[tdwg-phylo] Upcoming TDWG meeting

Arlin Stoltzfus arlin at umd.edu
Tue Aug 31 16:06:25 CEST 2010

To build momentum for a possible working session on linking trees, I  
put some parts of this thread on the twiki page here:


This is one place to indicate your interest by adding your name and  
describing what you can bring to the workshop (in terms of both real- 
world problems and possible solutions).

All of you should be able to access the twiki using credentials that  
you established as a TDWG member.


On Aug 30, 2010, at 2:08 PM, Arlin Stoltzfus wrote:

> On Aug 28, 2010, at 6:59 PM, Blum, Stan wrote:
>> Regarding #1, and assuming that this concerns molecular data where  
>> individuals often function as OTUs, I think it would be even more  
>> important for the long-term usefulness of the data to support the  
>> ability to reference the specimen with a resolvable GUID
>> ...
>> On the other hand, a full name backed up by a URL or source/GUID  
>> would be a big improvement on codes and abbreviations
> My main aim is to support data integration (rather than validation),  
> and the two most important integrating variables for the foreseeable  
> future (at least in my limited vision) are species name (or other  
> taxonomic identifier) and geographic coordinates.  These are  
> important partly because the great mass of users outside of TDWG are  
> committed to using the same kinds of species names and the same  
> kinds of coordinates.
> Most phylogeny information artefacts (e.g., files) out there don't  
> have either one of these , so integrating phylogenetic information  
> into the global web of data isn't going to get very far until we  
> make it easy for users to put this information into their trees.
> To the extent that the scientific community is committed in the same  
> way to specimen identifiers, then this makes the problem simpler  
> because the specimen source would become the integrating variable,  
> and would mediate the integration of data by species or location  
> (because the specimen would have a species and a location).  But I  
> don't think we are there yet.
> Arlin
>> On 8/27/10 8:27 AM, "Arlin Stoltzfus" <arlin at umd.edu> wrote:
>>> 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
>> <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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