[tdwg-content] DwC taxonomic terms

Tue Aug 18 19:04:09 CEST 2009

It seems we will need new definitions of each of the terms you propose
to change as well as any definitions or comments that reference the
names or proposed content of any of these terms.

On Sun, Aug 16, 2009 at 11:24 PM, Markus Döring<m.doering at mac.com> wrote:
>> I do have a few comments nonetheless. Along with many of these
>> proposed changes would have to be changes in the wording of the
>> definitions and examples. Markus, can you provider those?
>
> Me and David Remsen will be happy to do so.
> Which exactactly are the missing definitions currently?
>
>>
>> The one suggestion with which I disagree is the one for
>> higherTaxonName (Issue #50). The definition of the term currently
>> reflects its origin and a need that could not otherwise be met - a way
>> to provide a complete classification in Simple Darwin Core, in which
>> only one instance of a term may occur per record. I don't think this
>> functionality should be lost. However, I do agree that the term
>> higherTaxonName should be consistent with the related identifier term
>> higherTaxonNameID, which is specifically about the parent name of the
>> scientificName only. So, I recommend that the current higherTaxonName
>> term be renamed to higherClassification and that a new higherTaxonName
>> term be added with the following attributes (adjusted later or name
>> changes to terms, as necessary):
>>
>> Definition: The name that is the parent of the scientificName.
>>
>> Comment: "Examples: "Animalia", "Chordata", "Vertebrata", "Mammalia",
>> "Theria", "Eutheria", "Rodentia", "Hystricognatha", "Hystricognathi",
>> "Ctenomyidae", "Ctenomyini", "Ctenomys".
>>
>> ABCD 2.06:
>> DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/HigherTaxa/HigherTaxon/HigherTaxonName
>
> That would be the best option in my eyes too, I agree. And it nicely lines
> up with ABCD
>
>
>> Finally, to me the term name "nameUsage does nothing to suggest its
>> content. This may require people to read the definition, which would
>> be a good thing, but it might just as easily slip people's notice as
>> something they don't understand and therefore must be irrelevant. For
>> such important terms I think that is too dangerous. I'd suggest better
>> names, and definitely request clear definitions that let those
>> currently using the term called "scientificName" know where that same
>> information should go.
>
> I never wanted to challenge scientificName. My main concern is and was about
> the term providing an ID for the "taxon class". I have had great sucess so
> far using the taxonomic terms in different context, representing
> nomenclatural work, classic taxonomic or even concept based taxonomies.
> Especially using the different ID terms for the classification, the basionym
> and the pointer form synonyms to the accepted taxon works nicely if you have
> a single "primary key" to refer to and not different terms for pure names,
> taxa or taxon concepts. This is where I thought name usage (see global names
> usage database, GNUB) would be the least common denominator and better
> suited as a term than scientificNameID or taxonID. If we can provide a
> definition of scientificNameID that covers the use for taxa or any "name
> usage" as in a name that has been used somewhere aka publication or digital
> source, then I am glad to keep scientificNameID. It just sounds very
> nomenclaturally biased when you come across it without reading the
> documentation.
>
>
>
>
>>
>> John
>>
>> On Thu, Aug 6, 2009 at 5:31 AM, Markus Döring<m.doering at mac.com> wrote:
>>>
>>> Dear John & DwC friends,
>>>
>>> after finally having time to review the current dwc terms again I came
>>> across a couple of issues I'd like to see discussed or even changed. I
>>> am working for nearly 1 year now with the new terms during their
>>> development, especially with the new and modified taxonomic terms. So
>>> far they work very well in practice, but there are a few improvements
>>> I can think of, mostly related to the latest changes shortly before
>>> the public review started. I have added them as separate issues to the
>>> google code site, but list them here in one go. The number of issues
>>> is larger than I hoped for, but most of them are minor terminology
>>> issues for consistency and not touching the core meaning of the terms.
>>>
>>> Markus
>>>
>>> ---
>>> #47   rename basionym(ID) to originalName(ID)
>>> http://code.google.com/p/darwincore/issues/detail?id=47
>>> The intend for this term is really to reflect where a name originally
>>> comes from in case it is a recombination. The term basionym is mostly
