GUIDs for Taxon Names and Taxon Concepts

[Yde de Jong]

Dear Roger,

Thanks you for clear reply and Richard for his additions.

My problem in understanding your GUID system is that -if I am right-
it aims to integrate two functional properties for names, namely (1)
cross-referencing for nomenclatural mapping and (2) definite
identification of all name objects in the linked systems, which also
function as an input of user-cases.

The Semantic Web Applications for knowledge-based systems I know
always try's to separate those functions. The benefit of splitting is
that the functional constraints on (in our case) name objects will be
restricted depending their use on either the critical
cross-referencing or the usage context. When you merge both functions
you induce conflicting constraint on your name object and I think
that is what happens in your current discussion with Richard: For the
cross-referencing property you need nomenclatural exactness; for the
usage (modelling) context you would like to have a maximum of
flexibility and freedom to treat name objects.

Of course both methods have their pros and cons. A problem of
explicit cross-referencing is that it is an awful lot of work in the
beginning and you need to have certain standards, but once
established it's probably the best system. Merging cross-referencing
and user-cases has the benefit of having a quick start, however,
conflicting constraints on your data (=name) objects, a lot of
complex algorithmic modelling, and always the uncertainty of ending
with an sub-optimal system.

If I am right the GBIF attempt is not 'either-or', but a kind of
hybrid system. Since I am not an expert in this informatics area I
realise that some of the answers probably can be found in recent GBIF
documents on this issues and your wiki page. So time to do some
homework.

