<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Paul - I'll post some examples as soon as I can (I'm in a GBIF Science Committee meeting the next two days) that illustrate how we can use the DwC terms to create simple schemas for representing rich taxonomic data. Markus and I have modelled complex zoological and botanical taxonomies using it for testing the GBIF IPT and it works. I'll get these examples served in the next day or so. It includes some Euro+Med Plants data and a Smithsonian taxonomic bulletin on Cetacean taxonomy (zoological + botanical examples). It covers all of the components of taxonomic opinion to which you refer and more. It can represent all that I know are contained in Index Fungorum and Species Fungorum unless you are hiding a lot more, which you may well be. The only thing it doesn't do well are the explicit concept-to-concept assertions enabled by TCS but I have other strategies for achieving that. There are some homonym cases as well which I'm not sure we do well but which Markus thinks we can so I need to dig in there a bit.<div><br></div><div>If you have some sample taxonomic or nomenclatural data that you think will break it I would be happy to take it for a ride within the DwC-with-extensions approach that is employed within the IPT and see if it can't be effectively addressed. I don't mind being wrong about it so long so as I or someone else can provide some clues as where to go from here.</div><div><br></div><div>DR.<br></div><div><br></div><div><div>On Apr 27, 2009, at 4:20 PM, Paul Kirk wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"> <div style="WORD-WRAP: break-word; webkit-nbsp-mode: space; webkit-line-break: after-white-space"> <div dir="ltr" align="left"><span class="289505913-27042009"><font face="Arial" color="#0000ff" size="2">I tend to agree with David ... but only to a point.</font></span></div> <div dir="ltr" align="left"><span class="289505913-27042009"><font face="Arial" color="#0000ff" size="2"></font></span> </div> <div dir="ltr" align="left"><span class="289505913-27042009"><font face="Arial" color="#0000ff" size="2">Are we not discussing the equivalent here of database normalization ... where two diametrically opposite opinions hold - fully normalized and it don't work (performance issue) or fully de-normalized and it don't work (integrity issues - accepting that a well designed UI can protect database content (and integrity) from the user)? Here we have DwC-with-extensions on the one hand and something like TCS/CDM? on the other. By taxonomic information I assume we mean that a taxonomic opinion on a name has been expressed (usually by a person). If so, the requirements are fairly basic - name with nomenclatorLSID, status, who, when and where. It gets complex, and it's what I do not think DwC supports, when everything in a complex taxonomic opinion (homotypic names, heterotypic names, misapplications, pro-parte synonyms etc) is placed in one 'object' - the equivalent of recursive joins to go back to a database analogy.</font></span></div> <div dir="ltr" align="left"><span class="289505913-27042009"><font face="Arial" color="#0000ff" size="2"></font></span> </div> <div dir="ltr" align="left"><span class="289505913-27042009"><font face="Arial" color="#0000ff" size="2">In haste,</font></span></div> <div dir="ltr" align="left"><span class="289505913-27042009"><font face="Arial" color="#0000ff" size="2"></font></span> </div> <div dir="ltr" align="left"><span class="289505913-27042009"><font face="Arial" color="#0000ff" size="2">Paul</font></span></div><br> <div class="OutlookMessageHeader" lang="en-us" dir="ltr" align="left"> <hr tabindex="-1"> <font face="Tahoma" size="2"><b>From:</b> tdwg-tag-bounces@lists.tdwg.org [<a href="mailto:tdwg-tag-bounces@lists.tdwg.org">mailto:tdwg-tag-bounces@lists.tdwg.org</a>] <b>On Behalf Of </b>David Remsen<br><b>Sent:</b> 27 April 2009 14:47<br><b>To:</b> Kevin Richards<br><b>Cc:</b> Technical Architecture Group mailing list; <a href="mailto:exec@tdwg.org">exec@tdwg.org</a><br><b>Subject:</b> Re: [tdwg-tag] darwin core terms inside tdwg ontology<br></font><br></div> <div></div> <div>Kevin, Can you tell me what the limitations are on being able to exchange taxonomic information with the DwC terms? As far as I can tell, you can exchange fairly complex taxonomic information short of concept-to-concept relations and I find the DwC-with-extensions approach we are using to exchanging information tied to taxa (not instances of taxa) to be a nice and practical compromise between complexity and practicality. My understanding is that the IPT can output TCS/RDF for those who want it. I am personally very happy to see the DwC taxon terms added. Finally I can provide format specifications that biologists can understand.