<HTML dir=ltr><HEAD><TITLE>Re: [tdwg-tag] NCBI taxonomy in RDF</TITLE>
<META http-equiv=Content-Type content="text/html; charset=unicode">
<META content="MSHTML 6.00.2900.5803" name=GENERATOR></HEAD>
<BODY>
<DIV id=idOWAReplyText75218 dir=ltr>
<DIV dir=ltr><FONT face=Arial color=#000000 size=2>Ideally all names in use anywhere should be accounted for in the appropriate nomenclator. I think we are beyond the days when only Code compliant names were included and we are certainly beyond the days when only names in agreement with the taxonomic opinion of the nomenclator compilor were included - as was the case for the first volumes of Index Kewensis, but now, I suspect, rectified. These restrictions were understandable in the context of 'only published names should be included' but that was in the days of 'published' meaning ink on paper ... I would hope we have moved (or are moving) on from that restrictive definition.</FONT></DIV>
<DIV dir=ltr><FONT face=Arial size=2></FONT> </DIV>
<DIV dir=ltr><FONT face=Arial size=2>I assume the TDWG vocabulary has no 'other' to cover informal ranks?</FONT></DIV>
<DIV dir=ltr><FONT face=Arial size=2></FONT> </DIV>
<DIV dir=ltr><FONT face=Arial size=2>Paul</FONT></DIV></DIV>
<DIV dir=ltr><BR>
<HR tabIndex=-1>
<FONT face=Tahoma size=2><B>From:</B> tdwg-tag-bounces@lists.tdwg.org on behalf of Roderic Page<BR><B>Sent:</B> Sun 12/07/2009 10:14<BR><B>To:</B> Technical Architecture Group mailing list<BR><B>Subject:</B> Re: [tdwg-tag] NCBI taxonomy in RDF<BR></FONT><BR></DIV>
<DIV>
<P><FONT size=2>Dear Kevin,<BR><BR>But the reality is that a taxon concept may have a rank that's not in <BR>the TDWG vocabulary (e.g., an informal rank), and existing name <BR>databases may disagree about the rank. For example, a nomenclator may <BR>have a name that was published as a subgenus, but a concept database <BR>(such as NCBI) may use it as a genus.<BR><BR>I guess I'm keen on capturing what is actually out there, not what <BR>ideally should be out their.<BR><BR>Regards<BR><BR>Rod<BR><BR>On 12 Jul 2009, at 06:59, Kevin Richards wrote:<BR><BR>> I suspect the rankString (as well as the rank property) was <BR>> deprecated from the TaxonConcept class because the rank and <BR>> rankString properties are also on the TaxonName class (<A href="http://rs.tdwg.org/ontology/voc/TaxonName">http://rs.tdwg.org/ontology/voc/TaxonName</A><BR>> ), where it is far more appropriate to have them - ie Taxon Concepts <BR>> are not the best place to put rank info.<BR>><BR>> Kevin<BR>><BR>> ________________________________________<BR>> From: tdwg-tag-bounces@lists.tdwg.org [tdwg-tag-<BR>> bounces@lists.tdwg.org] On Behalf Of Roderic Page [r.page@bio.gla.ac.uk<BR>> ]<BR>> Sent: Sunday, 12 July 2009 5:25 a.m.<BR>> To: Technical Architecture Group mailing list<BR>> Subject: [tdwg-tag] NCBI taxonomy in RDF<BR>><BR>> I've been playing with expressing the NCBI taxonomy in TDWG RDF. The<BR>> results are described at <A href="http://iphylo.blogspot.com/2009/07/ncbi-rdf.html">http://iphylo.blogspot.com/2009/07/ncbi-rdf.html</A><BR>> (see also <A href="http://iphylo.blogspot.com/2009/07/ncbi-taxonomy-tdwg-vocabularies-and-rdf.html">http://iphylo.blogspot.com/2009/07/ncbi-taxonomy-tdwg-vocabularies-and-rdf.html</A><BR>> for some background).<BR>><BR>> It's still incomplete (I've not put links up and down the tree yet),<BR>> but for now the focus is on expressing links to nomenclators that<BR>> support LSIDs (such as IPNI and Index Fungorum) so that I can annotate<BR>> the NCBI taxonomy via SPARQL queries.<BR>><BR>> One minor comment, the property "rankString" has been deprecated<BR>> (apparently), but it makes sense to retain this as there may well be<BR>> ranks that a classification has that aren't in the TDWG vocabulary.<BR>> Hence, I'd be keen for this NOT to be deprecated.