[tdwg-tag] NCBI taxonomy in RDF
J.Kennedy at napier.ac.uk
Sun Jul 12 21:55:18 CEST 2009
Dear Rod (et al)
On holiday and just checked my email and for once I had time to respond - how sad.... anyway, I agree with you that the rank in taxon concept should not be deprecated. It was originally included for several reasons (none of them nomenclators' views, although their view is as important as any other). For example, a taxonomist might want to record information about a concept he/she is defining and might have decided the rank before the name is formally published but still wants to be able to refer to it and pass the information around or someone like an ecologist might want to describe a taxon they see in the field and refer to some name but use it as a different rank. Sounds like you have yet another reason. I can't say why it was deprecated except that the nomenclators thought it belonged to names - but then they only see the world from their point of view which is what we tried to avoiding when defining TCS. WE tried to accommodate what users of names and concepts of all kinds wanted to do.
From: tdwg-tag-bounces at lists.tdwg.org [mailto:tdwg-tag-bounces at lists.tdwg.org] On Behalf Of Roderic Page
Sent: 12 July 2009 10:15
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
> 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
Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
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