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I read Rich's email as quoted in Nico's reply - I think maybe Rich's
post didn't actually go out on the tdwg-tag or RDF group lists. Rich
mentions that he is swamped and will reply later. For the moment it
may be helpful to cite an earlier email of Rich's which it took me some
time to dig out of the tdwg-content email list:<br>
<br>
<a class="moz-txt-link-freetext" href="http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001703.html">http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001703.html</a><br>
<br>
In that post, Rich was responding to a thread that started when I asked
how one would handle a real-life situation (the specimen pictured in
<a class="moz-txt-link-freetext" href="http://images.cyberfloralouisiana.com/images/specimensheets/lsu/0/0/4/28/LSU00000428_l.jpg">http://images.cyberfloralouisiana.com/images/specimensheets/lsu/0/0/4/28/LSU00000428_l.jpg</a>).
The relevant part begins about half way down the page with "In the web
example given by Steve, we have... ". In that section, Rich notes that
<br>
<br>
"Eventually, a third party may be able to deduce (perhaps through a
suite of<br>
other, external information) a RelationshipAssertion that maps the TNU<br>
"[Juncus] diffusissimus Buckl. sec L. Urbatsch 2009" to some other,
perhaps<br>
published and well-defined taxon concept (of the same or different
name).<br>
Also, if there are 100 specimens in the collection that L. Urbatsch<br>
identified as "Juncus diffusissimus Buckl." in 2009, then anchoring all
100<br>
Identification instances to the one TNU, allows all of those specimens
to<br>
inherit the mapping of the one "[Juncus] diffusissimus Buckl. sec L.<br>
Urbatsch 2009" TNU instance to some other better-defined taxon concept."<br>
<br>
>From that post, I understood that a TNU (a.k.a. "assertion" in Pyle
2004 <a class="moz-txt-link-freetext" href="http://systbio.org/files/phyloinformatics/1.pdf">http://systbio.org/files/phyloinformatics/1.pdf</a>) can be as vague
as an idea that some determiner had in his/her head about how
organism/specimen instances should be mapped to a name. I think from
what Rich said there that there is the potential that we as metadata
aggregators may at some later point be able to map how that idea in the
determiner's head fits in with a more well-defined (e.g. published)
taxon description which one may choose to call a taxon concept rather
than a TNU. <br>
<br>
As so often is the case, I think the problem here boils down to
identifiers and the metadata that we associate with them. Let's say in
the real-life example above, somebody (we can say GNUB) assigns a
persistent identifier (perhaps a URI constructed from an opaque UUID)
to "Juncus diffusissimus Buckl. sec L. Urbatsch 2009". We could say
with an rdf:type statement that the resource identified by the URI is a
TNU. We can give that resource a tc:hasName property linking it to the
name which is represented by the string "Juncus diffusissimus Buckl.".
(I'm not sure what property we use to say that L. Urbatch made the
assertion). Now let's say that L. Urbatsch publishes a paper
describing in detail her concept of Juncus diffusissimus Buckl. We can
now assign the resource identified by the URI a tc:accordingTo property
whose value is the DOI of the paper she wrote. If we want, we can
replace the previous rdf:type statement with different one stating that
the resource is a taxon concept rather than a TNU, or if we believe
that all taxon concepts are also TNUs we can leave the rdf:type
statement that we had before and just add a second one saying that the
resource is also of type taxon concept. <br>
<br>
The point I'm trying to make is that as long as this "thing" that we
are variously calling "taxon name usage", "taxon concept", "shallow
taxonomic concept", or "deep taxonomic concept" can be assigned an
identifier, what really matters is the metadata we associate with it,
not really what we call it. The more metadata that we can connect with
it, either through datatype properties like name strings or object
properties that describe how the "thing" is related to other resources,
the "deeper" the concept. On the other extreme, we may know nothing
more than the name string. In that case we could call it a "nominal
concept", but we could still assign it an identifier and maybe with
luck we could associate more metadata with it (make it "deeper") at
some point in the future. <br>
<br>
Returning to the original question of the thread (which was about the
utility of TCS), TCS tries to deal with this problem using a thing
called "signatures" (section 17.2, see
<a class="moz-txt-link-freetext" href="http://bioimages.vanderbilt.edu/pages/TCS-Schema-UserGuide-v1.3.pdf">http://bioimages.vanderbilt.edu/pages/TCS-Schema-UserGuide-v1.3.pdf</a>)
which are a somewhat crude attempt to make identifying strings unique
by standardizing their format. However, TCS was written in 2005-2006.
