[Zoobank-list] RE: ZooBank Data Objects

[Richard Pyle]

Hi Anna,

I think the input of a botanist is especially welcome, given the imminent
need to find ways to harmonize the way botanical names data, zoological
names data, bacteriological names data, and other names data should be
accessed (soemthing fundamental to the development of ZooBank).

> Chris & I have just been discussing how to generate GUIDs in 
> our context of individual works being marked up (which seems 
> to parallel Rich's usage instances--though I would appreciate 
> it if Rich could verify).  

I guess the way I would define a "usage instance" would be the treatment of
one "name" in one "documentation instance".  A publication would be the most
familiar form of "documentation instance", but I prefer to keep it broad and
generalized. I think the logical unit of a "name" would be a reference to a
basionym-usage instance (although the word "basionym" is probably not the
best, for reasons too subtle to go into now**).  This definition is based on
the idea that, for the vast majority of taxonomic literature, authors treat
each "basionym" (see asterisked note below) in one particular way, and can
therefore be regarded as a single "usage instance".  If, in a publication,
the name "Aus bus" is used consistently four times on page 4, and 2 times on
page 8 and again in a table on page 9, I would not think of that as 7
discrete usage instances; but rather as one usage instance, representing the
treatment of a name within the context of a specific unit of documentation
instance (e.g., a publication).

**The reason why "basionym" may not be the best word here is that I
understand that word to represent a *relationship* between a subsquent
combination and an original combination in botany -- not the original
combination itself.  In other words, a name used in its original combination
is not itself thought of as a "basionym".  What I mean by "basionym" above
is really just "original usage instance" for a monomial or a
specific/infraspecific epithet. For Taxonomer, I used the word "Protonym",
but only later found out that this word has another meaning (see comments by
F. Bungartz under "Protonym" here:
http://wiki.cs.umb.edu/twiki/bin/view/UBIF/LinneanCoreDefinitions).

> It is clearly important that we 
> are able to generate a GUID for each taxon treated in a work. 
>  In addition, we favor generating a GUID for each synonym 
> (whether defined as a botanist or a zoologist--i.e., 
> taxonomic/heterotypic, nomenclatural/homotypic, junior or 
> senior synonyms (I confess I always get confused about the 
> meaning of junior/senior, sorry) misspellings, misusage, etc. 
>  Whatever is listed.  In addition, other names may be used in 
> discussion, or even in keys (I'm looking at a weevil 
> treatment at this moment where this is the case) which are 
> also some sort of synonym, which also should have a GUID.

I think I mostly agree, and this is mostly consistent with what I advocate
-- but we would need to parse out that word "synonym" a bit more.
Fundamentally, I think I agree in the sense that if Jones treated Aus bus L.
as a valid name, and also treated Aus pylei Smith as an (invalid) synonym of
Aus bus L., then there should be usage instances by Jones for *both* Aus bus
L. and Aus pylei Smith -- with the latter referring to the latter as the
"valid" link.

Where it might become a bit dicey comparing Zoology to Botany is if we have
a listing in the publication of Jones that looks this:

Aus xus L.
	Aus pylei Smith
	Anothergenus xus (L.) Brown
	Anothergenus pylei (Smith) Weitzman

...assuming the first line represents the valid treatment by Jones, and the
indented lines underneath represent what Jones regarded the synonymy of Aus
xus L.

If usage instances are anchored to "basionyms" (Protonyms...whatever), then
we have two species-level usage instances for the Jones publication:  One
declaring the basionym-usage instance of Aus xus L. to be valid in that
combination, and another declaring the basionym-usage instance of 	Aus
pylei Smith to be treated as a junior synonym of Aus xus L.  The references
to Anothergenus xus (L.) Brown and Anothergenus pylei (Smith) Weitzman would
be pointers to other usage instances (i.e., Brown's usage instance of the
basionym Aus xus L., where he first combined the species epithet with the
genus "Anothergenus"; and Weitzman's usage instance of the basionym Aus
pylei Smith, where she was the first to combine the species epithet with the
genus "Anothergenus").

