[tdwg-tag] NCBI taxonomy in RDF

Mon Jul 13 23:41:14 CEST 2009

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,
NCBI<fcannderhen at 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 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.
>>>
>>> Regards
>>>
>>> Rod
>>>
>>> ---------------------------------------------------------
>>> 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
>>> http://lists.tdwg.org/mailman/listinfo/tdwg-tag
>>>
>>> Please consider the environment before printing this email
>>> Warning:  This electronic message together with any attachments is
>>> confidential. If you receive it in error: (i) you must not read,
>>> use, disclose, copy or retain it; (ii) please contact the sender
>>> immediately by reply email and then delete the emails.
>>> The views expressed in this email may not be those of Landcare
>>> Research New Zealand Limited. http://www.landcareresearch.co.nz
>>>
>>
>> ---------------------------------------------------------
>> 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
>> http://lists.tdwg.org/mailman/listinfo/tdwg-tag
>
> _______________________________________________
> tdwg-tag mailing list
> tdwg-tag at lists.tdwg.org
> http://lists.tdwg.org/mailman/listinfo/tdwg-tag
>

-- 
_________________
Jim Croft ~ jim.croft at gmail.com ~ +61-2-62509499 ~
http://www.google.com/profiles/jim.croft

... in pursuit of the meaning of leaf ...