[tdwg-phylo] Upcoming TDWG meeting

Dan Rosauer dan.rosauer at yale.edu
Fri Aug 27 20:45:32 CEST 2010

Hi Arlin and others


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, Biodiverse
<http://www.purl.org/biodiverse/> , 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.





From: tdwg-phylo-bounces at lists.tdwg.org
[mailto:tdwg-phylo-bounces at lists.tdwg.org] On Behalf Of Arlin Stoltzfus
Sent: Friday, August 27, 2010 11:27 AM
To: tdwg-phylo at lists.tdwg.org
Subject: Re: [tdwg-phylo] Upcoming TDWG meeting


I'm sending this reply to only the tdwg-phylo list (sending to everyone
seems like overkill). 


Here are two ideas based on the use of phylogenies: 


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


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.  




On Aug 26, 2010, at 9:40 PM, Nico Cellinese wrote:

Hi all,

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.

Any feedback or ideas, wild or not, that you have would be welcome - send
those our way.

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.



Nico & Hilmar



Nico Cellinese, Ph.D.

Assistant Curator, Herbarium & Informatics

Adjunct Assistant Professor, Department of Biology


Florida Museum of Natural History

University of Florida

354 Dickinson Hall, PO Box 117800

Gainesville, FL 32611-7800, U.S.A.

Tel. 352-273-1979

Fax 352-846-1861

http://www.flmnh.ufl.edu <http://www.flmnh.ufl.edu/> 






Arlin Stoltzfus (arlin at 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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