[tdwg-tag] NCBI taxonomy in RDF

[Scott Federhen, NCBI]

Hi Rod:

In case it helps at all, our rank list is -

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
>>
>>
>>
>>
>>
>>
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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
>
>
>
>
>
>
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