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@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. _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
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