[tdwg-tag] NCBI taxonomy in RDF
Scott Federhen, NCBI
federhen at ncbi.nlm.nih.gov
Mon Jul 13 16:53:48 CEST 2009
In case it helps at all, our rank list is -
Several of these are not on the TDWG list (cohort, parvorder,
species group & subgroup) or are spelled differently
Unranked nodes can appear anywhere in the classification,
and sibling nodes may be of different rank.
On Jul 12, 2009, at 5:14 AM, Roderic Page wrote:
> Dear Kevin,
> 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
>> 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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> 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
> tdwg-tag mailing list
> tdwg-tag at lists.tdwg.org
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