[Zoobank-list] RE: ZooBank Data Objects

Tue Mar 6 23:03:42 GMT 2007

Hi Rich,

Thanks for the welcome!

You said:
>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. 

as I said, parallel, but not equal.  A "usage instance" could also include a specimen determination, among other things.

You said:
> 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).

I could not agree more.  In fact, it has been my intention to make sure that all those 'mentions' (if I may use that term) in the same work are linked to a single GUID.

You gave the example:

>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.

I have discussed examples similar to this one with a number of zoologists over many years.  We disagree on the term (Zoo: senior/junior synonyms = Bot. taxonomic synonyms).  We also (botanists and zoologists) have different definitions of nomenclatural acts.  Botanists would say that Brown and Weitzman had made new combinations, which are nomenclatural acts.  However, for zoologists, these are not nomenclatural acts--however, they are still combinations (or forms of a name) that you use in the literature.  For that reason, I would argue that the place where these combinations are first made is worth recording (if for no other reason than that someone doesn't have to search for where it was done the first time each time someone works on a species--and we are, after all, trying to speed up the rate that taxonomy can be done by creating these databases and linking GUIDs, etc.).  Most zoologists I have discussed this with have agreed with me that recording the 'homotypic' synonyms and where they were first made is useful and convenient whether or not they have nomenclatural standing. 

You said that in this case, the later combinations would be 'pointers' to the basionyms.  I think that is where we diverge.  As a botanist, I would give all four a GUID, but each of the homotypic synonyms should have 'pointers' to their basionym as well (within the work and within a registry), and in this particular work the 3 would also have pointers to the 'accepted name'='senior synonym' (although most botanists would only see 3 synonyms and not differentiate them, except implicitly in their minds).  

In terms of 'usage instances' in this example, I am somewhat less clear--as I had not actually thought much about the term.  My initial reaction, is that in fact this is one 'usage instance' of an accepted name with 3 synonyms (of different kinds as explained above).

You said further:
>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".  

Agreed.

>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.

This is an interesting point, and I see your point since in a functioning database it would not matter, since all of the homotypic synonyms would move together no matter what we did.  However, I fear that it will be a long time before most botanists will accept this.  Though perhaps if we could agree that there is a different kind of linkage between heterotypic and homotypic synonyms--which is not a usage instance link or GUID we could all be happy :-) ?

You make an interesting point about the word "basionym".  I have struggled for years to find a widely accepted definition--or one sanctioned by the botanical Code.  It has been used both in the way that you use it, and for database purposes at least, also in place of your protonym.  However, it is only the new Code (published last fall) that finally includes a glossary.  In that glossary the word is finally defined: 

"basionym. A previously published legitimate name-bringing or epithet-bringing synonym from which a new name is formed for a taxon of different rank or position (Art. 33.4, 49.1 and 52.3)."

This definition does indeed read the way that you have used it and excludes 'a previously published legitimate name' that has not been used to form a new name at a different rank or position.  So I guess we will have to adopt your term protonym.

I've got to head home now, but I'm sure we will continue this later tonight or tomorrow!

Cheers,

Anna

Anna L. Weitzman, PhD
Informatics Branch Chief, ITO
Informatics, Botany and Biodiversity Research
National Museum of Natural History
Smithsonian Institution

202.633.0846
weitzman at si.edu

________________________________

From: zoobank-list-bounces at afriherp.org on behalf of Richard Pyle
Sent: Tue 06-Mar-07 5:10 PM
To: 'Zoobank Discussion List (ICZN)'
Subject: RE: [Zoobank-list] RE: ZooBank Data Objects

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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