</div> <div><br></div> <div>David Remsen</div> <div><br></div><br> <div> <div>On Apr 25, 2009, at 9:52 AM, Kevin Richards wrote:</div><br class="Apple-interchange-newline"> <blockquote type="cite"><span class="Apple-style-span" style="WORD-SPACING: 0px; FONT: 12px Helvetica; TEXT-TRANSFORM: none; COLOR: rgb(0,0,0); TEXT-INDENT: 0px; WHITE-SPACE: normal; LETTER-SPACING: normal; BORDER-COLLAPSE: separate; orphans: 2; widows: 2; webkit-border-horizontal-spacing: 0px; webkit-border-vertical-spacing: 0px; webkit-text-decorations-in-effect: none; webkit-text-size-adjust: auto; webkit-text-stroke-width: 0px"> <div ocsi="x"> <div dir="ltr"><font face="Tahoma" color="#000000" size="2">I see the ontology as a model of ALL (hopefully, eventually all) the data in our domain of biodiversity informatics. </font></div> <div dir="ltr"><font face="Tahoma" size="2">I would love to see it as a standard (at the least it might give it a bit more clout).</font></div> <div dir="ltr"><font face="Tahoma" size="2">I agree that the ontology is useful to tie other TDWG schemas together, using it as a core/master model. I would be happy to see it used for ALL tasks within TDWG, but I understand the usefulnes of the more specific schemas/standards - horses for courses.</font></div> <div dir="ltr"><font face="Tahoma" size="2"></font> </div> <div dir="ltr"><font face="Tahoma" size="2">If I understand Stan here, I agree with him about the dubious use of DwC for representing Taxon Concepts/Names. As far as I know, it was really intended as a transfer standard for observation records?? It contains very limited taxon information! It really is not a overly difficult job to use a more suitable schema/ontology. I think the popularity of Darwin Core is due to its simplicity - and I wonder if what Roger is proposing will help with this - ie an XML implementation of the ontology as well as an RDF version. This will allow people to create very simple XML documents with reasonably simple/flat data, eg an xml document of TaxonName entities, with perhaps 6 or 7 or so key fields - even simpler than DwC. :-)</font></div> <div dir="ltr"><font face="Tahoma" size="2"></font> </div> <div dir="ltr"><font face="Tahoma" size="2">Kevin</font></div> <div dir="ltr"><font face="Tahoma" size="2"></font> </div> <div id="divRpF910076" style="DIRECTION: ltr"> <hr tabindex="-1"> <font face="Tahoma" size="2"><b>From:</b><span class="Apple-converted-space"> </span><a href="mailto:tdwg-tag-bounces@lists.tdwg.org">tdwg-tag-bounces@lists.tdwg.org</a><span class="Apple-converted-space"> </span>[<a href="mailto:tdwg-tag-bounces@lists.tdwg.org">tdwg-tag-bounces@lists.tdwg.org</a>] On Behalf Of Blum, Stan [<a href="mailto:sblum@calacademy.org">sblum@calacademy.org</a>]<br><b>Sent:</b><span class="Apple-converted-space"> </span>Saturday, 25 April 2009 6:12 a.m.<br><b>To:</b><span class="Apple-converted-space"> </span>Technical Architecture Group mailing list;<span class="Apple-converted-space"> </span><a href="mailto:exec@tdwg.org">exec@tdwg.org</a><br><b>Subject:</b><span class="Apple-converted-space"> </span>Re: [tdwg-tag] darwin core terms inside tdwg ontology<br></font><br></div> <div></div> <div> <div id="idOWAReplyText927" dir="ltr"> <div dir="ltr"><font face="Arial" color="#000000" size="2"><font face="Tahoma"><strong>From:</strong><span class="Apple-converted-space"> </span><a href="mailto:tdwg-tag-bounces@lists.tdwg.org">tdwg-tag-bounces@lists.tdwg.org</a><span class="Apple-converted-space"> </span>on behalf of John R. WIECZOREK<br><b>Sent:</b><span class="Apple-converted-space"> </span>Fri 2009-04-24 8:58 AM<br><b>To:</b><span class="Apple-converted-space"> </span>Roger Hyam<br><b>Cc:</b><span class="Apple-converted-space"> </span>Technical Architecture Group mailing list<br><b>Subject:</b><span class="Apple-converted-space"> </span>Re: [tdwg-tag] darwin core terms inside tdwg ontology<br><br></font></font></div><font face="Arial" color="#000000" size="2"><font face="Tahoma"></font> <div dir="ltr"> <div style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><font size="2">Anything I should do on the DwC side in anticipation of harmony?