[tdwg-content] Idea for Discussion, Differentiating between "type's" of identifiers

[Arlin Stoltzfus]

This issue came up in the phylogenetic standards subgroup, which (at  
the TDWG meeting last week) started to assess current best practices  
for publishing a phylogenetic tree electronically.  One of the issues  
that came up is that there is no standard way of making a link between  
a tree (a clade or node) and a species.  Some of the file formats used  
in phylogenetics can do this explicitly, and others can't.  I made  
some toy examples of encodings on our twiki here:

   http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/LinkingTrees2010#A_set_of_toy_files_for_illustrat

Here is how it is done in phyloXML:

<clade>
      <taxonomy>
           <id provider="UBio">http://www.ubio.org/authority/metadata.php?lsid=urn:lsid:ubio.org:namebank:3854553 
</id
           <scientific_name>Gallus gallus</scientific_name>
      </taxonomy>
</clade>

and here is how it is rendered in the nexml output from TreeBase:

     <otu id="otu4" label="Gallus_gallus_CAA25046.1">
         <meta href="http://www.ubio.org/authority/metadata.php?lsid=urn:lsid:ubio.org:namebank:3854553 
" id="meta5" rel="skos:closeMatch" xsi:type="nex:ResourceMeta"/>
         <meta content="Gallus gallus" datatype="xsd:string"  
id="meta6" property="skos:altLabel" xsi:type="nex:LiteralMeta"/>
     </otu>

phyloXML and NeXML are emerging XML standards for phylogenetics.

Arlin

On Oct 7, 2010, at 11:49 AM, Rutger Vos wrote:

>> As an example I am of the growing opinion that taxonomic  
>> classifications
>> would be rendered perfectly adequately in SKOS - each  
>> classification being a
>> free standing thesaurus linked to other thesauri/classifications  
>> using the
>> standard SKOS terms.
>
> This is how TreeBASE shows links between OTU labels submitted to it
> and their matches to uBio NameBank records and NCBI taxonomy records,
> using the skos:closeMatch predicate (this was deemed appropriate also
> because the TreeBASE webapp determines these links mostly just by
> string matching).
>
> -- 
> Dr. Rutger A. Vos
> School of Biological Sciences
> Philip Lyle Building, Level 4
> University of Reading
> Reading
> RG6 6BX
> United Kingdom
> Tel: +44 (0) 118 378 7535
> http://www.nexml.org
> http://rutgervos.blogspot.com
> _______________________________________________
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> tdwg-content at lists.tdwg.org
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-------
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