[tdwg-content] DwC taxonomic terms

"Markus Döring (GBIF)" mdoering at gbif.org
Thu Sep 10 23:33:49 CEST 2009


in case of a specimen I would just create an occurrence record like  
this using verbatim terms:

dwc:occurrenceID=BPBM-13492
dwc:collectionCode=BPBM
dwc:catalogNumber=13492
dwc:scientificName=Centropyge flavicauda Fraser-Brunner 1933
dwc:acceptedTaxon=Centropyge fisheri (Snyder 1904)

if I understand you correct the orignal name is the one for the  
accepted name.
So I cannot state this in the above record, as it would mean the  
original name of C. flavicauda

I would have to create another taxon record:

dwc:scientificName=Centropyge fisheri (Snyder 1904)
dwc:acceptedTaxon=Centropyge fisheri (Snyder 1904)
dwc:originalName= Holacanthus fisheri Snyder 1904


The problem here is that I dont think it is a good idea to mix  
occurrence and taxon records in one dataset.
But they could easily be separate datasets for specimen and taxa.

Also you could use ID terms instead of the verbatim one, which is less  
error prone and cleaner to grasp:

dwc:taxonID=431
dwc:scientificName=Centropyge flavicauda Fraser-Brunner 1933
dwc:taxonomicStatus=synonym
dwc:acceptedTaxonID=432

dwc:taxonID=432
dwc:scientificName=Centropyge fisheri (Snyder 1904)
dwc:taxonomicStatus=accepted
dwc:originalNameID=433

dwc:taxonID=433
dwc:scientificName=Holacanthus fisheri Snyder 1904




On Sep 10, 2009, at 11:11 PM, Richard Pyle wrote:

