[tdwg-phylo] Upcoming TDWG meeting

[Arlin Stoltzfus]

Is anyone else interested?  If there is interest, I'll start a  
planning document (TDWG phylo twiki?).

Arlin

On Aug 27, 2010, at 2:45 PM, Dan Rosauer wrote:

> 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, 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.
>
> cheers
> Dan
>
> 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 you).
>
> 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.
>
> Arlin
>
> 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.
>
> Cheers,
> 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
>
>
>
> <ATT00001.txt>
>
> -------
> 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
>
> <ATT00001.txt>

-------
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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