[tdwg-tag] [tdwg-content] canonicalScientificName

Roderic Page r.page at bio.gla.ac.uk
Wed Mar 14 18:32:57 CET 2012


So what I'm hearing is people can't figure out how to use Darwin Core without getting confused about pretty much the most basic thing, the taxonomic name. And we're OK with that?!

In many ways I don't actually care about Darwin Core, all I want is for people to serve canonical names whenever they can (and if they actually want people to use their data without those people pulling their hair out).



On 14 Mar 2012, at 17:11, Richard Pyle wrote:

> There has in the past been discussions about a term for this purpose (in fact I believe the proposed term was canonicalScientificName).  It's been a few years, and it would take me some time to dig up the details, but my recollection of the conclusion of those discussions was along the lines of the following:
> - When providers had only a "text blob" to represent the scientific name, with or without authorship, with or without rank abbreviations and formatting, etc., and these providers lacked the time, inclination, skills, and/or local data structure to parse these text blobs, then the scientificName term fulfilled their needs.
> - When providers had a text blob for the name, separate from the text blob for the authorship, they could concatenate the two for presentation in scientificName, and also provide the authorship bit in scientificNameAuthorship, and the consumers could easily strip the authorship from scientificName to produce the functional equivalent of a canonical name.
> - When providers did have the time, inclination, skills, and local data structure to parse these text blobs, the elements of a canonical name could be provided via the genus | subgenus | specificEpithet | infraspecificEpithet | taxonRank | verbatimTaxonRank terms, and the consumer could easily assemble these into a single string with canonical form.
> This led to the conclusion that the addition of yet another term in the dwc:Taxon class would have provided very little benefit, at the cost of confusion about what information to provide in which term, and inconsistent use.
> Aloha,
> Rich
> Richard L. Pyle, PhD
> Database Coordinator for Natural Sciences
> Associate Zoologist in Ichthyology
> Dive Safety Officer
> Department of Natural Sciences, Bishop Museum
> 1525 Bernice St., Honolulu, HI 96817
> Ph: (808)848-4115, Fax: (808)847-8252
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> http://hbs.bishopmuseum.org/staff/pylerichard.html
> Note: This disclaimer formally apologizes for the disclaimer below, over which I have no control.
>> -----Original Message-----
>> From: tdwg-content-bounces at lists.tdwg.org [mailto:tdwg-content-
>> bounces at lists.tdwg.org] On Behalf Of Peter Desmet
>> Sent: Tuesday, March 13, 2012 12:59 PM
>> To: TDWG content mailing list; Roderic D. M. Page; TDWG TAG mailing list
>> Subject: Re: [tdwg-content] canonicalScientificName
>> Sorry, forgot to include TAG mailing list.
>> On Tue, Mar 13, 2012 at 15:27, Peter Desmet <peter.desmet at umontreal.ca>
>> wrote:
>>> Hi everyone,
>>> In a recent tweet [1] Roderic Page reminded me that in Darwin Core, we
>>> don't have a ready-to-use scientificName field. The definition for
>>> scientificName [2] asks for the full verbose name, including authors.
>>> I think this is a good definition (see below), but it also means that
>>> in a lot of use cases, names need to be parsed before they can be used
>>> or matched. I am currently helping collections publish their data for
>>> Candensys [3] and as a data producer I am happy we can provide all the
>>> information we have in scientificName, but as a data user, I get
>>> frustrated every time I see those long verbose botanical names with
>>> multiple authors. I am convinced that our data would be more usable if
>>> we had an additional canonicalScientificName term.
>>> Which is why I am now officially requesting it on the Darwin Core code
>>> site: http://code.google.com/p/darwincore/issues/detail?id=150 (see
>>> below). This has been discussed in detail before [4], but no consensus
>>> was reached. I hope we can get our act together this time!
>>> Regards,
>>> Peter Desmet
>>> --
>>> [1] https://twitter.com/#!/rustyrussell22/status/179500954901692417
>>> [2] http://rs.tdwg.org/dwc/terms/index.htm#scientificName
>>> [3] http://www.canadensys.net
>>> [4]
>>> http://lists.tdwg.org/pipermail/tdwg-content/2010-
>> November/thread.html
>>> #1976
>>> ==New Term Recommendation==
>>> Submitter: Peter Desmet
>>> Justification: The scientific name is probably the most used element
>>> of an occurrence/taxon, but currently Darwin Core does not provide a
>>> single ready-to-use-field for this. A canonicalScientificName with the
>>> scientific name as a uninomial, binomial or trinomial could solve this
>>> problem.
>>> The current terms are not sufficient:
>>> - scientificName: verbose, used to record all components of a
>>> scientific name (if available), including authorship(s) and
>>> rankmarker(s). It is critical to keep this definition, as this term is
>>> sometimes the only place to share certain information, e.g.:
>>> quadrinomials, intermediate botanical authors, hybrid formulas, etc.
>>> The disadvantage of only having this verbose notation is that the user
>>> needs to parse the name before he/she can use or match it.
>>> - genus, specificEpithet, infraspecificEpithet: concatenated, this
>>> terms are identical to the canonicalScientificName for genera, species
>>> and infraspecific taxa. For higher taxa or infrageneric taxa, these
>>> terms are not sufficient. In addition, there is some ambiguity
>>> regarding the genus definition: for synonyms, is it the accepted genus
>>> or the genus that is part of the synonym name? See:
>>> http://lists.tdwg.org/pipermail/tdwg-content/2010-
>> November/002052.html.
>>> In the former case, the genus cannot be used to concatenate a
>>> canonicalScientificName.
>>> The need for this term has been discussed thoroughly already (see:
>>> http://lists.tdwg.org/pipermail/tdwg-content/2010-
>> November/thread.html
>>> #1976), but no consensus was reached. I'd like to reopen the
>>> discussion and I hope that a consensus can be reached quickly, so our
>>> data can be used more easily.
>>> Definition: The scientific name as a uninomial, binomial or trinomial.
>>> When forming part of an Identification, this should be the name in
>>> lowest level taxonomic rank that can be determined. This term should
>>> not contain authorship(s), rankmarker(s) or identification
>>> qualifications. If the scientific name cannot be expressed as a uni-,
>>> bi- or trinomial (e.g. hybrid formulas), do not use this term (use
>>> scientificName instead).
>>> Comment: Examples: "Carex" (genus), "Vulpes vulpes" (species),
>>> "Anaphalis margaritacea occidentalis" (plant variety)
>>> Refines:
>>> Has Domain:
>>> Has Range:
>>> Replaces:
>>> ABCD 2.06:
>>> --
>>> Peter Desmet
>>> Biodiversity Informatics Manager
>>> Canadensys - www.canadensys.net
>>> Université de Montréal Biodiversity Centre
>>> 4101 rue Sherbrooke est
>>> Montreal, QC, H1X2B2
>>> Canada
>>> Phone: 514-343-6111 #82354
>>> Fax: 514-343-2288
>>> Email: peter.desmet at umontreal.ca / peter.desmet.cubc at gmail.com
>>> Skype: anderhalv
>>> Public profile: http://www.linkedin.com/in/peterdesmet
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Roderic Page
Professor of Taxonomy
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