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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Makes sense too.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Nicolas.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Absent from tomorrow to Saturday.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Richard Pyle [mailto:pylediver@gmail.com]
<b>On Behalf Of </b>Richard Pyle<br>
<b>Sent:</b> Thursday, March 20, 2014 2:05 AM<br>
<b>To:</b> Bailly, Nicolas (WorldFish); 'Roderic Page'; 'Hilmar Lapp'<br>
<b>Cc:</b> 'TDWG Content Mailing List'<br>
<b>Subject:</b> RE: [tdwg-content] synonyms in DwC Archives<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks, Nicolas – that makes sense.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I guess I’ve come to the view that the most sensible path is to split nomenclatural data management processes into two tracks:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Track 1: Names as text strings. This is the GNI track, and it literally treats a sequence of UTF-8 characters as a unique “thing”. These are different records
in GNI, all of which refer to the same Protonym (“bus”):<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Aus bus Linnaeus 1758<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Aus bus Linnaeus, 1758<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Aus bus L. 1758<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Aus bus Linnaeus<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Aus bus Linn.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Aus bus Lin.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Aus bus L.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Aus bus<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Aus buus Linnaeus<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Xus bus (L.)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Xus bus (Linn.)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Xus bus (Linn., 1758)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Xus bus (Linn. 1758)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">[and so on….]<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">It doesn’t matter if “Aus bus” is a homonym – there is still only one record in GNI for each unique UTF-8-encoded text string.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Track 2: Names as objects. This is the GNUB track, where the subset of all Taxon Name Usage instances (TNUs) that represent Protonyms also represent the “name”
as an object. As such, the text string is just a property of that object, (i.e. metadata). Records in GNUB look something like this (Simplified):<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">TNUID ProtID Reference ParTNUID ValidTNUID Rank Namestring<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">---------------------------------------------------------------------------------------------------------------<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">1 1 Linnaeus 1758 - 1 Gen. Aus<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">2 2 Linnaeus 1758 1 2 Sp. bus<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">3 1 Smith 1850 - 3 Gen. Aus<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">4 2 Smith 1850 3 4 sp. buus<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">5 5 Jones 1900 - 5 Gen. Aus<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">6 6 Jones 1900 5 6 sp. bus<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">7 7 Brown 1950 - 7 Gen. Xus<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">8 2 Brown 1950 7 8 sp. bus<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">9 9 Brown 1950 7 9 sp. cus<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">10 7 Pyle 2000 - 10 Gen. Xus<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">11 2 Pyle 2000 10 11 sp. bus<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">12 9 Pyle 2000 - 11 - cus<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">TNUIDs 1, 2, 5, 6, 7 & 9 are Protonyms; the others are subsequent usages (as indicated by the ProtID).<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">TNUID 5 represents a genus-level homonym for TNUID 1; and TNUID 6 is a species-level primary homonym for TNUID 2.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">TNUID 4 is a misspelling of the species epithet, representing a homotypic “synonym” of Aus bus.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">TNUID 7 puts an existing species in a different genus, representing a homotypic “synonym” of Aus bus.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">TNUID 12 establishes Aus cus Brown 1950 as a junior heterotypic “synonym” of Aus bus Linnaeus 1758 (according to Pyle 2000)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">The “Reference” column represents the “According to”.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">No – it cannot be “entirely” automated. However, Rob Whitton has been developing tools that allow us to photograph a checklist table or index (or both!) in
a book or published article, OCR it, clean up the OCR, disambiguate against Protonyms in GNUB, and then insert TNUs in GNUB – at a rate of about 100 TNUs in 8 minutes. For example, just during the past week or two while developing & testing the tools, Rob
has processed nearly 4,000 TNUs from ten different publications (regional checklists, books, etc.). The key is in having the Protonyms already in GNUB to anchor the new TNUs to. In April we will flesh out some tools that focus on capturing Protonyms in a
similar fashion (bulk import).<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Aloha,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Rich<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Bailly, Nicolas (WorldFish) [<a href="mailto:N.Bailly@cgiar.org">mailto:N.Bailly@cgiar.org</a>]
<br>
<b>Sent:</b> Wednesday, March 19, 2014 1:36 AM<br>
<b>To:</b> Richard Pyle; 'Roderic Page'; 'Hilmar Lapp'<br>
<b>Cc:</b> 'TDWG Content Mailing List'<br>
<b>Subject:</b> RE: [tdwg-content] synonyms in DwC Archives<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Using the string as the key …<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">The way we manage the synonymy pro parte would not work (we repeat the string and have 2 different syn records), but it is because of compromises we do for
simplicity.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">For homonyms, you would need mandatorily to include the authorship, but maybe it means that assigning a numeric Id is adding more meaning than the strict string,
which is again a compromise. To say it in other words, we don’t have a repository of meaningless strings like GNI, our synonym table is thus closer to a subset of the GNUB implicitly.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">So ok you got a point: what I call NameAsString with its Id in FishBase is not strictly a name as string. I suppose it is the difference I saw comparing FishBase
and GNA, but I did not pay attention enough to the vocabulary. …<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Agree with the rest of your analyses and suggestions. And with the less sexy part of it: populate the GNUB! With the most tedious part: the “according to”!