>
> Thanks Markus -- this is very helpful.  I'll need to wrap my head  
> around
> what is meant.  However, it would be useful if you or someone could  
> show me
> how I would populate a DwC record for the sample I gave:
>
> Specimen BPBM 13492.
> Last identified as "Centropyge flavicauda Fraser-Brunner 1933".
> We (provider) treat this species is as a synonym of "Centropyge  
> fisheri
> (Snyder 1904)".
> The original description "fisheri" by Snyder (1904) placed it in the  
> genus
> "Holacanthus".
>
> I'll take a look at the example, and see if I can understand from  
> that.
>
> Thanks,
> Rich
>
>
>> -----Original Message-----
>> From: "Markus Döring (GBIF)" [mailto:mdoering at gbif.org]
>> Sent: Thursday, September 10, 2009 11:03 AM
>> To: Richard Pyle
>> Cc: tdwg-content at lists.tdwg.org
>> Subject: Re: [tdwg-content] DwC taxonomic terms
>>
>> Rich,
>> as usual no time to write a long mail, but I wanted to
>> quickly respond to your 3 intended uses below.
>> The idea is that everyone of them has a dwc:scientificName
>> term and potentially also the other terms you listed at the
>> end like rank.
>>
>> originalTaxonNameID and acceptedTaxonID are still properties
>> of the described dwc:scientificName and act like foreign keys
>> linking one name/taxon to another. So if you have some sort
>> of synonym (indicated by dwc:taxonomicStatus) the
>> dwc:acceptedTaxonID will point to what is considered the
>> accepted taxon. While originalTaxonNameID will point to the
>> original name  record. The verbatim non ID versions of these
>> two terms do essentially the same, but are based on name
>> string matching.
>> They are not meant to replace the use of dwc:scientificName
>> in a record.
>>
>> Maybe its best to look at the examples Dave put together:
>> (the tax/nom status columns are subject to change)
>>
>> http://code.google.com/p/gbif-ecat/wiki/GNAsynonymsExample
>>
>>
>>
>> Markus
>>
>>
>>
>> On Sep 10, 2009, at 5:47 AM, Richard Pyle wrote:
>>
>>>
>>> Dear All,
>>>
>>> After a series of off-list conversations with Peter DeVries, Dave
>>> Remsen, and others; and thanks to John W. for pointing me to the
>>> active list of terms, I would like to offer some additional
>> thoughts
>>> on the "Core Taxon"
>>> terms; but before I do, I want to make sure I understand how the
>>> existing terms are intended to be used.
>>>
>>>> From the perspective of an Occurrence (specimen/observation/etc.)
>>>> record
>>> represented through DwC, it seems to me that there are
>> three sets of
>>> name/taxon terms:
>>>
>>> 1. "As Identified"
>>> [Information about how the record is currently identified.]
>>>
>>> - scientificName
>>> - scientificNameID
>>> - scientificNameAuthorship
>>> - taxonAccordingTo
>>> - taxonAccordingToID
>>>
>>> 2. "As originally established"
>>> [Information about the original name as established under the Code]
>>>
>>> - originalTaxonName
>>> - originalTaxonNameID
>>> - namePublishedIn
>>> - namePublishedInID
>>>
>>> 3. "Opinion of Data Provider"
>>> [Information about how the data provider interprets the
>> correct name.]
>>>
>>> - acceptedTaxon
>>> - acceptedTaxonID
>>>
>>>
>>> I'm not entirely certain which "set" of names the following terms
>>> would apply to:
>>>
>>> - rank
>>> - verbatimRank
>>> - higherTaxonName
>>> - higherTaxonNameID
>>> - higherClassification
>>> - kingdom
>>> - phylum
>>> - class
>>> - order
>>> - family
>>> - genus
>>> - subgenus
>>> - specificEpithet
>>> - infraspecificEpithet
>>>
>>> According to the current draft spreadsheet
>>>
>> (http://spreadsheets.google.com/pub? 
>> key=tZ3c04UGzRgalNxZMmcijcQ&output
>>> =html
>>> )
>>> , it seems that the first two apply specifically to the
>>> "scientificName", and therefore belong in the first set (i.e., rank
>>> according to how it was identified; not necessarily how the Data
>>> Provider now treats it, or what the original rank was).  I
>> assume the
>>> rest all apply to "Opinion of Data Provider"; but this is not
>>> explicitly stated.
>>>
>>> For example, consider the specimen BPBM 13492. It was most recently
>>> identified as "Centropyge flavicauda Fraser-Brunner 1933".  Our
>>> current treatment of this species is as a junior synonym of
>>> "Centropyge fisheri (Snyder 1904)".  The original description
>>> "fisheri" by Snyder (1904) placed it in the genus "Holacanthus".
>>>
>>> I'm assuming that I would present this record via DwC using
>> the above
>>> terms as follows:
>>>
>>> 1. As Identified:
>>>
>>> scientificName: Centropyge flavicauda
>>> scientificNameID:
>>>
>> http://research.calacademy.org/research/ichthyology/catalog/ 
>> fishcatget
>>> .asp?s
>>> pid=53548
>>> scientificNameAuthorship: Fraser-Brunner 1933
>>> taxonAccordingTo: Allen, G.R. 1980. Butterfly and
>> angelfishes of the
>>> world.
>>> Volume II. Mergus Publishers. Pp. 149-352.
>>> taxonAccordingToID:
>>>
>> http://research.calacademy.org/research/ichthyology/catalog/ 
>> getref.asp
>>> ?id=22
>>> 764
>>>
>>> 2. As originally established:
>>>
>>> - originalTaxonName: Centropyge flavicauda Fraser-Brunner 1933
>>> - originalTaxonNameID:
>>>
>> http://research.calacademy.org/research/ichthyology/catalog/ 
>> fishcatget
>>> .asp?s
>>> pid=53548
>>> - namePublishedIn: Fraser-Brunner, A. 1933. A revision of the
>>> chaetodont fishes of the subfamily Pomacanthinae.
>> Proceedings of the
>>> General Meetings for Scientific Business of the Zoological
>> Society of
>>> London 1933 (pt 3, no.
>>> 30): 543-599, Pl. 1.
>>> - namePublishedInID:
>>>
>> http://research.calacademy.org/research/ichthyology/catalog/ 
>> getref.asp
>>> ?id=67
>>> 1
>>>
>>> 3. Opinion of Data Provider:
>>>
>>> acceptedTaxon: Centropyge fisheri
>>> acceptedTaxonID:
>>>
>> http://research.calacademy.org/research/ichthyology/catalog/ 
>> fishcatget
>>> .asp?s
>>> pid=53548
>>>
>>> If my assumptions are correct, then "specificEpithet" would be
>>> "fisheri", not "flavicauda" -- correct?
>>>
>>> Once I get a sense from this list whether I am interpreting
>> the terms
>>> correctly (or not), I'll offer some specific comments on the taxon
>>> terms.
>>>
>>> Aloha,
>>> Rich
>>>
>>>
>>>
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>>
>
>
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