Since then, the development of DOIs, the TDWG GUID Applicability
Statement standard, and best practices in the Linked Data world have
provided well-established and standardized ways to create persistent
and dereferenciable identifiers. So there isn't any reason I can see
why we can't use them. <br>
<br>
I am going to be bold and say that we already have the minimum tools
required to get started implementing TNUs/TaxonConcepts: <br>
- URI GUIDs (which if one preferred could be UUIDs or LSIDs -- HTTP
proxied to make Linked Data people happy; see the TDWG GUID
Applicability Statement standard if you don't know how to do this) to
identify the TNU/concepts, <br>
- the two terms tc:hasName and tc:accordingTo (from the TDWG Taxon
Concept ontology) to relate the TNUs/TaxonConcepts to names and sec.
references, and <br>
- some sources for name and publication URI GUIDs. <br>
There are deficiencies all over the place for that last item, but they
can be addressed over time by improving the scope of the relevant
databases and the quality of the metadata provided. uBio has URIs for
almost every name I've ever looked for. BHL has a growing collection
of old literature which has been assigned identifiers by Rod Page's
BioStor, new literature usually has an assigned, dereferenceable
proxied DOI, and one can even make valid URIs from ISBNs of books
(although they aren't resolvable). I'm not sure how one should address
the situation where the "sec." reference of a TNU is a person and date
since there isn't a standard database of people (as far as I know).
But that could be remedied. Ultimately, one could create the kinds of
mapping tools that Nico and Rich are talking about which relate
different taxon concepts/TNUs which have set theory relationships.
Whether that would be done with RDF, OWL, or something completely
different I don't know, but the basic anchoring of persistent
identifiers for the TNU/concepts to the names and sec. references
wouldn't have to wait on that. We could also get hung up about what
terms to use to express the metadata describing the basic TNU/name/sec.
resources, but there is nothing that says that metadata can't change or
be improved over time. It's the identifier that shouldn't change. <br>
<br>
Am I wrong about this???<br>
<br>
Steve<br>
<br>
Nico Franz wrote:
<blockquote
cite="mid:CALZMekkx431h=OB7t0dOtcvate85BgLQQiF2uCLALJxCP+Sp1g@mail.gmail.com"
type="cite">Thank you, Rich.<br>
<br>
So we seem to agree on something like this:<br>
<br>
Rich Nico<br>
taxon name usage <===> "shallow" taxonomic concept<br>
taxon concept <===> "deep" taxonomic concept<br>
<br>
Both: labeling is via name sec. author<br>
Both: authoring concepts/usages vs. identifying to those => slippery
issue; ideally requires proper speaker awareness.<br>
<br>
Why the latter? - well, because (again) the desirable effect of
using concepts - the desirable situation where these would have a
justification that goes beyond just really meticulous data management
and advances to the level of facilitating better science qua more
precise taxonomic semantics - only obtains if a great number of name
occurrences in a wide range of shallow-ish sources is linked via
identification to a presumably smaller number of occurrences where
those names are well defined and where successive definitions of names
are semantically linked. So there needs to be an emerging culture of
minimizing concept inflation. Otherwise we obtain what we have now
(mostly just names) and on top of that add new baggage (lots of really
shallow concepts) that nobody can do good semantics with. <br>
<br>
Here is where I think we disagree, perhaps just in terms of sales
strategy:<br>
<br>
You seem to suggest that making an a priori distinction between TNUs
and concepts is (1) possible in a good number of cases, (2) is
desirable perhaps in the form of registry, and (3) even necessary for
building and populating databases, etc.<br>
<br>
Here I disagree, for a number of reasons. First off I do believe
that not defining certain things too soon or too narrowly is sometimes
actually really good science and on the other hand, doing so can be a
show stopper if other people don't share this narrowness and find it
limiting. Second, while we can perhaps readily agree that a lengthy
monograph published in American Museum Novitates rises to the level of
authoring next concepts whereas a label saying "Family Carabidae" on a
specimen submitted as part of an insect student collection does not,
there are enough in-between cases where only time will tell.<br>
<br>
Example: USDA Plants promotes a particular perspective of
groundcherry taxonomy, genus-level concept Physalis - <a
