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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Hi Arlin and others<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>I think that idea 1 below is a really valuable topic to address.
The ability to link tree tips to other sources of data by taxon name or identifier
is a threshold step for automating a whole range of analyses and
displays. For example, the software I work on, <a
href="http://www.purl.org/biodiverse/">Biodiverse</a>, links phylogenies to
species location data for visualisation and analysis. It would be great
to have it running automatically online, linking (for example) trees from
treebase to distributions from GBIF. To do this (and many other things)
however we need a better solution to the taxon matching problem you describe.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>cheers<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Dan<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
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<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> tdwg-phylo-bounces@lists.tdwg.org
[mailto:tdwg-phylo-bounces@lists.tdwg.org] <b>On Behalf Of </b>Arlin Stoltzfus<br>
<b>Sent:</b> Friday, August 27, 2010 11:27 AM<br>
<b>To:</b> tdwg-phylo@lists.tdwg.org<br>
<b>Subject:</b> Re: [tdwg-phylo] Upcoming TDWG meeting<o:p></o:p></span></p>
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<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>I'm sending this reply to only the tdwg-phylo list (sending
to everyone seems like overkill). <o:p></o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal>Here are two ideas based on the use of phylogenies: <o:p></o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal>1. For various reasons, its important to be able to
associate valid species sources or other universal identifiers (e.g., NCBI gis)
with the human-readable OTU identifiers used in tree files, but this typically
isn't done and it's not always easy. The goal of this project is to
enable ordinary phylogenetics & systematics users to use current standards
(Newick, NHX, phyloxml, ...) to associate species names (possibly other tax
ids) with phylogenies in their usual workflows. The focus is on
developing short-term tools and strategies that might lead to better long-term
solutions. In some cases, its just a matter of knowing how to use the
file format properly, possibly aided by better tools for data input. For
users whose workflows rely on Newick, we would need a way to keep a separate
mapping of OTU ids and tax ids, along with tools to interconvert or translate
to one of the other formats (this could be as simple as an Excel spreadsheet or
as complex as a web service that maintains your mapping and does the
translation for you). <o:p></o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal>2. There is a huge variety of tree viewers. To
some extent, users need this variety due to their having different feature
sets. But users shouldn't have to choose the viewer based on data format
restrictions. The goal of this project is to improve the usability of
tree viewers. Assess the interoperability (standards compatibility) of
tree viewing software, develop strategies to improve it, and get started on any
strategies that can be implemented. Its not possible to modify viewers
whose source code is unavailable, but there may be ways to work around this
with scripts and translation tools. <o:p></o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal>Arlin<o:p></o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal>On Aug 26, 2010, at 9:40 PM, Nico Cellinese wrote:<o:p></o:p></p>
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<br>
<o:p></o:p></p>
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<p class=MsoNormal>Hi all,<br>
<br>
we have reserved one full day for a Phylogenetics Standards hands-on activity
at the upcoming TDWG conference. We asked for power strips and wireless network
and tables that we can sit around and work together. The only thing that's
missing right now is what exactly we should target. The options are wide open
right now, with the two only major constraints being that (a) we have no
funding this year to bring people in who wouldn't otherwise be there, and (b)
abstract submission deadline is next Wednesday.<br>
<br>
Any feedback or ideas, wild or not, that you have would be welcome - send those
our way.<br>
<br>
And BTW currently this workshops seems to be placed on the Wednesday of the
conference week, so those of you blitzing the local biosphere will
unfortunately have a conflict.<o:p></o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal>Cheers,<o:p></o:p></p>
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<p class=MsoNormal>Nico & Hilmar<o:p></o:p></p>
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<p class=MsoNormal style='margin-bottom:12.0pt'><o:p> </o:p></p>
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color:black'><><><><><><><><><><><><><><><><><><><><><o:p> </o:p></span></p>
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<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'>Nico Cellinese, Ph.D.<o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'>Assistant Curator, Herbarium & Informatics<o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'>Adjunct Assistant Professor, Department of Biology<o:p></o:p></span></p>
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color:black'><o:p> </o:p></span></p>
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<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'>Florida Museum of Natural History<o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'>University of Florida<o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'>354 Dickinson Hall, PO Box 117800<o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'>Gainesville, FL 32611-7800, U.S.A.<o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'>Tel. 352-273-1979<o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'>Fax 352-846-1861<o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'><a href="http://www.flmnh.ufl.edu/">http://www.flmnh.ufl.edu</a><o:p></o:p></span></p>
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<ATT00001.txt><o:p></o:p></p>
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<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'>-------<o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'>Arlin Stoltzfus (<a href="mailto:arlin@umd.edu">arlin@umd.edu</a>)<o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'>Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST<o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'>IBBR, 9600 Gudelsky Drive, Rockville, MD<o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'>tel: 240 314 6208; web: <a href="http://www.molevol.org">www.molevol.org</a><o:p></o:p></span></p>
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