On Tue, Aug 25, 2009 at 2:04 AM, David Remsen (GBIF)dremsen@gbif.org wrote:
Upon re-read of your post I see that taxonAccordingTo has been retained. Therefore I can interpret taxonPublication to simply be a change in the name of namePublishedIn. I have worked up various examples using the terms in combination with some extensions we (Markus and I) have been drafting. They are listed below with comments. Note that given the instability around the taxon identifier names they might not be congruent with the current terminology. Euro+Med Example (http://spreadsheets.google.com/pub?key=tnoVriNunOOMzYp709vtauQ&output=ht...) We hit a snag with this example when the source database did not provide identifiers for the misapplied names and we therefore had to manufacture local identifiers for them. In this example namePublishedIn holds the unparsed primary citation and taxonAccordingTo holds the misapplied name reference. Peabody Museum Zoological and Botanical Synonyms Example Source Document (http://www.peabody.yale.edu/other/PROTEM/TAXSIG/taxonomy_synonyms_examples.p...) Transformed Document (http://spreadsheets.google.com/pub?key=ts5YVtLnXCBvv8X-prpprOg&output=ht...) Transformed Document with Comments (http://code.google.com/p/gbif-ecat/wiki/GNAsynonymsExample) These examples best illustrates my reasoning for the use of the term "taxon Reference" There is a comments part of the wiki that highlights some of the issues I hit. Lastly, this is a mapping of the DwC terms to the Catalogue of Life Standard Dataset http://code.google.com/p/gbif-ecat/wiki/CoL_Comparison I refer to a "GNA standard" in this document to refer to our use of the draft terms in combination with other draft terms structured as extensions according to the text guidelines. In this case I used taxonAccordingTo to reference the latest taxonomic scrutiny property of the standard dataset. 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@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 Döringm.doering@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.p...
#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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