<br><br><a href="http://rs.tdwg.org/dwc/terms/index.htm#theterms" target="_blank">http://rs.tdwg.org/dwc/terms/index.htm#theterms</a><br></font></div></div></font></div> <div style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><font face="Arial" color="#000000" size="2">===========================================================</font></div><font face="Arial" color="#000000" size="2"> <div dir="ltr">John,</div> <div dir="ltr"> </div></font> <div dir="ltr"><font face="Arial" color="#000000" size="2">At some point, all or (most) of the DarwinCore terms need to be added to the TDWG ontology.</font></div> <div dir="ltr"><font face="Arial" size="2"></font> </div> <div dir="ltr"><font face="Arial" size="2">But having said that, I also need to say that I'm uncomfortable with:</font></div> <div dir="ltr"><font face="Arial" size="2"></font> </div> <div dir="ltr"><font face="Arial" size="2">1) The current state of the TDWG ontology (primarily the naming conventions; lets just use terms names), and our understanding of the role it plays in TDWG and how it will be managed (entry of terms, integration of terms into the conceptual [is-a / has-a] relationships to other terms); and</font></div> <div dir="ltr"><font face="Arial" size="2"></font> </div> <div dir="ltr"><font face="Arial" size="2">2) the fact that the new DarwinCore straddles or overlaps the roles of an ontology and an application schema.</font></div> <div dir="ltr"><font face="Arial" size="2"></font> </div> <div dir="ltr"><font face="Arial" size="2">I understood the past TAG roadmaps to indicate that we were adopting an approach in which the TDWG Ontology would be a repository for data concepts that are present in (or implied by) TDWG standards; and that real data transmission would be accomplished with application schemas. The ontology itself would not be a standard, but would be a tool that helps integrate standards. I thought our standards would be created to function as application schemas or components of application schemas (as in the DwC and its extensions). I am now pretty confused. <span class="Apple-converted-space"> </span></font><font face="Arial" size="2">I'd like to hear the rationale for combining taxonomic name/concept with organism occurrence. I haven't gone over all the existing docs, so apologies if I've missed that, but I think it's confusing that a (new) DarwinCore record could be either a taxonomic name or an organism occurrence, or maybe something else. Maybe I'm too attached to object orientation and just don't GET the semantic web, but it feels to me like we are stepping into squishy ground.</font></div> <div dir="ltr"><font face="Arial" size="2"></font> </div> <div dir="ltr"><font face="Arial" size="2">Also, I the the DCMI maintenance procedures are also more appropriately applied to the ontology than a TDWG standard. The existing process for ratifying TDWG standards and the procedure in the DwC seem to be pretty explicitly in conflict; one can change the other cannot (without becoming another thing).</font></div> <div dir="ltr"><font face="Arial" size="2"></font> </div> <div dir="ltr"><font face="Arial" size="2">Is anyone else having these same trepidations? I don't think I've been as much of a Rip Van Winkle as Jim Croft, but I clearly missed some important shifts. </font></div> <div dir="ltr"><font face="Arial" size="2"></font> </div> <div dir="ltr"><font face="Arial" size="2">-Stan</font></div> <div dir="ltr"><font face="Arial" size="2"></font> </div> <div dir="ltr"><font face="Arial" size="2"></font> </div> <div dir="ltr"> </div></div><br> <hr> <font face="Arial" color="green" size="1">Please consider the environment before printing this email<br>Warning: This electronic message together with any attachments is confidential. 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