Unfortunately, I don’t see that it can be entirely automated …<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">And yes, I dream about it … !!!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">BW<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Nicolas.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Richard Pyle [<a href="mailto:pylediver@gmail.com">mailto:pylediver@gmail.com</a>]
<b>On Behalf Of </b>Richard Pyle<br>
<b>Sent:</b> Wednesday, March 19, 2014 6:16 PM<br>
<b>To:</b> Bailly, Nicolas (WorldFish); 'Roderic Page'; 'Hilmar Lapp'<br>
<b>Cc:</b> 'TDWG Content Mailing List'<br>
<b>Subject:</b> RE: [tdwg-content] synonyms in DwC Archives<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I’m reluctant to dive into this conversation, because there are so many things going on. Very briefly, Rod and Nicolas come the closest to reflecting my own
interpretation of the “simple” explanation. One question for Nicolas – why do you need “NameAsStringID”? Why not just NameString (literal)? What value is there for assigning an identifier to what is effectively a string of UTF-8-encoded characters?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">The key here, as Rod (and others) alluded to, is that different people have different meanings for the word “Synonym” in this context; and this is further confused
by the whole names vs. concepts thing.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Ignoring the names v. concepts issue altogether, we have various interpretations of “synonym” as including or excluding homotypic synonyms, heterotypic synonyms,
and orthographic variations. That is further confounded by the “names as conceptual objects” vs, “names as literal text strings” issues.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">The answer is obvious: reduce everything to atomized Taxon Name Usage instances (where the word “usage” comes from n DwC) to track “names as objects”, and
index every unique text string to track the strings themselves. GNUB is well along this path on the former for the groups that have been populated, and we are now ramping up our efforts to bulk-populate the content from various sources. Once you populate
the Protonym (~=Basionym) Usages (the hardest part, by far), then you can start to capture subsequent usages en masse to represent the spectrum of how names have been actually used through history -- different spellings, different classifications and genus
combinations, different ranks (e.g., as a full species vs. as a subspecies of another species), and treatments of names as valid (=accepted) or as junior heterotypic synonyms. With that properly captured & index, you can do all sorts of wonderful, magical,
amazing things that have only been dreamed about.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">So, the problem is well understood. And the solution is also well understood (as a result of the development of GNUB and GNI and associated services via GNA,
guided by a series of NOMINA meetings going back several years). What we need to do now is populate the content (particularly GNUB), and then implement the services.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I realize this is getting pretty far away from Hilmar’s original question – but that has been reasonably well addressed by others (particularly Markus, Tony,
Rod and Nicholas).<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">One final point to keep in mind when discussing this stuff – particularly in a flattened DwC sort of structure:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">The unqualified statement “Aus bus is a synonym of Aus cus” should never be represented in the form of metadata without an “According to” to go along with it.
