[tdwg-phylo] Upcoming TDWG meeting

Arlin Stoltzfus arlin at umd.edu
Mon Aug 30 20:08:31 CEST 2010

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  

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.


> 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

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