Hi Nico,<div><br></div><div>I don&#39;t think that we are very far apart.<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div bgcolor="#ffffff" text="#000000">
   The way I recall discussions as the TCS was designed, the role
    for the DarwinCore was to allow data providers to include sufficient
    information in the DC so that the vouchers/observations could be
    identified to a suitably authoritative concept. In another realm of
    the biodiversity informatics net, that concept would be represented
    in more depth, and ideally have multiple relationships mapped and/or
    inferred to relevant past, present, and future concepts.<br></div></blockquote><div><br></div><div>In my mind it would be best to link to an open resolvable concept since even the original descriptions often not very informative regarding what individuals should considered instances of the same concept.</div>
<div>One reading of the TCS is that this is something that is applied long after the specimen is collected and identified, most likely by someone that did not collect or may not have even seen the actual specimen.</div><div>
So in some sense this is probably more error prone than the imperfectly defined concepts I am proposing. Or at least more likely to differ in the intended meaning of the original observer / identifier.</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div bgcolor="#ffffff" text="#000000">
    <br>
       For what it&#39;s worth (really not much), I agree that the eBird
    project is finding a (the?) pragmatic solution to expanding their
    contributor base, and in all likelihood have a pretty good to
    excellent taxonomy to work with already. Keep in mind that I study
    weevils, with 65k species described and 220k species
    (conservatively) estimated to exist, and a ~ 200 tribes mid-level
    classifications based largely on Lacordaire&#39;s 1-2 external character
    system established in 1863 (claws single, versus paired; virtually
    none of these have any phylogenetic value). So experientially I come
    from that part of the knowledge spectrum where we&#39;re likely
    centuries away from a sufficiently stable naming system that
    includes, say, more than 2/3 of the actual species diversity.<br></div></blockquote><div><br></div><div>Yes this is one reason most of my examples involve entities that are not particularly controversial in their own right. </div>
<div><br></div><div>For now the idea is to concentrate on the model and how different things are related to each other. </div><div><br></div><div>For instance,I noticed that I had some parrot&#39;s that were incorrectly marked up as &quot;expected in&quot; North American.</div>
<div><br></div><div>This will be fixed in the next RDF dump, along with the freebase cougar link which is now fixed in the online RDF put not in the RDF dump.</div><div><br></div><div>This is less about having everything perfect and more about figuring out how one might markup these kinds of relations.</div>
<div><br></div><div>I had been watching for URI changes in DBpedia and Wikipedia but not Freebase.</div><div><br></div><div>I read a blog recently that described GBIF&#39;s efforts to clean up their occurrence records and thought that their 1 degree areas might make good candidates for URI&#39;s.</div>
<div><br></div><div><a href="http://ff.im/-DwvMu">http://ff.im/-DwvMu</a><br></div><div><br></div><div>This would allow them to make cleaned version of species occurrences that tags each species occurrence to a particular &quot;degree_area&quot;</div>
<div><br></div><div>If they existed I would try to add them to my examples.</div><div><br></div><div>Also note that I include name variations that link to the GNI. These are not true synonyms they should be interpreted as &quot;<i>someone said this might be a synonym of the current name</i>&quot;,</div>
<div><br></div><div>In addition, what I call BasionymName is not the same as what others call it. </div><div><br></div><div>I use this field to put in what appears to be the first name used for the species. In Zoology this would be the name that does not contain ().</div>
<div><br></div><div>It might be best to change to some other term in the future to avoid confusion.</div><div><br></div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div bgcolor="#ffffff" text="#000000">   I&#39;m not opposed to pragmatic solutions for taxa where it makes
    sense (again, as if anyone cared..). But, trying to foresee the very
    substantive classificatory shifts that many other groups likely
    still will experience 10, 20, 50, 100 years down the road from now,
    I think just the same that there are solid grounds for working out
    an admittedly non-pragmatic, but sematically maximally powerful
    solution. I think it&#39;s not unreasonable to assume that from some
    groups, classification in 250 years from now will look just as
    different from today&#39;s system as Linnaeus&#39; 1758 system looks to us
    today. He recognized 2 weevil genera and about 90 species. Now we
    have 5800 genera. We may end up with 15,000. <br>
    <br></div></blockquote><div><br></div><div>Yes, you are correct. I am particularly concerned about tying the concepts to one taxonomic hierarchy.</div><div><br></div><div>For your weevil&#39;s, I think that there would be some advantages in marking up what you think exists, documenting those with photos and links specimens and name variations. </div>
<div>Open accessible versions of these are much more likely to be improved that ones that are hidden in a dispersed collection of hard to find journals - many which have limits on the number of photographs etc.</div><div>
<br></div><div>This woud certainly make it easier for someone with a specimen that they think applies to find you and the other potential concept candidates.</div><div><br></div><div>I don&#39;t have many weevils so you might want to think about doing this yourself. My only concern is how to keep the vocabularies etc in sync while everything is being discussed.</div>
<meta charset="utf-8"><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div bgcolor="#ffffff" text="#000000">   The problem that at present only taxonomic experts can understand
    how to retrace the meanings of concepts proposed in the history of
    the field, and computers can&#39;t yet do this because the data are not
    marked up and linked to each other precisely enough (as precisely as
    an ontological representation would demand it), is not just going to
    go away by some top-down adherence to a &quot;consensus&quot;. Most
    taxonomists jump into the field precisely because they come to
    realize that the &quot;consensus&quot; has serious problems (read: &quot;sucks&quot;).
