[Tcs-lc] concepts of Higher taxa

[Richard Pyle]

> From a nomenclatural point of view I agree but from a TC point
> of view I still disagree for there is new information about
> what constitutes Aus Smith SEC. [everyone up to now] after
> Jones made his observations of the Johnston Atoll population.
> Which is where I came in to this whole discussion some time
> ago last year by observing that every (well, almost every)
> name usage instance is a new TC.

O.K., I think I now understand where you are coming from on this, and I
basically agree.  My approach to modelling this stuff is that every
Author-Date-NameUsage instance could be treated as a "potential" concept.
However, Stan's (and others') point about reusability is an important one.
But I should point out that treating every NameUsage as a potentially
distinct Concept does not make Concepts non-reusable (stated again without
the double-negative: treating every name usage as a potentially distinct
Concept still allows for reusability).  They are reusable in the sense that
later Concepts can define themselves by refering to (in a sense, re-using)
earlier Concepts.

But, I digress....

In the TCS world, there are two ways to handle the specific case I outlined:

Option 1:

<Dataset>
  <Publications>
    <Publication id="P1">
      <PublicationSimple>Smith 1950</PublicationSimple>
    <Publication>
    <Publication id="P2">
      <PublicationSimple>Jones 1970</PublicationSimple>
    <Publication>
  </Publications>
  <TaxonConcepts>
    <TaxonConcept id="TC1" type="original">
      <Name type="scientific">
        <NameSimple>Aus Smith 1950</NameSimple>
        <Rank>genus</Rank>
      </Name>
      <AccordingTo>
        <AccordingToSimple>Smith 1950</AccordingToSimple>
        <AccordingToDetailed>
          <AuthorTeam>Smith</AuthorTeam>
          <Date>1950</Date>
          <PublishedIn ref="P1"/>
        </AccordingToDetailed>
      </AccordingTo>
      <Relationships>
        <Relationship type="includes">
          <ToTaxonConcept ref="TC2"/>
        </Relationship>
        <Relationship type="includes">
          <ToTaxonConcept ref="TC3"/>
        </Relationship>
      </Relationships>
    </TaxonConcept>
    <TaxonConcept id="TC2" type="original">
      <Name type="scientific">
        <NameSimple>Aus bus Smith 1950</NameSimple>
        <Rank>species</Rank>
      </Name>
      <AccordingTo>
        <AccordingToSimple>Smith 1950</AccordingToSimple>
        <AccordingToDetailed>
          <AuthorTeam>Smith</AuthorTeam>
          <Date>1950</Date>
          <PublishedIn ref="P1"/>
        </AccordingToDetailed>
      </AccordingTo>
      <Relationships>
        <Relationship type="is included in">
          <ToTaxonConcept ref="TC1"/>
        </Relationship>
      </Relationships>
    </TaxonConcept>
    <TaxonConcept id="TC3" type="original">
      <Name type="scientific">
        <NameSimple>Aus xus Smith 1950</NameSimple>
        <Rank>species</Rank>
      </Name>
      <AccordingTo>
        <AccordingToSimple>Smith 1950</AccordingToSimple>
        <AccordingToDetailed>
          <AuthorTeam>Smith</AuthorTeam>
          <Date>1950</Date>
          <PublishedIn ref="P1"/>
        </AccordingToDetailed>
      </AccordingTo>
      <Relationships>
        <Relationship type="is included in">
          <ToTaxonConcept ref="TC1"/>
        </Relationship>
      </Relationships>
    </TaxonConcept>
    <TaxonConcept id="TC11" type="original">
      <Name type="scientific">
        <NameSimple>Aus jus Jones 1970</NameSimple>
        <Rank>species</Rank>
      </Name>
      <AccordingTo>
        <AccordingToSimple>Jones 1970</AccordingToSimple>
        <AccordingToDetailed>
          <AuthorTeam>Jones</AuthorTeam>
          <Date>1970</Date>
          <PublishedIn ref="P2"/>
        </AccordingToDetailed>
      </AccordingTo>
      <Relationships>
        <Relationship type="is included in">
          <ToTaxonConcept ref="TC1"/>
        </Relationship>
        <Relationship type="is included in">
          <ToTaxonConcept ref="TC2"/>
        </Relationship>
      </Relationships>
    </TaxonConcept>
    <TaxonConcept id="TC12" type="revision">
      <Name type="scientific">
        <NameSimple>Aus bus Smith 1950</NameSimple>
        <Rank>species</Rank>
      </Name>
      <AccordingTo>
        <AccordingToSimple>Jones 1970</AccordingToSimple>
        <AccordingToDetailed>
          <AuthorTeam>Jones</AuthorTeam>
          <Date>1970</Date>
          <PublishedIn ref="P2"/>
        </AccordingToDetailed>
      </AccordingTo>
      <Relationships>
        <Relationship type="is included in">
          <ToTaxonConcept ref="TC1"/>
        </Relationship>
        <Relationship type="is included in">
          <ToTaxonConcept ref="TC2"/>
        </Relationship>
        <Relationship type="excludes">
          <ToTaxonConcept ref="TC11"/>
        </Relationship>
      </Relationships>
    </TaxonConcept>
</Dataset>

