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

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

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.

Jessie

-----Original Message----- From: tdwg-tag-bounces@lists.tdwg.org [mailto:tdwg-tag-bounces@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

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

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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surprised that the infrageneric ranks not infrequently used in Botanical nomenclature are not included - viz. Section, Subsection, Series and Subseries

And confused as to the logic of using 'varietas' and 'forma' when, for example, kingdom is used rather than regnum ... I would suggest either all Latin forms or both Latin and English forms of the rank terms. Accepting that 'variety' has been used used as an alternative to what might be the more correct cultivar.

Paul

-----Original Message----- From: tdwg-tag-bounces@lists.tdwg.org [mailto:tdwg-tag-bounces@lists.tdwg.org] On Behalf Of Scott Federhen, NCBI Sent: 13 July 2009 15:54 To: Roderic Page Cc: Technical Architecture Group mailing list Subject: Re: [tdwg-tag] NCBI taxonomy in RDF

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@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-an d-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@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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...

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@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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