    So, as long as there is justified taxonomic research, there will be
    reclassification. ]And no, IMO coming up with a synapomorphy-based
    or node-pointing naming system will not miraculously allow us to
    have a reliable system.]<br>
    <br></div></blockquote><div><br></div><div>Yes, this will never really go away. My point with eBird and The Plant List is that there are groups doing this, seemingly without much controversy, so why is what I propose so controversial? </div>
<div><br></div><div><meta charset="utf-8"><blockquote class="gmail_quote" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex; ">
<div bgcolor="#ffffff" text="#000000">   To the extent that there is a discussion here on the list as to where the DC and a possible successor of the TCS is going, I think that&#39;s a worthwhile discussion to have.<br></div>
<div><br></div></blockquote></div><div><br></div><div>I hope that others agree with you. :-)</div><div><br></div><div>- Pete</div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div bgcolor="#ffffff" text="#000000">
    Regards,<br>
    <br>
    Nico<div><div></div><div class="h5"><br>
    <br>
    <br>
    On 5/13/2011 4:41 PM, Peter DeVries wrote:
    </div></div><blockquote type="cite"><div><div></div><div class="h5">Hi Nico,
      <div><br>
      </div>
      <div>Thanks for posting this.</div>
      <div><br>
      </div>
      <div>I have something in the concept model to indicate the basis
        for the species concept.</div>
      <div><br>
      </div>
      <div>For now I have three types. An individual species concept can
        have a combination of one, two or all three</div>
      <div><br>
      </div>
      <div>In the RDF they look like this</div>
      <div><br>
      </div>
      <div><font face="&#39;courier new&#39;,
          monospace">&lt;txn:speciesConceptBasedOn rdf:resource=&quot;<a href="http://lod.taxonconcept.org/ontology/txn.owl#ObjectiveSpeciesModel" target="_blank">http://lod.taxonconcept.org/ontology/txn.owl#ObjectiveSpeciesModel</a>&quot;/&gt;</font><br>

        <br>
      </div>
      <div>The first is what I call the #ObjectiveSpeciesModel - this
        indicates that it is a species concept because we say it is.</div>
      <div><br>
      </div>
      <div>All the species concepts are at least
        an #ObjectiveSpeciesModel</div>
      <div><br>
      </div>
      <div>*This is in part a way to handle things like the domestic cat
        which you want to be seen as different from the African Wildcat.</div>
      <div><br>
      </div>
      <div>There are also tags for </div>
      <div><br>
      </div>
      <div>
        txn:PhylogeneticSpeciesModel</div>
      
      <div>txn:BiologicalSpeciesModel</div>
      
      <div><br>
      </div>
      <div>For now I don&#39;t have these other models set in the example
        data, but fields are in the database and the code for that an
        editor could state the basis for the model.</div>
      <div><br>
      </div>
      <div>I can think of a couple of different ways to handle the issue
        of alternative species concepts.</div>
      <div><br>
      </div>
      <div>* Note that the identifications as proposed by DarwinCore
        don&#39;t seem to indicate what kind of model the identifications
        were based on.</div>
      <div>  So it is not clear to me if a straight DarwinCore data set
        would allow the analysis above.</div>
      <div><br>
      </div>
      <div>Instead of having multiple different statements like </div>
      <div><br>
      </div>
      <div><b>txn:occurrenceHasSpeciesConcept &lt;&gt; </b>in the
        record for each occurrence</div>
      <div><br>
      </div>
      <div>one could use different predicates to link to different kinds
        of species concepts.</div>
      <div><br>
      </div>
      <div>
        
        <b>txn:occurrenceHasUniprotConcept</b> =&gt; &lt;<a href="http://purl.uniprot.org/taxonomy/9696" target="_blank">http://purl.uniprot.org/taxonomy/9696</a>&gt;</div>
      <div><br>
      </div>
      <div>This would allow someone to query for the occurrences of &lt;<a href="http://purl.uniprot.org/taxonomy/9696" target="_blank">http://purl.uniprot.org/taxonomy/9696</a>&gt;</div>
      <div><br>
      </div>
      <div>That said, it is not clear to me what people mean by
        different identifications.</div>
      
      <div><br>
      </div>
      <div>Is the intent to have identifications with different
        homotypic synonyms to be an identification of the same thing or
        not?</div>
      <div><br>
      </div>
