[tdwg-tag] NCBI taxonomy in RDF
p.kirk at cabi.org
Sun Jul 12 12:00:57 CEST 2009
Ideally all names in use anywhere should be accounted for in the appropriate nomenclator. I think we are beyond the days when only Code compliant names were included and we are certainly beyond the days when only names in agreement with the taxonomic opinion of the nomenclator compilor were included - as was the case for the first volumes of Index Kewensis, but now, I suspect, rectified. These restrictions were understandable in the context of 'only published names should be included' but that was in the days of 'published' meaning ink on paper ... I would hope we have moved (or are moving) on from that restrictive definition.
I assume the TDWG vocabulary has no 'other' to cover informal ranks?
From: tdwg-tag-bounces at lists.tdwg.org on behalf of Roderic Page
Sent: Sun 12/07/2009 10:14
To: Technical Architecture Group mailing list
Subject: Re: [tdwg-tag] NCBI taxonomy in RDF
But the reality is that a taxon concept may have a rank that's not in
the TDWG vocabulary (e.g., an informal rank), and existing name
databases may disagree about the rank. For example, a nomenclator may
have a name that was published as a subgenus, but a concept database
(such as NCBI) may use it as a genus.
I guess I'm keen on capturing what is actually out there, not what
ideally should be out their.
On 12 Jul 2009, at 06:59, Kevin Richards wrote:
> I suspect the rankString (as well as the rank property) was
> deprecated from the TaxonConcept class because the rank and
> rankString properties are also on the TaxonName class (http://rs.tdwg.org/ontology/voc/TaxonName
> ), where it is far more appropriate to have them - ie Taxon Concepts
> are not the best place to put rank info.
> From: tdwg-tag-bounces at lists.tdwg.org [tdwg-tag-
> bounces at lists.tdwg.org] On Behalf Of Roderic Page [r.page at bio.gla.ac.uk
> Sent: Sunday, 12 July 2009 5:25 a.m.
> To: Technical Architecture Group mailing list
> Subject: [tdwg-tag] NCBI taxonomy in RDF
> I've been playing with expressing the NCBI taxonomy in TDWG RDF. The
> results are described at http://iphylo.blogspot.com/2009/07/ncbi-rdf.html
> (see also http://iphylo.blogspot.com/2009/07/ncbi-taxonomy-tdwg-vocabularies-and-rdf.html
> for some background).
> It's still incomplete (I've not put links up and down the tree yet),
> but for now the focus is on expressing links to nomenclators that
> support LSIDs (such as IPNI and Index Fungorum) so that I can annotate
> the NCBI taxonomy via SPARQL queries.
> One minor comment, the property "rankString" has been deprecated
> (apparently), but it makes sense to retain this as there may well be
> ranks that a classification has that aren't in the TDWG vocabulary.
> Hence, I'd be keen for this NOT to be deprecated.
> Roderic Page
> Professor of Taxonomy
> DEEB, FBLS
> Graham Kerr Building
> University of Glasgow
> Glasgow G12 8QQ, UK
> Email: r.page at bio.gla.ac.uk
> Tel: +44 141 330 4778
> Fax: +44 141 330 2792
> AIM: rodpage1962 at aim.com
> Facebook: http://www.facebook.com/profile.php?id=1112517192
> Twitter: http://twitter.com/rdmpage
> Blog: http://iphylo.blogspot.com <http://iphylo.blogspot.com/>
> Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
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Professor of Taxonomy
Graham Kerr Building
University of Glasgow
Glasgow G12 8QQ, UK
Email: r.page at bio.gla.ac.uk
Tel: +44 141 330 4778
Fax: +44 141 330 2792
AIM: rodpage1962 at aim.com
Blog: http://iphylo.blogspot.com <http://iphylo.blogspot.com/>
Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
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