[tdwg-content] DwC taxonomic terms

Tue Aug 25 07:00:22 CEST 2009

Right, that all makes sense now, and is exactly the kind of
simplification that was already in place in the Location class, where
the locationID refers to the Location as a whole, not some part of it,
such as a country in one case or a city in another case. So, I agree,
remove the taxonConceptID.

I've been struggling with trying to come up with a better term name
than nameUsage. After reading the arguments again with every
alternative I can come up with (scientificName, taxonName, taxon_name,
nameAsUsed, nameAsPublished, publishedName, publishedTaxon) I'm not
sure I can really do any better for a name that states specifically
what you are trying to encompass with that term. Nevertheless, the
term seems awkward, especially on first encounter. The terms would
have to be very carefully described (but I guess all terms should be).
The problem is, I think the same problem with recognizing what the
term is for would happen on the second encounter as well ("What was
that term for again?"). I don't think that would happen with terms
that were more familiar, even if their meaning is broad. To me,
"taxon" works, because it could be a name or a concept - exactly what
we're trying to encompass.

So here's what I'd do in an attempt to be clear, concise, and consistent.

Given that the Class is Taxon (which captures the idea of a name as
well as it does a concept), consistency would argue that the id term
for a record of the class should be taxonID. The list of terms under
this scenario would be:
taxonID, acceptedTaxonID, higherTaxonID, originalTaxonID,
scientificName, acceptedTaxon, higherTaxon, originalTaxon,
higherClassification, kingdom, phylum, class, order, family, genus,
subgenus, specificEpithet, infraspecificEpithet, taxonRank,
verbatimTaxonRank, scientificNameAuthorship, nomenclaturalCode,
taxonPublicationID, taxonPublication, taxonomicStatus,
nomenclaturalStatus, taxonAccordingTo, taxonRemarks, vernacularName.

I retained "scientificName " for two big reasons. First, the obvious
alternative "taxon" would be too easily confused with the name of the
Class "Taxon". Second, scientificName has broad current usage and will
immediately suggest the appropriate content for most users. An
additional minor reason is that the term contrasts with and is nicely
consistent with "vernacularName".

The rest is all dependent on good definitions. Here are some drafts
for new definitions for terms that need them. Please suggest any
necessary revisions.

taxonID: An identifier for a specific taxon-related name usage (a
Taxon record). May be a global unique identifier or an identifier
specific to the data set.

acceptedTaxonID: A unique identifier for the acceptedTaxon.

higherTaxonID: A unique identifier for the taxon that is the parent of
the scientificName.

originalTaxonID: A unique identifier for the basionym (botany),
basonym (bacteriology), or replacement of the scientificName.

scientificName: The taxon name (with date and authorship information
if applicable). When forming part of an Identification, this should be
the name in the lowest level taxonomic rank that can be determined.
This term should not contain Identification qualifications, which
should instead be supplied in the IdentificationQualifier term.

acceptedTaxon: The currently valid (zoological) or accepted
(botanical) name for the scientificName.

higherTaxon: The taxon that is the parent of the scientificName.

originalTaxon: The basionym (botany), basonym (bacteriology), or
replacement of the scientificName..

higherClassification: A list (concatenated and separated) of the names
for the taxonomic ranks less specific than that given in the
scientificName.

kingdom, phylum, class, order, family, genus, subgenus,
specificEpithet, infraspecificEpithet - all unchanged.

taxonRank: The taxonomic rank of the scientificName. Recommended best
practice is to use a controlled vocabulary.

verbatimTaxonRank: The verbatim original taxonomic rank of the scientificName.

scientificNameAuthorship, nomenclaturalCode - unchanged

taxonPublicationID: A unique identifier for the publication of the Taxon.

taxonPublication: A reference for the publication of the Taxon.

taxonomicStatus, nomenclaturalStatus, taxonAccordingTo, taxonRemarks,
vernacularName - unchanged.

On Mon, Aug 24, 2009 at 4:15 PM, "Markus Döring
(GBIF)"<mdoering at gbif.org> wrote:
> John,
> I think this is based on the different understanding of the other IDs we are
> having.
> If ScientificNameID is purely for the name as the term suggests, I do agree
> with you that taxonConceptID is still needed. But as me and David have
> argued we would prefer a wider definition closer to the originally suggested
> taxonID (which was turned into scientificNameID at some point). An
> identifier for anything that is described by the taxonomic terms, let it be
> a name, a taxon (concept) or any other use of a name. So the same name
> effectively can have different IDs if it has been used in different places,
> thereby representing different taxonomic concepts. This would make the
> conceptID superflous. If the taxon(Concept)ID is to take on this role and
> the scientificNameID is a purely nomenclatural name identifier only, I am
> with you.
>
> One thing I would like to avoid very much though is that some ID terms would
> refer to the scientificNameID (like originalNameID) while others like the
> higherTaxonID would reference the taxonConceptID.
> I think it all becomes a lot simpler if there is a single taxon/nameID for
> all purpuses. Similarly I dont think we would want a separate occurrenceID,
> specimenID and fossilID.
>
> Markus
>
>
>
> On Aug 25, 2009, at 0:55, John R. WIECZOREK wrote:
>
>> While thinking further in trying to implement the suggested changes
>> another question occurred to me. The recommendation was made in Issue
>> #48 to remove taxonConceptID. If it is removed, how would anyone be
>> able to capture the proposition that a given specimen was a member of
>> a circumscription identified by a registered (having a resolvable
>> GUID) taxon concept? I pose that one could not, because we would be
>> left only with name terms. Unless I'm getting something wrong, I
>> believe this term cannot be removed.
>>
>> 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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