>>> used with botanists and covers only the cases when an epithet remains
>>> the same, i.e. not replacement names. The best matching, broader term
>>> therefore is originalName I think. Changes have to be done to both the
>>> verbatim name and the ID.
>>>
>>> Good examples for synonyms, basionyms, replaced names etc can be found
>>> in this document:
>>>
>>> http://www.peabody.yale.edu/other/PROTEM/TAXSIG/taxonomy_synonyms_examples.pdf
>>>
>>> ---
>>> #48   remove taxonConceptID
>>> http://code.google.com/p/darwincore/issues/detail?id=48
>>> The conceptID is intended to state that 2 name usages / potential taxa
>>> are the same, even if they use a different name. This is a special
>>> case of true concept relations and I would much prefer to see this
>>> covered in a dedicated extension treating all concept relations,
>>> especially frequent cases such as includes, overlaps, etc. I am more
>>> than willing to define such an extension
>>>
>>> ---
>>> #49   rename scientificNameID, acceptedScientificNameID and
>>> higherTaxonNameID
>>> http://code.google.com/p/darwincore/issues/detail?id=49
>>> no matter what the final term names are I think the 3 ones should be
>>> consistent. Originally it was intended to call them   taxonID,
>>> acceptedTaxonID and higherTaxonID
>>> with a loose definition of a taxon, more based on the idea of that all
>>> terms here are taxonomic terms and therefore contain taxon in their
>>> name. The current version  scientificNameID, acceptedScientificNameID
>>> and higherTaxonNameID intends to do the same I believe, but the
>>> terminology invites people to use them not referring to each other
>>> from what I have seen so far in practice.
>>> Concrete recomendations:
>>>
>>> #49a   replace scientificNameID with nameUsageID
>>> There is the need to uniquely identify a taxon concept with a given
>>> name, a name usage. A nameID suggests the name is unique which it isnt
>>> if combined with an sec reference aka taxonAccordingTo. A taxonID
>>> suggests to refer to a distinct taxon concept. A name usage seems the
>>> smallest entity and can therefore be used to act as a sort of unique
>>> key for names, taxa, taxon concepts or just usages of a name. All
>>> other taxonomic dwc ID terms can and should point to a name usage id
>>> then. This makes me think if most/all other IDs should reflect this in
>>> their names, see below.
>>>
>>> It could make sense to keep scientificNameID as a ID to the name as
>>> defined by a nomenclator. But this ID can also be used as a name usage
>>> id, so in order to gain clarity I would prefer to have the term removed.
>>>
>>> #49b rename acceptedScientificName(ID) to acceptedNameUsage(ID)
>>> this term should point to the name usage that reflects the "accepted"
>>> taxon in case of synonyms, no matter if they are objective or
>>> subjective. AcceptedScientificName sounds more like a nomenclatural
>>> exercise and in accordance with #3 (nameUsageID) the term
>>> acceptedNameUsage(ID) would be the best fit in my eyes.
>>>
>>> #49c rename higherTaxonName(ID) to higherNameUsage(ID)
>>> in consistency with nameUsage & acceptedNameUsage
>>>
>>> ---
>>> #50 remove recommendation to concatenate multiple values, especially
>>> for higherTaxonName/higherNameUsage
>>> http://code.google.com/p/darwincore/issues/detail?id=50
>>>
>>> similar to originalName or acceptedNameUsage this term is meant to be
>>> a verbatim pointer to the higher taxon as an alternative way of using
>>> higherTaxonNameID. Therefore it should only contain a single name, the
>>> direct parent, in my eyes. There are also already the 7 mayor ranks as
>>> separate terms that can be used to express a flattened hierarchy.
>>> I am aware DwC suggests to use concatenated lists in a single term in
>>> other places, e.g. , but I believe it would be better to keep the
>>> meaning singular and use multiple instances of that term to express
>>> multiple values. Dublin Core also recommends to use multiple XML
>>> elements for multiple values, see recommendation 5 in
>>> http://dublincore.org/documents/dc-xml-guidelines/
>>>
>>> ---
>>> #51 rename namePublicationID to namePublishedInID
>>> http://code.google.com/p/darwincore/issues/detail?id=51
>>> for consistency with namePublishedIn
>>>
>>> ---
>>> #52 rename (verbatim)scientificNameRank to (verbatim)rank
>>> http://code.google.com/p/darwincore/issues/detail?id=52
>>> to avoid discussions about whether the rank belongs to the name or the
>>> taxon and also because its nice and short and there is no clash in
>>> biological terminology.
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>>>
>
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