Even objective synonyms should be understood in the context of the relevant Code (i.e., where the “According To” is effectively the Code of Nomenclature itself). This is why the “usage” qualifiers were added to the various DWC terms in the Taxon class – to
emphasize that the status of a name as being either accepted, or as representing a synonym of another name, is implied to be in the context of a particular usage (i.e., a particular “according to”).<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Aloha,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Rich<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">
<a href="mailto:tdwg-content-bounces@lists.tdwg.org">tdwg-content-bounces@lists.tdwg.org</a> [<a href="mailto:tdwg-content-bounces@lists.tdwg.org">mailto:tdwg-content-bounces@lists.tdwg.org</a>]
<b>On Behalf Of </b>Bailly, Nicolas (WorldFish)<br>
<b>Sent:</b> Tuesday, March 18, 2014 8:57 PM<br>
<b>To:</b> Roderic Page; Hilmar Lapp<br>
<b>Cc:</b> TDWG Content Mailing List<br>
<b>Subject:</b> Re: [tdwg-content] synonyms in DwC Archives<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Dear Hilmar,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I completely concur with Rod. An additional remark is that Biodiversity Informatics has unfortunately twisted the meaning of the word ‘synonym’ as it is used
in the different codes where it designates primarily a relationship between taxa and only secondarily by extension a relationship between names (because we designate taxa by using names). Formally, two different combinations of the same basionym are not synonyms:
they are different combinations.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">The flat DarwinCore cannot handle (easily) the 3 necessary Ids that have to be managed:<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-18.0pt;mso-list:l0 level1 lfo2"><![if !supportLists]><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><span style="mso-list:Ignore">-<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">TaxonId<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-18.0pt;mso-list:l0 level1 lfo2"><![if !supportLists]><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><span style="mso-list:Ignore">-<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">BasionymId<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-18.0pt;mso-list:l0 level1 lfo2"><![if !supportLists]><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><span style="mso-list:Ignore">-<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">NameAsStringId<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Technically, the NameAsStringId could be used alone, but only if there is a second field that precises if it is a Basionym or not, and a third that indicates
if it is the current accepted name: in the latter case, then the NameAsStringId can be used as the TaxonId. So in any case, a triplet has to be managed, otherwise, if you give an id alone, you cannot know what it is beyond a simple NameAsString.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">But to be honest I prefer for clarity to have 3 different codes. It is what we have in FishBase, a SpecCode as TaxonId, a SynCode as NameAsStringId, and we
use the Catalog of Fishes (CofF) CAS_SPC as the BasionymId – so we do exactly what Rod suggests, we use the acknowledged nomenclator. Strictly speaking and referring to my remark above, CofF has ids for all basionyms, whatever they are linked to valid taxa
or synonym taxa. What CofF does not have is an id for the new combinations and misspellings.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Where FishBase is not completely consistent is that we use a SynCode also for the misidentifications and the misapplied names, while these relationships should
be managed in another table than the table of NameAsStrings. Also like Markus described, the current accepted NameAsString is repeated both in our Taxon and our NameAsString tables. These were compromises to simplify the structure of the database.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">BW<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Nicolas.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">
<a href="mailto:tdwg-content-bounces@lists.tdwg.org">tdwg-content-bounces@lists.tdwg.org</a> [<a href="mailto:tdwg-content-bounces@lists.tdwg.org">mailto:tdwg-content-bounces@lists.tdwg.org</a>]
<b>On Behalf Of </b>Roderic Page<br>
<b>Sent:</b> Wednesday, March 19, 2014 1:38 PM<br>
<b>To:</b> Hilmar Lapp<br>
<b>Cc:</b> TDWG Content Mailing List<br>
<b>Subject:</b> Re: [tdwg-content] synonyms in DwC Archives<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Hilmar,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I think the phrase “simply names” summarises part ot the problem here. Many taxon databases seem determined to conflate names and taxa, and treat names as dumb strings rather than entities of interest (or worse, as taxa, rather than names
of taxa). Many synonyms are relationships between names (e.g., names that change because we move species to different genera are the “same” name), others are relationships between taxa (e.g., this set of things and that set of things are the members of the
same set of things).<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">We could model things much more cleanly if we distinguished between taxa and names for taxa, and made use of the fact that we have databases of names (the nomenclators) that have been serving name data and stable identifiers for almost
a decade. It is a pity that most taxonomic databases make little or no use of this. Map names to those ids, have ids for taxa, and link all the names to the taxa to which they’ve been applied. Instead we have a flat Darwin Core with row upon row of things
