[SEEK-Taxon] LinneanCore Group Work - PART 2

[Richard Pyle]

Continuing where I left off...(in case anyone is still intersted...)

> Based on these points it seems to me that the discussion on the
> Wiki is introducing concept issues into the requirements even
> though some people are trying hard to keep it concept free. If
> this continues  what in my mind will eventually happen (even if
> you try your hardest to ignore information that is unequivocally
> only about concepts) is that you will still come up with an
> abstract model that needs to deal with everything that the TCS
> already does, e.g. names will have: specimens, relationships
> between them of different types (whether you choose to model this
> as relationships or embed them in the data type), citations,
> authors, (descriptions?), other people's opinions on the
> relationships someone else asserted about a name etc.... So we
> will have two schemas to handle taxonomic names and concepts -
> does the community really need this?

No, the community does not need two schemas for handling concepts -- but I
am a bit of a loss for why you feel that the LC group is heading in this
direction.  Again, I guess I will rely on you for providing specific
examples that illustrate your concerns.  I already explained in "Part 1" of
this long-winded response why I believe that a name-object needs to point to
publication instances, separately from why a concept-object needs to point
to publication instances -- and in some cases there will seem to be
duplicated information (when technically, there is not).

Following up on my previous example of "Aus bus Smith, 1949 sensu Smith
1949".  Based on my understanding of TCS, I can imagine two TCS records that
look (in abridged form, with some ad-hoc modifications to the current LC
schema) something like this (I hope I've rendered the XML properly):

<DataSet>
  <Publications>
    <Publication id="9876" type="Article">
      <PublicationSimple>
         Smith, J.D. 1949. Aus bus, a new species of Cidae from the Hawaiian
Islands. Journal of the Linnean Core. 1(1):15-20
      <PublicationSimple>
      <PublicationDetailed>
        [Insert full "AlexandriaCore" schema instance here for publication
details of Smith, 1949]
      </PublicationDetailed>
    </Publication>
  </Publications>
  <TaxonConcepts>
    <TaxonConcept type="Nominal" id="1234">
      <Name id="1234">
        <NameSimple>Aus bus</NameSimple>
        <NameDetailed>
          <Label>Aus bus Smith, 1949</Label>
          <CanonicalName>
            <Text>Aus bus</Text>
            <Genus>Aus</Genus>
            <SpecificEpithet>bus</SpecificEpithet>
          </CanonicalName>
          <CanonicalAuthorship>
            <Text>Smith, 1949</Text>
            <ProtonymCitation id="9876" />
          </CanonicalAuthorship>
          <Rank code="sp" text="species" />
          <AuthorsTaxonOrthograpy>Aus bus</AuthorsTaxonOrthograpy>
        </NameDetailed>
      </Name>
    </TaxonConcept>
    <TaxonConcept type="Original" id="5678">
      <Name id="1234">
        <NameSimple>Aus bus</NameSimple>
        <NameDetailed>
          <Label>Aus bus Smith, 1949</Label>
          <CanonicalName>
            <Text>Aus bus</Text>
            <Genus>Aus</Genus>
            <SpecificEpithet>bus</SpecificEpithet>
          </CanonicalName>
          <CanonicalAuthorship>
            <Text>Smith, 1949</Text>
            <ProtonymCitation id="9876" />
          </CanonicalAuthorship>
          <Rank code="sp" text="species" />
          <AuthorsTaxonOrthograpy>Aus bus</AuthorsTaxonOrthograpy>
        </NameDetailed>
      </Name>
      <AccordingTo>
        <AccordingToSimple>Smith</AccordingToSimple>
        <AccordingToDetailed>
          <AuthorTeam>Smith</AuthorTeam>
          <Date>1949</Date>
          <PublishedIn ref="9876" />
        </AccordingToDetailed>
      </AccordingTo>
    </TaxonConcept>
  </TaxonConcepts>
</Dataset>

The first thing to notice is that the Publication details ("Alexandria
Core") have been moved out of LC ProtonymCitation, and instead referenced
via the TCS method (Jessie -- correct me if I interpret TCS correctly here).
It has the GUID "9876".

