Re: [tdwg-content] proposed term: dwc:verbatimScientificName
Ebird and NCBI have just genus and specific epithet, most publications have just the genus and specific epithet.
That is what you have to match against first and then try to determine what is the most appropriate or intended authority.
Essentially you have a has many relationship with
scientificName hasMany authorities (authorship strings)
Also what is not made clear in your earlier example is that
Every scientificName: Lobelia spicata var. spicata
is an instance of
scientificName: Lobelia spicata
In relation to occurrence records you will have specimens of Lobelia spicata var. spicata that were identified as Lobelia spicata.
This should be done in away where those searching for specimens etc of Lobelia spicata also get those entries labeled Lobelia spicata var. spicata and Lobelia spicata ssp. spicata etc.
Respectfully,
- Pete
On Thu, Dec 9, 2010 at 10:54 AM, Richard Pyle deepreef@bishopmuseum.orgwrote:
They cannot provide a verbatimScientificName???? That would imply they have no text field whatsoever.
*From:* Peter DeVries [mailto:pete.devries@gmail.com] *Sent:* Thursday, December 09, 2010 6:47 AM *To:* Richard Pyle *Subject:* Re: [tdwg-content] proposed term: dwc:verbatimScientificName
So basically what you are saying is that the entire NCBI taxonomy database as well as the ebird database cannot output the required format.
- Pete
On Thu, Dec 9, 2010 at 9:44 AM, Richard Pyle deepreef@bishopmuseum.org wrote:
I think this is **exactly** the right solution. I would go further to make it clear that:
verbatimScientificName is the required field (withscientificName and scientificNameAuthorship as optional)
When a source database maintains separate fields correspondingto scientificName and scientificNameAuthorship, they should be concatenated (with a single space between them) to form the required verbatimScientificName
Aloha,
Rich
*From:* tdwg-content-bounces@lists.tdwg.org [mailto: tdwg-content-bounces@lists.tdwg.org] *On Behalf Of *David Remsen (GBIF) *Sent:* Wednesday, December 08, 2010 6:10 AM *To:* tdwg-content@lists.tdwg.org List *Subject:* [tdwg-content] proposed term: dwc:verbatimScientificName
Markus and I wanted to try to consolidate the issues related to the current use and definition of scientificName that have been the focus of last weeks discussion in as simple a way as we can and leave it with a simple proposal which we will add to the issue tracking on the project site.
- We propose that a new term, dwc:verbatimScientificName carry the
existing definition for dwc:scientificName and
- dwc:scientificName follow the more accepted convention that is better
represented by the earlier proposed definition for Canonical Name
The intention is to enable data publishers to distinguish unparsed, complex scientific names from more cleanly separated scientific name data. This will relieve consumers of these data from testing each instance of a name for one of these two conditions.
Here are the definitions for the two existing terms that have been part of the discussion:
*dwc:scientificName * - The full scientific name, with authorship and date information if known. 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 identification qualifications, which should instead be supplied in the IdentificationQualifier term.
*dwc:scientificNameAuthorship* - The authorship information for the scientificName formatted according to the conventions of the applicable nomenclaturalCode.
Here are terms and definitions used in the following 5 source data configurations we came up with. They don't have to be exact for this purpose.
*canonical name* - The nomenclatural components of a scentific name without authorship information.
*authorship* - the authorship information that follows a scientific name
*verbatim name* - the verbatim text stored in a source database when it differs from or combines the two definitions above. This is a bit more broad than the def for scientificName.
We identified the following configurations in a source database and how they would be mapped to the existing terms. In cases 4 and 5 we also propose how we would map these were there a 3rd available term (called 'mapping b:')
When a source database contains:
- canonical names only
Mapping: canonical name -> dwc:scientificName
- canonical name and authorship in two fields
Mapping: canonical name -> dwc:scientificName / authorship->dwc:scientificNameAuthorship
- verbatim name only
Mapping: verbatim name -> dwc:scientificName
- all three: canonical name, authorship, and verbatim name in 3 diff.
columns
Mapping a: verbatim name -> dwc:scientificName / authorship->dwc:scientificNameAuthorship
Mapping b: canonical name -> dwc:scientificName / authorship->dwc:scientificNameAuthorship / verbatim name -> dwc:verbatimScientificName
- a mix of canonical and verbatim names in a single column
Mapping a: verbatim name + canonical names -> dwc:scientificName
Mapping b: verbatim name + canonical names -> dwc:verbatimScientificName
Summary - with the current two terms are left with no choice but to support both canonical and verbatim names in a single term, which makes consuming these data difficult.
