[tdwg-phylo] Upcoming TDWG meeting

[Roderic Page]

The mapping can get complicated. At the level of taxa, one could do a  
one-to-one mapping of  TreeBASE taxa to NCBI taxa. At the level of  
OTUs, the mapping may be one to many. An OTU may correspond to a  
single specimen, a single sequence, or a set of sequences from  
multiple individuals of the same taxon, or, indeed, a composite of  
exemplar taxa representing a higher taxon. So, OTUs map onto sets of  
observations.

Mapping OTUs to one or more specimen URIs would be great, if we had  
these. But as a rule we don't. Most individual data providers don't  
make individual specimens addressable. GBIF does, but we'd have to  
assume that these were stable over time, and that we have tools in  
place to map museum specimen codes to GBIF specimen URLs, and in  
general we don't. This isn't a huge obstacle if GBIF were to provide  
some guarantee that it's specimen URLs were stable, we'd then "just"  
need some tools to convert "Museum addreviation specimen code xxx" to  
a URL.

Regards

Rod

On 28 Aug 2010, at 23:59, 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 or at least  
> a collection code and catalog number.  A simple assertion that “this  
> sequence came from [an unknown specimen identified to be] this  
> taxon” can’t be re-examined or validated except by the sequence  
> data.  If you know what specimen it came from, the identification  
> can be updated (by  more methods).
>
> On the other hand, a full name backed up by a URL or source/GUID  
> would be a big improvement on codes and abbreviations
>
> -Stan
>
>
> 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
>>
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