that we call “taxa” but which, in many cases, aren’t. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I get why we like flat Darwin Core, but sometimes the world isn’t flat.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Regards<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Rod<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On 19 Mar 2014, at 02:44, Hilmar Lapp <<a href="mailto:hlapp@nescent.org">hlapp@nescent.org</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><o:p> </o:p></p>
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<p class="MsoNormal">Tony - your example matches pretty much what GBIF does.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">John - yes indeed, if using ResourceRelationship terms, it would have to be in an extension and not the core taxon file.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Markus and all - yes, I realized after I emailed how GBIF does this. I agree that this has advantages. However, this way of doing synonyms requires that there is an identifier for the synonym. For the core use-case I'm interested in synonyms
are metadata of taxon records and do not have their own identifier. For example, synonyms in NCBI don't have identifiers, and they don't in Catalog of Fishes. (I'm not sure they do in PaleoDB.)<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">One could of course invent identifiers on behalf of the taxonomy providers in these cases, but that's a hack. I think if there is an extension for vernacularNames, there ought to be one as well for synonyms that are simply names.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> -hilmar<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><o:p> </o:p></p>
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<p class="MsoNormal">On Tue, Mar 18, 2014 at 6:35 PM, Markus Döring <<a href="mailto:m.doering@mac.com" target="_blank">m.doering@mac.com</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal">Hi Hilmar,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">GBIF, Catalog of life and others have produced guidelines for how to express taxonomies with synonyms and these are in widespread use already since over a year. I will forward links tomorrow when Im back at my desk.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">The common idea is to include synonyms together with accepted taxa in the core file. This allows one to also add extension data to synonyms, for example bibliographic references, types data, etc. The term acceptedNameUsageID is used to
link to the accepted record in the core file (targeting taxonID), originalNameUsageiD for the basionym and taxonomicStatus to declare a specific type of synonym such as homo/heterotypic or later/junior synonym. The scientificName is used both for accepted
and synonym records.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">You should be able to find many dwca examples in the gbif dataset search when filtered for checklists: <a href="http://www.gbif.org/dataset/search?type=CHECKLIST" target="_blank">http://www.gbif.org/dataset/search?type=CHECKLIST</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">For example try these:<o:p></o:p></p>
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<p class="MsoNormal"><a href="http://data.canadensys.net/ipt/archive.do?r=vascan" target="_blank">http://data.canadensys.net/ipt/archive.do?r=vascan</a><o:p></o:p></p>
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<p class="MsoNormal"><a href="http://ipt.speciesfile.org:8080/archive.do?r=orthoptera" target="_blank">http://ipt.speciesfile.org:8080/archive.do?r=orthoptera</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Cheers,<o:p></o:p></p>
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<p class="MsoNormal">Markus<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
Am 18.03.2014 um 22:44 schrieb Chuck Miller <<a href="mailto:Chuck.Miller@mobot.org" target="_blank">Chuck.Miller@mobot.org</a>>:<o:p></o:p></p>
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<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hilmar,</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Sticking strictly to Darwin Core and not adding RDF, I think there are a couple of DwC terms that
are attributes that can be used to identify a synonym:</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">taxonomicStatus -
</span><span style="font-size:10.0pt;font-family:"Verdana","sans-serif"">The status of the use of the scientificName as a label for a taxon. Requires taxonomic opinion to define the scope of a taxon. Rules of priority then are used to define the taxonomic status
of the nomenclature contained in that scope, combined with the experts opinion. It must be linked to a specific taxonomic reference that defines the concept. Recommended best practice is to use a controlled vocabulary. Examples: "invalid", "misapplied", "homotypic
synonym", "accepted".</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif""> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif"">relationshipofResource - The relationship of the resource identified by relatedResourceID to the subject (optionally
identified by the resourceID). Recommended best practice is to use a controlled vocabulary. Examples: "duplicate of", "mother of", "endoparasite of", "host to", "sibling of", "valid synonym of", "located within".</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif""> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D">There’s also acceptedNameUsage and acceptedNameUsageID, which if used infer that the name the terms
are associated with is a synonym of the AcceptedName.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D">But, so far there is no guideline for how to organize synonyms in a Darwin Core Archive. They can
be embedded in the core file using relationshiopofResource from a synonym name to an accepted name in the same file. Or they can be in an extension file, where the extension file may be called Synonyms and thus define a one-to-many “synonym relationship”
