<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Chris - you probably know the Triplify project? <a href="http://triplify.org/">http://triplify.org/</a><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>-hilmar</div><div><br><div><div>On Oct 19, 2010, at 1:03 PM, Chris Baron wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">I've written a plugin to transform relational database data into RDF : <a href="http://www.web2py.com/semantic">http://www.web2py.com/semantic</a><br><br>If anyone keeps their data in a relational database, this would be useful. <br> <br><div class="gmail_quote">On Tue, Oct 19, 2010 at 11:58 AM, Arlin Stoltzfus <span dir="ltr"><<a href="mailto:arlin@umd.edu">arlin@umd.edu</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;"> <div style="word-wrap: break-word;">Chris-- <div><br></div><div>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: </div> <div><br></div><div> <a href="http://www.cs.nmsu.edu/%7Ecdaostore/phylows.php" target="_blank">http://www.cs.nmsu.edu/~cdaostore/phylows.php</a></div><div><br></div><div>If you know about other tools, that would be great. </div> <div><br></div><div>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. </div> <div><br></div><div>Arlin</div><div><br><div><div><div></div><div class="h5"><div>On Oct 19, 2010, at 12:33 PM, Chris Baron wrote:</div><br></div></div><blockquote type="cite"><div><div></div><div class="h5">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" target="_blank">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;"> Send tdwg-phylo mailing list submissions to<br> <a href="mailto:tdwg-phylo@lists.tdwg.org" target="_blank">tdwg-phylo@lists.tdwg.org</a><br> <br> To subscribe or unsubscribe via the World Wide Web, visit<br> <a href="http://lists.tdwg.org/mailman/listinfo/tdwg-phylo" target="_blank">http://lists.tdwg.org/mailman/listinfo/tdwg-phylo</a><br> or, via email, send a message with subject or body 'help' to<br> <a href="mailto:tdwg-phylo-request@lists.tdwg.org" target="_blank">tdwg-phylo-request@lists.tdwg.org</a><br> <br> You can reach the person managing the list at<br> <a href="mailto:tdwg-phylo-owner@lists.tdwg.org" target="_blank">tdwg-phylo-owner@lists.tdwg.org</a><br> <br> When replying, please edit your Subject line so it is more specific<br> than "Re: Contents of tdwg-phylo digest..."<br> <br> <br> Today's Topics:<br> <br> 1. publishing trees in CDAO as linked open data? (Arlin Stoltzfus)<br> <br> <br> ----------------------------------------------------------------------<br> <br> Message: 1<br> Date: Mon, 18 Oct 2010 12:32:39 -0400<br> From: Arlin Stoltzfus <<a href="mailto:arlin@umd.edu" target="_blank">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" target="_blank">cdao-discuss@lists.sourceforge.net</a>>, Phylogenetics<br> Standards Interest Group <<a href="mailto:tdwg-phylo@lists.tdwg.org" target="_blank">tdwg-phylo@lists.tdwg.org</a>><br> Message-ID: <<a href="mailto:BAAFA68C-2622-409A-B530-1CABADC36016@umd.edu" target="_blank">BAAFA68C-2622-409A-B530-1CABADC36016@umd.edu</a>><br> Content-Type: text/plain; charset="US-ASCII"; format=flowed; delsp=yes<br> <br> 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" target="_blank">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> <br> <br> <br> ------------------------------<br> <br> _______________________________________________<br> tdwg-phylo mailing list<br> <a href="mailto:tdwg-phylo@lists.tdwg.org" target="_blank">tdwg-phylo@lists.tdwg.org</a><br> <a href="http://lists.tdwg.org/mailman/listinfo/tdwg-phylo" target="_blank">http://lists.tdwg.org/mailman/listinfo/tdwg-phylo</a><br> <br> <br> End of tdwg-phylo Digest, Vol 2, Issue 3<br> ****************************************<br> </blockquote></div><br><br clear="all"><br>-- <br>Chris Baron<br> </div></div><span><ATT00001.txt></span></blockquote> </div><div class="im"><br><div> <span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; font-size: medium;"><div style="word-wrap: break-word;"> <div><div style="font-size: 12px;">-------</div><div style="font-size: 12px;">Arlin Stoltzfus (<a href="mailto:arlin@umd.edu" target="_blank">arlin@umd.edu</a>)</div><div style="font-size: 12px;">Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST</div> <div style="font-size: 12px;">IBBR, 9600 Gudelsky Drive, Rockville, MD</div><div style="font-size: 12px;">tel: 240 314 6208; web: <a href="http://www.molevol.org" target="_blank">www.molevol.org</a></div></div></div></span> </div> <br></div></div></div></blockquote></div><br><br clear="all"><br>-- <br>Chris Baron<br> _______________________________________________<br>tdwg-phylo mailing list<br><a href="mailto:tdwg-phylo@lists.tdwg.org">tdwg-phylo@lists.tdwg.org</a><br><a href="http://lists.tdwg.org/mailman/listinfo/tdwg-phylo">http://lists.tdwg.org/mailman/listinfo/tdwg-phylo</a><br></blockquote></div><br><div> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><font class="Apple-style-span" face="Monaco" size="3"><span class="Apple-style-span" style="font-size: 11px; ">-- </span></font></div><div><font class="Apple-style-span" face="Monaco" size="3"><span class="Apple-style-span" style="font-size: 11px; ">===========================================================</span></font></div><div><font class="Apple-style-span" face="Monaco" size="3"><span class="Apple-style-span" style="font-size: 11px; ">: Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org :</span></font></div><div><font class="Apple-style-span" face="Monaco" size="3"><span class="Apple-style-span" style="font-size: 11px; ">===========================================================</span></font></div><div><br class="webkit-block-placeholder"></div></div></span><br class="Apple-interchange-newline"> </div><br></div></body></html>