<BR>><BR>> Regards<BR>><BR>> Rod<BR>><BR>> ---------------------------------------------------------<BR>> Roderic Page<BR>> Professor of Taxonomy<BR>> DEEB, FBLS<BR>> Graham Kerr Building<BR>> University of Glasgow<BR>> Glasgow G12 8QQ, UK<BR>><BR>> Email: r.page@bio.gla.ac.uk<BR>> Tel: +44 141 330 4778<BR>> Fax: +44 141 330 2792<BR>> AIM: rodpage1962@aim.com<BR>> Facebook: <A href="http://www.facebook.com/profile.php?id=1112517192">http://www.facebook.com/profile.php?id=1112517192</A><BR>> Twitter: <A href="http://twitter.com/rdmpage">http://twitter.com/rdmpage</A><BR>> Blog: <A href="http://iphylo.blogspot.com/">http://iphylo.blogspot.com</A><BR>> Home page: <A href="http://taxonomy.zoology.gla.ac.uk/rod/rod.html">http://taxonomy.zoology.gla.ac.uk/rod/rod.html</A><BR>><BR>><BR>><BR>><BR>><BR>><BR>> _______________________________________________<BR>> tdwg-tag mailing list<BR>> tdwg-tag@lists.tdwg.org<BR>> <A href="http://lists.tdwg.org/mailman/listinfo/tdwg-tag">http://lists.tdwg.org/mailman/listinfo/tdwg-tag</A><BR>><BR>> Please consider the environment before printing this email<BR>> Warning: This electronic message together with any attachments is <BR>> confidential. If you receive it in error: (i) you must not read, <BR>> use, disclose, copy or retain it; (ii) please contact the sender <BR>> immediately by reply email and then delete the emails.<BR>> The views expressed in this email may not be those of Landcare <BR>> Research New Zealand Limited. <A href="http://www.landcareresearch.co.nz/">http://www.landcareresearch.co.nz</A><BR>><BR><BR>---------------------------------------------------------<BR>Roderic Page<BR>Professor of Taxonomy<BR>DEEB, FBLS<BR>Graham Kerr Building<BR>University of Glasgow<BR>Glasgow G12 8QQ, UK<BR><BR>Email: r.page@bio.gla.ac.uk<BR>Tel: +44 141 330 4778<BR>Fax: +44 141 330 2792<BR>AIM: rodpage1962@aim.com<BR>Facebook: <A href="http://www.facebook.com/profile.php?id=1112517192">http://www.facebook.com/profile.php?id=1112517192</A><BR>Twitter: <A href="http://twitter.com/rdmpage">http://twitter.com/rdmpage</A><BR>Blog: <A href="http://iphylo.blogspot.com/">http://iphylo.blogspot.com</A><BR>Home page: <A href="http://taxonomy.zoology.gla.ac.uk/rod/rod.html">http://taxonomy.zoology.gla.ac.uk/rod/rod.html</A><BR><BR><BR><BR><BR><BR><BR>_______________________________________________<BR>tdwg-tag mailing list<BR>tdwg-tag@lists.tdwg.org<BR><A href="http://lists.tdwg.org/mailman/listinfo/tdwg-tag">http://lists.tdwg.org/mailman/listinfo/tdwg-tag</A><BR></FONT></P></DIV></p>
<a href="http://www.cabiglobalsummit.com">
<IMG SRC="cid:0568-0d723b07@a6fb37f4.01ca02d7"></a>
<p> </p>
<p><span style="font-size:18.0pt;font-family:Webdings;
color:green">P</span><span style="mso-bidi-font-size:10.0pt;font-family:"Courier New";
color:#339966"> </span><font face="Arial">
<span style="font-size:8.0pt;mso-bidi-font-family:Arial;color:green;mso-bidi-font-weight:bold">Think Green -
don't print this email unless you really need to</span></font><span style="font-size:8.0pt;font-family:"Comic Sans MS";
mso-bidi-font-family:Arial;color:green;mso-bidi-font-weight:bold"><o:p>
</span>
<span style="font-size:8.0pt;font-family:"Comic Sans MS";
mso-bidi-font-family:Arial;mso-bidi-font-weight:bold">
<p><font face="Arial" size="1">
************************************************************************<br>
The information contained in this e-mail and any files transmitted with it is confidential and is for the exclusive use of the intended recipient. If you are not the intended recipient please note that any distribution, copying or use of this communication or the information in it is prohibited. <br>
<br>
Whilst CAB International trading as CABI takes steps to prevent the transmission of viruses via e-mail, we cannot guarantee that any e-mail or attachment is free from computer viruses and you are strongly advised to undertake your own anti-virus precautions.<br>
<br>
If you have received this communication in error, please notify us by e-mail at cabi@cabi.org or by telephone on +44 (0)1491 829199 and then delete the e-mail and any copies of it.<br>
<br>
CABI is an International Organization recognised by the UK Government under Statutory Instrument 1982 No. 1071.<br>
<br>
**************************************************************************</font>
</BODY></HTML>