[tdwg-content] DwC taxonomic terms
David Remsen (GBIF)
dremsen at gbif.org
Tue Aug 25 08:06:23 CEST 2009
John
in haste as I prepare for biking my son to school
as another option for nameUsage I've been favoring the term
"taxonReference"
it's more atomic than taxonID in the sense that a taxon can be
described by a series of taxon references
I think the other linked terms you listed could stay as they are but I
think taxonID and scientificNameID carry implications that don't match
the cardinality of the term, at least in some cases, whereas in all
cases there is a reference to a taxon.
I notice that namePublishedIn and taxonAccordingTo have been merged
into a single taxonPublication. In working through various use cases
for modelling published taxon concepts I used these different terms as
well as a bibliographic extension and will re-evaluate these with the
proposed changes when I get to work.
Cheers,
David
On Aug 25, 2009, at 7:00 AM, John R. WIECZOREK wrote:
> 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.
>>>> _______________________________________________
>>>> tdwg-content mailing list
>>>> tdwg-content at lists.tdwg.org
>>>> http://lists.tdwg.org/mailman/listinfo/tdwg-content
>>>>
>>
>>
> _______________________________________________
> tdwg-content mailing list
> tdwg-content at lists.tdwg.org
> http://lists.tdwg.org/mailman/listinfo/tdwg-content
>
More information about the tdwg-content
mailing list