeBASE submission process, which makes it possible to<br>
upload a NEXUS file and create associations of OTUs with taxon IDs,<br>
and of data rows with accessions, and so on. But there are also some<br>
other possibilities. The preliminary report is being assembled here:<br>
<br>
<a href="http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/LinkingTrees2010" target="_blank">http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/LinkingTrees2010</a><br>
<br>
Our plan is (over the next 6 weeks) to get feedback on this<br>
preliminary report, then analyze the results and prepare a more<br>
extensive report for publication.<br>
<br>
One possibility that we haven't examined yet is to publish a tree<br>
electronically by rendering it in RDF in the language of CDAO<br>
(Comparative Data Analysis Ontology) and then contributing it to the<br>
Linked-Open-Data cloud in some way.<br>
<br>
Does anyone out there want to explore this idea and contribute the<br>
results to the TDWG project? If so, please let me know.<br>
<br>
Arlin<br>
-------<br>
Arlin Stoltzfus (<a href="mailto:arlin@umd.edu">arlin@umd.edu</a>)<br>
Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST<br>
IBBR, 9600 Gudelsky Drive, Rockville, MD<br>
tel: 240 314 6208; web: <a href="http://www.molevol.org" target="_blank">www.molevol.org</a><br>
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End of tdwg-phylo Digest, Vol 2, Issue 3<br>
****************************************<br>
</blockquote></div><br><br clear="all"><br>-- <br>Chris Baron<br>