Kind regards,

Yde





>Hi Yde,
>
>TaxonNames
>
>Yes it is ambiguous as to whether a nomenclator may wish to issue a
>TaxonName GUID for 4 and/or 5. What I would do if I were a
>nomenclator is issue a TaxonName GUID for both. The GUID of the
>wrongly spelled one would return an object which included the GUID
>of the correctly spelled one. This is just what I would do not what
>a nomenclator may choose to do.
>
>TaxonConcepts
>
>TaxonConcepts depend on intention. From just a list of words it is
>usually impossible to say whether they represent something that
>should have a TaxonConcept GUID or not.
>
>If this list was entitled "Moths I have caught in my moth trap" I
>would argue strongly that you should not treat them as concepts.
>They are an attempt by some one to say which taxa they have found
>not an attempt to re-define taxa. The authors want to reference
>existing taxa not give objects an identity. The items on the list
>may get GUIDs from some recording scheme system though.
>
>If the exact same list was entitled "A treatment of  Zus  from Far
>Away Land" then it seems to me that they are all meant to be
>concepts (possibly with bad nomenclature). The authors want to
>tag/label these taxa so that other people can reference them when
>they go bird watching in Far Away Land - or whatever animal a Zus
>is...
>
>An Analogy
>
>I have in front of me a book called Everyman's Dictionary of First
>Names.  Here are some names from the book.
>
>Milli
>Mills
>Milly - see Milli
>Milo
>Milson
>Milton
>The question: "Should we issue National Insurance numbers for these
>people?" is not a good one. They are not people they are just names!
>But we only know that because I told you where I got them from. The
>people who compiled the book probably had a database with IDs on.
>They could try and set up a global system for names with GUIDs. This
>system would clearly be completely separate from a global system for
>identifying people by number for tax purposes although the tax
>system may refer to the name system and a credit reference agency
>might provide a service for getting an NI number from a person's
>name plus some other disambiguation data.
>
>So we can argue about the correct spelling of Milly and the register
>can have its own pointers to 'correct' spelling but Milly Smith
>still gets a tax bill because when she was born they gave her a
>number.
>
>(Incidentally I believe Denmark actual has this system. It has a
>national list of acceptable names for children and it has a system
>of issuing ID numbers to everyone at birth. The UK just gets
>confused with NI numbers and NHS numbers etc)
>
>Hope this helps,
>
>All the best,
>
>Roger
>
>[BTW I had the name book to hand because the children are choosing a
>name for our new cat. Milo is the favourite but we are open to
>suggestions. He is a ginger tom with a sister called Motlie].
>
>
>
>
>>Re: GUIDs for Taxon Names and Taxon Concepts
>>Dear Roger,
>>
>>One puzzling thing for me to be explained in more detail is the following:
>>
>>Extending the example of Richard:
>>
>>1. Aus Smith 1995
>>2. Xea Jones 2000
>>3. Aus bus Smith 1995
>>4. Xea bus (Smith 1995) Jones 2000
>>5. Xea ba (Smith 1995) Jones 2000
>>6. Xea bus (Smith 1995) Jones 2000 as it appears in Pyle 2005
>>    = Xea ba (Smith 1995) Jones 2000
>>
>>I agree with Richard that it is ambiguous whether nos 4 & 5 should
>>get TaxonName
>>GUIDs or TaxonConcept GUIDs, but I believe this is a matter of
>>defintion we can solve.
>>
>>However, how to discriminate between the TaxonConcept of no. 4 and
>>the TaxonConcept of no. 6 which includes subjective synonymy? I
>>assume you need a GUID for each documentable usage instance?
>>
>>Kind regards,
>>
>>Yde
>>
>>
>>
>>
>>
>>>Hi Rich,
>>>
>>>So you define a NameUsage as:
>>>
>>>"Any occurrence of a NameString as it appears or is explicitly implied
>>>within some form of static documentation."
>>>
>>>Let us explore this definition! Picking a volume almost at random
>>>(I like the cover) I chose Porley & Hodgett (2005) Mosses &
>>>Liverworts.
>>>
>>><http://www.tdwg.hyam.net/images/bryo_01.jpg>http://www.tdwg.hyam.net/images/bryo_01.jpg
>>>
>>>and picking a page at random - in this case 136
>>>
>>><http://www.tdwg.hyam.net/images/bryo_02.jpg>http://www.tdwg.hyam.net/images/bryo_02.jpg
>>>
>>>So we have a 'static' document and it is chuck full of
>>>NameStrings. I have circled some of them.
>>>
>>>We have Ditrichum cornubicum (a red data book moss). It is
>>>mentioned, with a picture on the previous page and at the top of
>>>this page it is mentioned a few more times. Further down this page
>>>we have Buxbaumia aphylla which is also mentioned twice. There is
>>>a picture of it on the next page.
>>>
>>>So how many name usages do we have here? There seem to be loads.
>>>
>>>Does each mention of the name on the page count as a usage? -
>>>would seem to be a silly thing to do.
>>>Does mentioning the name on different pages mean different usages?
>>>- would also be silly but we don't have anyway to judge (different
>>>pages within a journal or combined work for example?)
>>>How about same page but different context? The picture may be of a
>>>different moss to the one that they mention in the text.
>>>If a subspecies is mentioned does that count as a usage of the
>>>specific name (it has been used) and likewise a binomial implies a