The other thing to notice is that there are two TaxonConcept instances
represented here: one is "Nominal" type and the other is "Original" type.
The "Nominal" type contains only LC elements -- it is an "empty", name-only
concept (no "AccordingTo", etc.).  This is what I imagine a basic
concept-less LC instance would look like (i.e., enclosed within a TCS
wrapper). Notice that both TaxonConcept id="1234", *and* Name id="1234".
This is my attempt to illustrate how the same GUID series used for TCS
instances could be inherited by the LC schema where TaxonConcept
type="Nominal".

The second TaxonConcept instance is of "Original" type -- which, as I
understand it, implies that a concept is created at the same time that its
name is created (correct, Jessie?)  This TCS instance *is* intneded to
represent a specific taxon concept -- the concept asserted by Smith in the
original publication that created the name. Note that TaxonConcept id is
different ("5678"), but Name id is the same ("1234").

My main point here is that there are separate "name-only" and
"concept-bearing" TCS instances represented by the idea of "Aus bus Smith,
1949 sensu Smith 1949".

If I have totally misunderstood either TCS or LC, now would be a VERY good
time to clue me in.

> I believe that TCS is almost finalised or
> could be very soon and I hoped that the Linnean core would help
> that by getting agreement on the fields necessary to detail a
> name applied to a concept - currently the according to element
> and the name element (ABCD name) in TCS.

The LC group is not concered with the AccordingTo element in TCS.  There are
no AccordingTo's for names (unless you count "According to the IC_N Code of
Nomenclature").  We are really only concerned with what falls within the
<Name> element of TCS.

> The only other things we
> are waiting on is an agreed interface to the other schemas being
> developed, i.e. the elements we have marked with placeholders.

I think the point is that you should insert such a placeholder within the
<Name> element of TCS, and help the LC group fully develop the schema that
will be inserted there.

> Having read this far I hope you don't think I've made these
> comments because the Linnean core Wiki is suggesting changes to
> our proposal and I simply don't like it. I'm very happy to have
> good suggestions which improve the schema but if the suggestions
> fundamentally change it then I'm reluctant to start modelling TCS
> over again. If they are suggestions because of misunderstandings
> then it's a waste of time arguing back and forth until we explain
> TCS more clearly. So I am happy to reply to specific questions
> about the relationship between Linnean core and TCS but unless
> the philosophy of TCS is understood the discussion may become a
> bit pointless.

Thanks, Jessie.  I guess my two requests to you would be:

1) Tell us specifically where you think that LC is encroaching on TCS (i.e.,
overlapping concept information), so we can address your concerns in a more
specific way;

2) Please explain to us (or point us to a document that explains) the
detailed definitions of the different TaxonConcept types ("Nominal" [was
"nomenclatural"], ["Original"], etc.) in TCS, and what they were intended to
represent.

The primary issues that I think we need to discuss in terms of developing LC
as a seamless plug-in to TCS <Name> elements are:

1) Vocabulary (i.e., we should try as much as possible to follow similar or
identical element naming conventions).

2) Publications: looking at TCS (if I understand it correctly) I am now
leaning towards removing the "Publication" element of LC 0.1.4 from within
"ProtonymCitation" (under "CanonicalAuthorship_Proposal2"), and instead
adding a "ref" attribute to ProtonymCitation that points to a Publication
record stored in the TCS "wrapper" of an LC instance.

3) Perhaps eliminate "Kingdom" element of TCS, and either replace with
"NomenCode" (or similar); or move this element to within the "Name" element
(in the domain of LC.

4) Make sure we understand the respective roles of "Rank" in TCS and LC,
make sure they need to be separate (or decide how to combine them), and if
maintained as separate, make sure they are cross-consistent.

5) Resolve the Primary type specimen issue I discussed in the previous
message (e.g., move type specimen elements from LC to
SpecimenCircumscription, or prehaps create some sort of
"TypeSpecimenCircumscription" element somewhere -- I don't know.  As I said
before, I see this as the only real potential point of contention.

O.K., approaching midnight.  Time for me to sign off.

Aloha,
Rich

Richard L. Pyle, PhD
Natural Sciences Database Coordinator, Bishop Museum
1525 Bernice St., Honolulu, HI 96817
Ph: (808)848-4115, Fax: (808)847-8252
email: deepreef at bishopmuseum.org
http://www.bishopmuseum.org/bishop/HBS/pylerichard.html