moz-do-not-send="true"
href="http://plants.usda.gov/java/profile?symbol=physa" target="_blank">http://plants.usda.gov/java/profile?symbol=physa</a>
- with some 29 species-level concepts recognized. ASU's herbarium
curator Les Landrum is a bit of a groundcherry nerd (I say this with
admiration). If you go here: <a moz-do-not-send="true"
href="http://swbiodiversity.org/seinet/index.php" target="_blank">http://swbiodiversity.org/seinet/index.php</a>,
then Search Collections => Select All => Next => Scientific
Name = Physalis => Search, you get some 3700 pertinent specimen
records. If you then switch to the Species List tab, you see 115
concept listed overall. Switching to the USDA Plants Thesaurus will
give you only 46 concepts that these 3700 specimens are mapped to.
Using instead the ASU Taxonomic Thesaurus will yield 89 concepts
linking variously to those specimens. This is based on Les'
classification of groundcherries which is not further documented in the
SEINet environment at this moment.<br>
<br>
Now, saying a a priori whether Les' list represents a set of TNUs
versus concepts would presumably require you to assert that there is
nobody who is Les or very much like him that can provide a semantically
very accurate mapping of the 89 name usages in the SEINet-ASU Physalis
list to the much more thoroughly circumscribed USDA Plants concepts.
That could seem like a daring prediction given how little Les might
think of the USDA perspective. At the very moment that Les or someone
very much like him DOES provide the mapping, what looked like a list of
TNUs then all of a sudden acquires - via the mapping - a much deeper
semantic status where others can readily go from one classification to
the next, even though each come with very different amounts of
information in their original appearances. Some people may prefer Les'
concepts at least for Arizonan groundcherries, and in either case, the
mapping put both on an even playing field.<br>
<br>
So this exemplifies IMO why so far the concept approach has been too
abstract, the TCN has been too depauperate on the relationships/mapping
side (worrying instead almost needlessness about what constitutes a
concept per se), and definitions between identifications, name usages,
shallow, deep concepts have been too abstract as well. I believe we
should focus less discussion on those issues and more emphasis on
building mapping tools that can carry a wide range of input and
logically infer additional implied mappings from the initial
expert-given set. The actual semantic properties of that input will
emerge a posteriori and will be hard to predict in some cases. Some
descriptions are lengthy but nobody understands them. Some names lists
are profoundly informative if the context of their origin is well known
to an expert. <br>
<br>
There will be some obvious overreaches in both directions (too many
unconnected items, some items that are connected more precisely than
their inherent information would seem to justify). I think these
overreaches would be tolerable. What's less productive to me is a
restrictive set of definitions that provide an early blockage in they
way towards an environment where mapping is supposed to occur very
frequently. We're not at the registry stage yet. More at the "can this
work in principle" stage. As I mentioned before, the mappings ARE the
concepts under a certain viewpoint. We don't want to pre-determine
their fate by separating TNUs from concepts in a great number of cases.<br>
<br>
I hope this was not a misrepresentation of your view and also a
clarification of my view. In the end, we both advocate some sort of
balance for the same concerns, but perhaps disagree only strategically
about the moment where/when that balance will materialize - upfront via
precise definitions and registration or later on via the presence/lack
of actual mappings.<br>
<br>
Best,<br>
<br>
Nico<br>
<br>
<br>
<div class="gmail_quote">On Mon, Nov 26, 2012 at 5:18 PM, Richard
Pyle <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:deepreef@bishopmuseum.org" target="_blank">deepreef@bishopmuseum.org</a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div link="blue" vlink="purple" lang="EN-US">
<div>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">I
want to get into this topic in more detail (going back to Steve’s
original post), but this week is hell-week for me, so only a quick
comment now.</span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">I
generally agree with everything Nico says, but I think we need to be a
little more clear of what we mean by “name sec. author”</span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">The