Here's a summary:

TC1=Aus SEC. Smith
TC2=Aus bus SEC. Smith
TC3=Aus xus SEC. Smith
TC11=Aus jus SEC. Jones
TC12=Aus bus SEC. Jones

The important points are the relationships within TC11 and TC12.  TC11 "is
included in" both TC1 (Aus SEC. Smith), and TC2 (Aus bus SEC. Smith).
Similarly TC12 both "is included in" TC1, and "is included in" TC2.  I also
added the fact that TC12 "excludes" TC11, though that is probably
unnecessary.

But the important thing is that I conveyed all the important bits of
information, without creating an instance for "Aus SEC. Jones".  I can do
this because the Relationships of TC11 & TC12 point directly to Smith's
pre-existing concept definitions (i.e., it re-uses them).  There is one
piece of information missing though:  What did Jones make of Aus xus?
Perhaps he never mentioned it, in which case we don't know.  But what if he
did mention it?  How would we show that in the model above, without creating
another TC instance for Aus xus SEC. Jones?

That leads me to Option 2, which is identical to Option 1 above in all
respects except:

a) The addition of the following TC instance:

    <TaxonConcept id="TC13" type="revision">
      <Name type="scientific">
        <NameSimple>Aus Smith 1950</NameSimple>
        <Rank>genus</Rank>
      </Name>
      <AccordingTo>
        <AccordingToSimple>Jones 1970</AccordingToSimple>
        <AccordingToDetailed>
          <AuthorTeam>Jones</AuthorTeam>
          <Date>1970</Date>
          <PublishedIn ref="P2"/>
        </AccordingToDetailed>
      </AccordingTo>
      <Relationships>
        <Relationship type="is congruent to">
          <ToTaxonConcept ref="TC1"/>
        </Relationship>
        <Relationship type="includes">
          <ToTaxonConcept ref="TC3"/>
        </Relationship>
        <Relationship type="includes">
          <ToTaxonConcept ref="TC11"/>
        </Relationship>
        <Relationship type="includes">
          <ToTaxonConcept ref="TC12"/>
        </Relationship>
      </Relationships>
    </TaxonConcept>

b) Add the following relationship to both TC11 and TC12:

        <Relationship type="is included in">
          <ToTaxonConcept ref="TC13"/>
        </Relationship>

That way, we can sort out how Jones dealt with Aus xus (TC3) by virtue of
the fact that he included it in his definition of Aus (TC13), without having
to create a new instance of Aus xus SEC. Jones.

Having just gone through the process of manually creating the above, I am
prompted to ask these questions to the TCS designers:

1) When is it appropriate to provide an "excludes" Relationship?  Only when
there may be some confusion?  Only when names are the same (e.g.,
misidentifications & homonyms)?

2) In the example above, is it appropriate that I added this relationship to
TC12:
        <Relationship type="is included in">
          <ToTaxonConcept ref="TC2"/>
        </Relationship>

3) Would it be appropriate to include this relationship under TC13:
        <Relationship type="includes">
          <ToTaxonConcept ref="TC2"/>
        </Relationship>

I have more questions than these, but I'll stop here.

Aloha,
Rich