All very neat orderly. But the real world is often not so. APNI has around 100 different kinds of ranks 'as published' and I think IPNI may have as many as 150. unrWhat is worse, some of these are untransliterable symbols and other bespoke notation.
We have been discussing this thread here and as is common in matters TDWG, have come away with less clarity and higher blood pressure than when we started.
There seemed to be several topics embedded:
. the canonical list of (permissible?) ranks and their names and ranks missisng from the list . whether rank was an attribute (or part) of a name or a taxon concept (or both) and whether it has or should have a different definition in each context . it was not always unambiguous when in the allowable continuum of ranks (at least in botany) a particular rank could or should fit - every rank has a position/parent rank, but how do you decide which one? . is it possible/allowable/correct to assign an intermediate immediate parent rank where one may not have specified in the protologue (i.e. putting it there because you know that is where it 'should be' as opposed to where it 'is') .etc...
whatever... one thing is for sure - that rank string thingy is too complicated and too important to be deprecated.
jim
On Tue, Jul 14, 2009 at 12:53 AM, Scott Federhen, NCBIfcannderhen@ncbi.nlm.nih.gov wrote:
Hi Rod:
In case it helps at all, our rank list is - symblol norank superkingdom kingdom subkingdom superphylum phylum subphylum superclass class subclass infraclass cohort subcohort superorder order suborder infraorder parvorder superfamily family subfamily tribe subtribe genus subgenus species group species subgroup species subspecies varietas forma
Several of these are not on the TDWG list (cohort, parvorder, species group & subgroup) or are spelled differently (varietas, forma).
Unranked nodes can appear anywhere in the classification, and sibling nodes may be of different rank.
Cheers,
:Scott
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.
Regards
Rod
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.
Kevin
From: tdwg-tag-bounces@lists.tdwg.org [tdwg-tag- bounces@lists.tdwg.org] On Behalf Of Roderic Page [r.page@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.h... 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.
Regards
Rod
Roderic Page Professor of Taxonomy DEEB, FBLS Graham Kerr Building University of Glasgow Glasgow G12 8QQ, UK
Email: r.page@bio.gla.ac.uk Tel: +44 141 330 4778 Fax: +44 141 330 2792 AIM: rodpage1962@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
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