>>>usage of the genus name.
>>>There are around 1100 species mentioned in this publication. They
>>>are probably mentioned on average 3 times each (a guess) so that
>>>is 3300 new name usages. Plus they are all binomials or
>>>subspecific names so double that for the different usages or
>>>genera etc. So 6,600 name usages in this volume. I wonder how many
>>>publications like this come out a year globally?
>>>I really can't see how one would apply your definition. Perhaps if
>>>you restricted it to taxonomic works but then you have to define a
>>>taxonomic work and you are still limited to how it has to be
>>>stated to act as a 'usage'. It certainly isn't clear to me.
>>>
>>>We can easily define what a TaxonConcept is because it implies
>>>intent. If I want to create an object that I want you to refer to
>>>as a definition of a taxon then I am creating a TaxonConcept and
>>>should issue a GUID to make it easy for you to refer to it. If not
>>>then I shouldn't bother. If I want to use the services of a
>>>nomenclator to define the publication and typification of the name
>>>I am using then I can use a TaxonName GUID within my definition -
>>>but I don't have to.  I can't see how that can be any simpler than
>>>that.
>>>
>>>Porley & Hodgetts (2005) have no intension whatsoever of
>>>'committing' nomenclatural acts or of defining any taxa that
>>>people will later refer to. They are simple referring to existing
>>>concepts. Yet by your definition they have created over 6k name
>>>usages that a diligent publisher might issue GUIDs for.
>>>
>>>Have I completely misinterpreted you definition? If so could you
>>>define it a little tighter? If you imply that the author has to
>>>have meant to describe something then you are just creating the
>>>TaxonConcept definition I am working with here. How else can you
>>>subset all the times names appear in print?
>>>
>>>
>>>This is all great fun but we do need to nail it down and move on.
>>>
>>>All the best,
>>>
>>>Roger
>>>
>>>
>>>
>>>>Hi Roger,
>>>>
>>>>
>>>>>Could you attempt a concise definition of a
>>>>>
>>>>>UsageInstance we can all agree on then :)
>>>>>
>>>>
>>>>Sure: Any occurrence of a NameString as it appears or is explicitly implied
>>>>within some form of static documentation.
>>>>
>>>>"NameString" refers to a string of textual characters meant to represent a
>>>>name of biological organisms.  This can be defined more restrictively to
>>>>"ScientificNameString" (names that conform to one of a designated set of
>>>>nomenclatural Codes), or more broadly to include vernacular NameStrings.
>>>>
>>>>"static documentation" can be defined broadly, to include publications,
>>>>databases, and any other form of documented medium of human communication.
>>>>The "static" part means that it must represent a snapshot in time. In the
>>>>case of dynamic databases, this would require a "date stamp" for each
>>>>UsageInstance -- either for an individual record, or for a snapshot of the
>>>>entire dataset.
>>>>
>>>>The "explicitly implied" part addresses zoological-style nomenclatural
>>>>listings along the lines of what Yde has sent to this list, where
>>>>a genus is
>>>>listed once as a header, and species epithets are enumerated below,
>>>>explicitly implying a series of binomials, even if they are not actually
>>>>printed on papaer as such.
>>>>
>>>>The point is, the definition is highly flexible, yet mostly unambiguous
>>>>(assuming sufficient metadata for identifying a documentation instance).
>>>>
>>>>I think it only makes informatic sense to distinguish two "kinds" of GUID
>>>>for taxonomic objects if the distinction between the objects is
>>>>unambiguous.
>>>>Given these NameStrings:
>>>>
>>>>1. Aus Smith 1995
>>>>2. Xea Jones 2000
>>>>3. Aus bus Smith 1995
>>>>4. Xea bus (Smith 1995) Jones 2000
>>>>5. Xea ba (Smith 1995) Jones 2000
>>>>
>>>>It is ambiguous whether there are three, four, or five distinct NameObjects
>>>>represented (i.e., it is ambiguous whether #s 4 & 5 should get TaxonName
>>>>GUIDs, or TaxonConcept GUIDs via SEC instances).
>>>>
>>>>However, given this list:
>>>>
>>>>1. "Aus" as it appears in Smith 1995
>>>>2. "Xea" as it appears in Jones 2000
>>>>3. "Aus bus" as it appears in Smith 1995
>>>>4. "Xea bus" as it appears in Jones 2000
>>>>5. "Xea" as it appears in Pyle 2005
>>>>6. "Xea ba" as it appears in Pyle 2005
>>>>7. "Xea" as it appears in ITIS Nov. 11, 2005 snapshot dataset
>>>>8. "Xea bus" as it appears in ITIS Nov. 11, 2005 snapshot dataset
>>>>9. "Xea ba" as it appears in ITIS Nov. 11, 2005 snapshot dataset
>>>>
>>>>There is very little ambiguity that each item in this list gets its own
>>>>GUID.  Until a universal definition of a "NameObject" emerges,
>>>>certain usage
>>>>instances can serve as surrogates for basionyms (1, 2, 3), or botanical new
>>>>combinations (4), or TaxonConcepts (1-6) -- in whatever way that a data
>>>>manager needs or wishes to establish linkages among GUIDs (e.g., linking #s
>>>>4, 6, 8 & 9 to #3 via "is basionym of"; or linking #s 4, 6, 8 & 9 to #2 via
>>>>"is combined with"; or linking #5 to #6, #2 to #4, and #1 to #3 via
>>>>"contains").
>>>>
>>>>Several people have expressed a desire for "simple" and "flexible", and I
>>>>think this approach maximizes both.
>>>>
>>>>Aloha,
>>>>
>>>>Rich
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