      <div>The way it works now in many data sets is that Felis
        concolor, Puma concolor and Puma conncolor are treated as
        identifications of different things.</div>
      <div><br>
      </div>
      <div>This is another way of saying<i> is the namestring the
          concept?</i></div>
      <div><i><br>
        </i></div>
      <div>My understanding of the eBird project is that it allows
        citizen scientists to contribute their own observations. This
        creates a much larger data set for analysis etc.</div>
      <div><br>
      </div>
      <div>They have a created a curated list of species and a ~6 letter
        code for each. This serves as a guide for observers on how to
        encode their observations.</div>
      <div><br>
      </div>
      <div>I think their progress would be inhibited, the occurrence
        coding inconsistant, and contributors frustrated, if they have a
        list that included many overlapping species concepts.</div>
      <div><br>
      </div>
      <div>Thanks again for you comments,</div>
      <div><br>
      </div>
      <div>- Pete</div>
      </div></div><div> <br>
        <div class="gmail_quote"><div><div></div><div class="h5">On Fri, May 13, 2011 at 3:05 AM, Nico
          Franz <span dir="ltr">&lt;<a href="mailto:nico.franz@upr.edu" target="_blank">nico.franz@upr.edu</a>&gt;</span>
          wrote:<br>
          </div></div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">
            <div text="#000000" bgcolor="#ffffff"> Hello Pete (et al.):<br>
              <br>
                 For birds, Town Peterson at KU and colleagues have
              published these papers showing how alternative bird
              taxonomies affect the ranking of conservation priorities.<div><div></div><div class="h5"><br>
              <br>
              <a href="http://specify5.specifysoftware.org/Informatics/bios/biostownpeterson/PN_CB_1999.pdf" target="_blank">http://specify5.specifysoftware.org/Informatics/bios/biostownpeterson/PN_CB_1999.pdf</a><br>
              <a href="http://specify5.specifysoftware.org/Informatics/bios/biostownpeterson/NP_BN_2004.pdf" target="_blank">http://specify5.specifysoftware.org/Informatics/bios/biostownpeterson/NP_BN_2004.pdf</a><br>
              <a href="http://specify5.specifysoftware.org/Informatics/bios/biostownpeterson/P_BCI_2006.pdf" target="_blank">http://specify5.specifysoftware.org/Informatics/bios/biostownpeterson/P_BCI_2006.pdf</a><br>
              <br>
                 Here&#39;s the abstract of the 1999 paper:<br>
              <br>
              Analysis of geographic concentrations of endemic taxa is
              often used to determine priorities for conservation<br>
              action; nevertheless, assumptions inherent in the
              taxonomic authority list used as the basis for<br>
              analysis are not always considered. We analyzed foci of
              avian endemism in Mexico under two alternate species<br>
              concepts. Under the biological species concept, 101 bird
              species are endemic to Mexico and are concentrated<br>
              in the mountains of the western and southern portions of
              the country. Under the phylogenetic species<br>
              concept, however, total endemic species rises to 249,
              which are concentrated in the mountains and lowlands<br>
              of western Mexico. Twenty-four narrow endemic biological
              species are concentrated on offshore islands, but<br>
              97 narrow endemic phylogenetic species show a
              concentration in the Transvolcanic Belt of the mainland
              and<br>
              on several offshore islands. Our study demonstrates that
              conservation priorities based on concentrations of<br>
              endemic taxa depend critically on the particular taxonomic
              authority employed and that biodiversity evaluations<br>
              need to be developed in collaboration or consultation with
              practicing systematic specialists.<br>
              <br>
                 There was a debate recently on Taxacom that was started
              and subsequently neatly summarized by Fabian Haas. The
              topic was &quot;let&#39;s summarize reasons why &#39;donors&#39; seem to
              not fund taxonomy&quot;. One point from the summary was this:<br>
              <p class="MsoNormal">3) Taxonomy is over-accurate for most
                applications <br>
              </p>
              <p class="MsoNormal">Most (not all) decisions in e.g.