But...if you see four separate usage instances within Jones' publication in
the list above (i.e., Jones' use of "Aus xus L.", "Aus pylei Smith",
"Anothergenus xus (L.) Brown", and "Anothergenus pylei (Smith) Weitzman") --
each with their own usage-instance GUID; then we are back to the difference
between zoology and botany.

I would make this case, however:  the information can be adequately captured
using the basionym approach for both zoology and botany; but the latter
approach would make sense only in the context of of botany. Logically, if
Jones regarded "Aus pylei Smith" as a junior synonym of "Aus xus L.", then
isn't it also true (by definition) that he regarded "Anothergenus pylei
(Smith) Weitzman" to be a junior synonym as well?  If so, then recording
both as separate usage instances does not provide us with any additional
information for how Jones treated the relevant nomenclature.  All it does is
tell us is that Jones was aware of the combination by Weitzman of the
epithet "pylei" within "Anothergenus".  We certainly may want to record that
fact, of course (which is fine), but my point is that the linking of
"Anothergenus pylei (Smith) Weitzman" as a junior synonym of "Aus xus L."
tells us nothing nomenclaturally about Jones' treatments that we don't
already know by the listing of "Aus pylei Smith" as a junior synonym of "Aus
xus L."  Having a separate index to cross-reference Jones' usage-instance
GUID for "Aus xus L." to Weitzman's usage instance GUID for "Anothergenus
pylei (Smith) Weitzman" is great -- but I don't see a need to create yet
another usage instance GUID in the context of Jones' publication
specifically for this link. I see that more as metadata.

> While I agree, that only the treated name should be a top 
> priority for Zoobank, as long as we are marking the text up 
> and generating information with GUIDs, I would certainly hope 
> that Zoobank would want all (and take now as opposed to 
> coming back to us for later after the priority is 'finished') 
> of these names along with the information that we may 
> generate about what kind of synonym, even though they are 
> mostly 'non-Code-governed' uses.

I would agree with you on this completely!!

> Further, there are other names that are cited in this work 
> (e.g., host plants, vernacular names, parasites, etc.).  I 
> think that those too should have GUIDs from our work, but 
> whether or not Zoobank (or IPNI--currently an informal 
> botanical registry) wants them, GBIF and uBio should! 

Again, I agree completely.  They are all usage instances; the only
difference in the context of ZooBank is to what extent they have relevance
to nomenclatural acts governed by the ICZN.  I would say that the average
ZooBank user would certainly be very interested in publications that cited a
given name as a host or parasite or whatever -- even if it's not within
ZooBank's scope to authoritatively track and manage that broad a scope of
usage instances.  But this is where ZooBank fills a specific role within a
larger biodiversity informatics context (i.e., GBIF/EoL/etc.) -- just like
ITIS and Species2000 and IPNI and IF and uBio and FishBase and countless
other data sources serve specific roles.  The important (and urgent) need
now is to come up with an architecture that makes it easy to tie all these
different roles together.

> Again, 
> I would be interested in whether these fit into Rich's 
> definition of 'usage instance'--though there may not be a 
> formal taxonomic concept involved.

It sounds like we're pretty-much on the same page.  The only fuzzy bit (as
far as I can tell) is whether you would see usage instances as
"basionym"-based (i.e., two usage instance GUIDs for Jones's publication in
the example above), or if you see usages as combination-based (in which case
there might be four usage-instance GUIDs for Jones -- that is, for example,
separate GUIDs for the usage within Jones of "Aus pylei Smith" and
"Anothergenus pylei (Smith) Weitzman").

I'd be interested to know if I misunderstood any of your positions on this.
No doubt I have written the above in a sufficiently obscure way that many
readers will misunderstand my positions..... :-)

Aloha,
Rich

Richard L. Pyle, PhD
Database Coordinator for Natural Sciences
  and Associate Zoologist in Ichthyology
Department of Natural Sciences, Bishop Museum
1525 Bernice St., Honolulu, HI 96817
Ph: (808)848-4115, Fax: (808)847-8252
email: deepreef at bishopmuseum.org
http://hbs.bishopmuseum.org/staff/pylerichard.html





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