from the taxonID in the core file to synonym names in the extension file. There are probably other ways. RDF adds the ability to be more explicit about the relationships.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D">Rich Pyle has lectured prolifically on this so I’m sure he has good advice to offer.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D">Chuck</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">
<a href="mailto:tdwg-content-bounces@lists.tdwg.org" target="_blank">tdwg-content-bounces@lists.tdwg.org</a> [<a href="mailto:tdwg-content-bounces@lists.tdwg.org" target="_blank">mailto:tdwg-content-bounces@lists.tdwg.org</a>]
<b>On Behalf Of </b>Hilmar Lapp<br>
<b>Sent:</b> Tuesday, March 18, 2014 2:55 PM<br>
<b>To:</b> TDWG Content Mailing List<br>
<b>Cc:</b> Dan Leehr<br>
<b>Subject:</b> [tdwg-content] synonyms in DwC Archives</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I'm looking for recommendations on how best to put synonyms for taxon records into DwC Archive format.<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I'm assuming that these would go into an extension file. Do I have this right? What I'm having more trouble with is determining the right column term. there's dwc:vernacularName,
which is also in the examples, but what about synonyms of different types that come with taxonomies (such as NCBI's) or that result from merging taxonomies. There isn't an obvious candidate in DwC, and the list at <a href="http://rs.gbif.org/core/dwc_taxon.xml" target="_blank">http://rs.gbif.org/core/dwc_taxon.xml</a>
doesn't have a suggestion either that would seem pertinent.<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Any suggestions, pointers to documentation or examples?<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> -hilmar<br clear="all">
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">--
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hilmar Lapp -:-
<a href="http://informatics.nescent.org/wiki" target="_blank">informatics.nescent.org/wiki</a> -:-
<a href="http://lappland.io/" target="_blank">lappland.io</a><o:p></o:p></p>
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<p class="MsoNormal">_______________________________________________<o:p></o:p></p>
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<p class="MsoNormal"><br>
tdwg-content mailing list<br>
<a href="mailto:tdwg-content@lists.tdwg.org" target="_blank">tdwg-content@lists.tdwg.org</a><br>
<a href="http://lists.tdwg.org/mailman/listinfo/tdwg-content" target="_blank">http://lists.tdwg.org/mailman/listinfo/tdwg-content</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">-- <o:p></o:p></p>
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<p class="MsoNormal">Hilmar Lapp -:- <a href="http://informatics.nescent.org/wiki" target="_blank">
informatics.nescent.org/wiki</a> -:- <a href="http://lappland.io/" target="_blank">
lappland.io</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">_______________________________________________<br>
tdwg-content mailing list<br>
<a href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a><br>
<a href="http://lists.tdwg.org/mailman/listinfo/tdwg-content">http://lists.tdwg.org/mailman/listinfo/tdwg-content</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-family:"Helvetica","sans-serif";color:black">---------------------------------------------------------<br>
Roderic Page<br>
Professor of Taxonomy<br>
Institute of Biodiversity, Animal Health and Comparative Medicine<br>
College of Medical, Veterinary and Life Sciences<br>
Graham Kerr Building<br>
University of Glasgow<br>
Glasgow G12 8QQ, UK<br>
<br>
Email: <span class="apple-tab-span"> </span><a href="mailto:r.page@bio.gla.ac.uk">r.page@bio.gla.ac.uk</a><br>
Tel:<span class="apple-converted-space"> </span><span class="apple-tab-span">
</span>+44 141 330 4778<br>
Fax:<span class="apple-converted-space"> </span><span class="apple-tab-span">
</span>+44 141 330 2792<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Helvetica","sans-serif";color:black">Skype:<span class="apple-converted-space"> </span><span class="apple-tab-span">
</span>rdmpage<br>
Facebook: <span class="apple-tab-span"> </span><a href="http://www.facebook.com/rdmpage">http://www.facebook.com/rdmpage</a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Helvetica","sans-serif";color:black">LinkedIn: <span class="apple-tab-span">
</span><a href="http://uk.linkedin.com/in/rdmpage">http://uk.linkedin.com/in/rdmpage</a><br>
Twitter: <span class="apple-tab-span"> </span><a href="http://twitter.com/rdmpage">http://twitter.com/rdmpage</a><br>
Blog: <span class="apple-tab-span"> </span><a href="http://iphylo.blogspot.com">http://iphylo.blogspot.com</a><br>
Home page: <span class="apple-tab-span"> </span><a href="http://taxonomy.zoology.gla.ac.uk/rod/rod.html">http://taxonomy.zoology.gla.ac.uk/rod/rod.html</a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Helvetica","sans-serif";color:black">Wikipedia: <span class="apple-tab-span">
</span><a href="http://en.wikipedia.org/wiki/Roderic_D._M._Page">http://en.wikipedia.org/wiki/Roderic_D._M._Page</a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Helvetica","sans-serif";color:black">Citations: <span class="apple-tab-span">
</span><a href="http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ">http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ</a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Helvetica","sans-serif";color:black">ORCID:<span class="apple-converted-space"> </span><span class="apple-tab-span">
</span><a href="http://orcid.org/0000-0002-7101-9767">http://orcid.org/0000-0002-7101-9767</a><o:p></o:p></span></p>
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