                modelling and conservation are done and can be done
                without complete knowledge of taxa. As it is, decisions
                for conservation areas are often based on flagship
                species (e.g. elephants), on taxa which have an
                excellent research background, e.g. birds (IBAs), on
                availability of land (e.g. land with a high Tsetse
                burden), importance as corridor and other factors, but
                never on a complete view on an all biodiversity in a
                specific area. Even if an inventory existed, it would be
                an illusion that we could collect data on ecological
                requirements and population dynamics for most of the
                species necessary for informed decisions. A complete
                inventory does not seem to provide an advantage for
                conservation.</p>
                 I personally think there&#39;s some truth to that. I also
              think that, while it&#39;s understandable that an accurate
              representation of the (sometimes) fleetingness of
              taxonomic consensus it not a priority for applied
              ecological projects, if taxonomists themselves don&#39;t find
              better ways to document and link these alternatives
              perspectives, then it&#39;s not the best science we can do.
              That would be fine too if adopted outright as a pragmatic
              stance.<br>
              <br>
              Regards,<br>
              <br>
              Nico
              <div>
                <div><br>
                  <br>
                  <br>
                  On 5/13/2011 1:08 AM, Peter DeVries wrote: </div>
              </div>
              <blockquote type="cite">
                <div>
                  <div>I thought that I would also mention
                    that in addition to The Plants List, the eBird
                    project also uses on overlapping concepts in its
                    bird list (it does have concepts for common hybrids)
                    <div><br>
                    </div>
                    <div>What is clear to me is that you cannot create
                      graphs like these if every observation can have X
                      number of species (especially those that
                      overlapping ) without any indication which is is
                      the most appropriate one.</div>
                    <div><br>
                    </div>
                    <div>eBird Occurrence Maps Northern Cardinal</div>
                    <div><a href="http://ebird.org/content/ebird/about/occurrence-maps/northern-cardinal" target="_blank">http://ebird.org/content/ebird/about/occurrence-maps/northern-cardinal</a><br clear="all">
                      <br>
                    </div>
                    <div>NCBI is also similar.</div>
                    <div><br>
                    </div>
                    <div>Perhaps a member of the consensus committee can
                      comment?</div>
                    <div><br>
                      -- Pete<br>
------------------------------------------------------------------------------------<br>
                      Pete DeVries<br>
                      Department of Entomology<br>
                      University of Wisconsin - Madison<br>
                      445 Russell Laboratories<br>
                      1630 Linden Drive<br>
                      Madison, WI 53706<br>
                      Email: <a href="mailto:pdevries@wisc.edu" target="_blank">pdevries@wisc.edu</a><br>
                      <a href="http://www.taxonconcept.org/" target="_blank">TaxonConcept</a>  &amp;  <a href="http://about.geospecies.org/" target="_blank">GeoSpecies</a> Knowledge Bases<br>
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        </div><div><div></div><div class="h5">
        <br>
        <br clear="all">
        <br>
        -- <br>
------------------------------------------------------------------------------------<br>
        Pete DeVries<br>
        Department of Entomology<br>
        University of Wisconsin - Madison<br>
        445 Russell Laboratories<br>
        1630 Linden Drive<br>
        Madison, WI 53706<br>
        Email: <a href="mailto:pdevries@wisc.edu" target="_blank">pdevries@wisc.edu</a><br>
        <a href="http://www.taxonconcept.org/" target="_blank">TaxonConcept</a>  &amp;  <a href="http://about.geospecies.org/" target="_blank">GeoSpecies</a> Knowledge Bases<br>
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</blockquote></div><br><br clear="all"><br>-- <br>







------------------------------------------------------------------------------------<br>Pete DeVries<br>Department of Entomology<br>University of Wisconsin - Madison<br>445 Russell Laboratories<br>1630 Linden Drive<br>Madison, WI 53706<br>
Email: <a href="mailto:pdevries@wisc.edu" target="_blank">pdevries@wisc.edu</a><br><a href="http://www.taxonconcept.org/" target="_blank">TaxonConcept</a>  &amp;  <a href="http://about.geospecies.org/" target="_blank">GeoSpecies</a> Knowledge Bases<br>
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