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_...
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:3... </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 _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
------- Arlin Stoltzfus (arlin@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