core unit of the data model we’ve been building towards (GNUB, which
underlies ZooBank) uses as its fundamental unit something we’ve been
calling a “Taxon Name Usage Instance” (TNU). The scope of what can be
a TNU is intentionally very broad – anything from an original taxon
name description, to a mention in a newspaper article, and potentially
even a scribbled hand-written label or letter. The only requirement is
that it be static – that is, a snapshot in time. I mention this
because database records can be represented as TNUs, but only as a
static snapshot of the record. If the essence of the database record
changes over time (e.g., due to changing taxonomic opinion), then a new
TNU is generated for a different snapshot in time.</span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">A
very small subset of the universe of TNUs represent Code-governed
Nomenclatural Acts (original descriptions of new names and other
code-governed nomenclatural actions). In the case of such TNUs
involving the ICZN Code (for example), the TNUs are registered in
ZooBank. But the point is, one subset of all TNUs are those that
involve actions governed by a Code of nomenclature.</span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">The
reason I mention this is that, if I read Nico’s email correctly, I
think he’s saying that not all TNUs de-facto represent taxon concepts.
Rather, analogous to the nomenclatural subset of TNUs, there is a
subset of TNUs that rise to the level of representing Taxon Concept
definitions. In the case of nomenclatural acts, someone must make some
sort of declaration (assertion) that a specific TNU constitutes a
Code-governed nomenclatural act, along with relevant metadata relating
to that assertion and the nature of the Act. In the case of zoological
names, ZooBank is intended to facilitate this role (i.e., when a person
registers a TNU in ZooBank, there is an implied assertion that the TNU
represents a nomenclatural act under the ICZN Code).</span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">What
would be nice to have (and what TDWG could play a helpful role in
facilitating), is a registry of sorts (analogous to ZooBank) for those
TNUs that represent taxon concepts. In other words, a mechanism for
people to “register” the subset of all TNUs that represent taxon
concepts. Secondarily, there would also be a mechanism to make
assertions about how registered taxon concepts map to each other (via
some sort of set theory relationship[s]).</span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">In
summary, my points are </span></p>
<p><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><span>1)<span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></span></span><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">We
should be clear when we say “name sec. author” whether we mean it sensu
lato (i.e., all TNUs); or sensu stricto (i.e., only those TNUs that
rise to the level of representing taxon concepts).</span></p>
<p><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><span>2)<span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></span></span><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">There
ought to be a registry (perhaps administered by CoL?) for identifying
the subset of TNUs that represent concept definitions, and it should
include a mechanism for making set-theory relationship assertions among
registered concept-TNUs.</span></p>
<p><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><span>3)<span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></span></span><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">The
two things mentioned in #2 should be separate; that is, one can assert
that a particular TNU represents a taxon concept separately from
(potentially multiple) assertions about how that taxon concept relates
to other taxon concepts.</span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">More
later.</span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Aloha,</span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Rich</span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">P.S
By my standards that WAS quick!</span></p>
</div>
</div>
</blockquote>
</div>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences
postal mail address:
VU Station B 351634
Nashville, TN 37235-1634, U.S.A.
delivery address:
2125 Stevenson Center
1161 21st Ave., S.
Nashville, TN 37235
office: 2128 Stevenson Center
phone: (615) 343-4582, fax: (615) 343-6707
<a class="moz-txt-link-freetext" href="http://bioimages.vanderbilt.edu">http://bioimages.vanderbilt.edu</a>
</pre>
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