Summary of Nomenclature and GUIDs

[Roderic Page]

>
> A detail I would like to discuss  within this context in the near  
> future is the best possible way to link species names to genetic  
> resources (e.g. DNA barcodes).
>

Well, the simplest way is if the genetic resources themselves have  
GUIDs (such as an LSID, Biopathways.org provides some for NCBI, and I'm  
playing with this as well). Then one simply adds one or more tags to  
the metadata associated with the resource. For example, using RDF a DNA  
sequence could have a tag such as

<dc:source rdf:resource="urn:lsid:ncbi.nlm.nih.gov:TaxId:345788" />

indicating it comes from the taxonomy with NCBI's TaxId 345788.

For the taxon one could use a tag like

<dcterms:isReferencedBy  
rdf:resource="urn:lsid:ncbi.nlm.nih.gov:genbank:AF234577" />

indicating that sequence AF234577 comes from this taxon [both LSIDs are  
made up, I could create functional ones if it woulod help the  
discussion].

The "dc" and "dcterms" are from the Dublin Core namespace  
(http://dublincore.org). This illustrates a point I've made elsewhere,  
but one of my biggest gripes about current XML efforts in taxonomy is  
the use of XML schema and custom namespaces for everything, whereas I  
think RDF is much leaner and we can employ existing namespaces for most  
(but not all) of what we need. Plus we can embed our efforts in a much  
larger community of projects. Again, I recommend keeping things simple  
and using existing standards wherever possible.

Regards

Rod



------------------------------------------------------------------------ 
----------------------------------------
Professor Roderic D. M. Page
Editor, Systematic Biology
DEEB, IBLS
Graham Kerr Building
University of Glasgow
Glasgow G12 8QP
United Kingdom

Phone:    +44 141 330 4778
Fax:      +44 141 330 2792
email:    r.page at bio.gla.ac.uk
web:      http://taxonomy.zoology.gla.ac.uk/rod/rod.html
reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html

Subscribe to Systematic Biology through the Society of Systematic
Biologists Website:  http://systematicbiology.org
Search for taxon names at http://darwin.zoology.gla.ac.uk/~rpage/portal/
Find out what we know about a species at http://ispecies.org