We propose that a new term, dwc:verbatimScientificName carry the existing definition for dwc:scientificName and that dwc:scientificName follow the more accepted convention that is better represented by the definition for Canonical Name
Best,
David Remsen / Markus Döring
tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
--
Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 TaxonConcept Knowledge Base http://www.taxonconcept.org/ / GeoSpecies Knowledge Base http://lod.geospecies.org/ About the GeoSpecies Knowledge Base http://about.geospecies.org/
No problem. Concatenate them and put them in verbatimScietificName and, if canonical, in scientificName as well.
These are just text strings; they have no other implications. The relationships to taxa re inferred afterward.
I still dont understand your statement that the entire NCBI taxonomy database as well as the ebird database cannot output the required format.
Rich
From: Peter DeVries [mailto:pete.devries@gmail.com] Sent: Thursday, December 09, 2010 7:12 AM To: Richard Pyle; tdwg-content@lists.tdwg.org Subject: Re: [tdwg-content] proposed term: dwc:verbatimScientificName
Ebird and NCBI have just genus and specific epithet, most publications have just the genus and specific epithet.
That is what you have to match against first and then try to determine what is the most appropriate or intended authority.
Essentially you have a has many relationship with
scientificName hasMany authorities (authorship strings)
Also what is not made clear in your earlier example is that
Every scientificName: Lobelia spicata var. spicata
is an instance of
scientificName: Lobelia spicata
In relation to occurrence records you will have specimens of Lobelia spicata var. spicata that were identified as Lobelia spicata.
This should be done in away where those searching for specimens etc of Lobelia spicata also get those entries labeled Lobelia spicata var. spicata and Lobelia spicata ssp. spicata etc.
Respectfully,
- Pete
On Thu, Dec 9, 2010 at 10:54 AM, Richard Pyle deepreef@bishopmuseum.org wrote: They cannot provide a verbatimScientificName???? That would imply they have no text field whatsoever. From: Peter DeVries [mailto:pete.devries@gmail.com] Sent: Thursday, December 09, 2010 6:47 AM To: Richard Pyle Subject: Re: [tdwg-content] proposed term: dwc:verbatimScientificName So basically what you are saying is that the entire NCBI taxonomy database as well as the ebird database cannot output the required format. - Pete On Thu, Dec 9, 2010 at 9:44 AM, Richard Pyle deepreef@bishopmuseum.org wrote: I think this is *exactly* the right solution. I would go further to make it clear that: - verbatimScientificName is the required field (with scientificName and scientificNameAuthorship as optional) - When a source database maintains separate fields corresponding to scientificName and scientificNameAuthorship, they should be concatenated (with a single space between them) to form the required verbatimScientificName Aloha, Rich From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of David Remsen (GBIF) Sent: Wednesday, December 08, 2010 6:10 AM To: tdwg-content@lists.tdwg.org List Subject: [tdwg-content] proposed term: dwc:verbatimScientificName Markus and I wanted to try to consolidate the issues related to the current use and definition of scientificName that have been the focus of last weeks discussion in as simple a way as we can and leave it with a simple proposal which we will add to the issue tracking on the project site. 1. We propose that a new term, dwc:verbatimScientificName carry the existing definition for dwc:scientificName and 2. dwc:scientificName follow the more accepted convention that is better represented by the earlier proposed definition for Canonical Name The intention is to enable data publishers to distinguish unparsed, complex scientific names from more cleanly separated scientific name data. This will relieve consumers of these data from testing each instance of a name for one of these two conditions. Here are the definitions for the two existing terms that have been part of the discussion: dwc:scientificName - The full scientific name, with authorship and date information if known. 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 identification qualifications, which should instead be supplied in the IdentificationQualifier term. dwc:scientificNameAuthorship - The authorship information for the scientificName formatted according to the conventions of the applicable nomenclaturalCode. Here are terms and definitions used in the following 5 source data configurations we came up with. They don't have to be exact for this purpose. canonical name - The nomenclatural components of a scentific name without authorship information. authorship - the authorship information that follows a scientific name verbatim name - the verbatim text stored in a source database when it differs from or combines the two definitions above. This is a bit more broad than the def for scientificName. We identified the following configurations in a source database and how they would be mapped to the existing terms. In cases 4 and 5 we also propose how we would map these were there a 3rd available term (called 'mapping b:') When a source database contains: 1. canonical names only Mapping: canonical name -> dwc:scientificName 2. canonical name and authorship in two fields Mapping: canonical name -> dwc:scientificName / authorship->dwc:scientificNameAuthorship 3. verbatim name only Mapping: verbatim name -> dwc:scientificName 4. all three: canonical name, authorship, and verbatim name in 3 diff. columns Mapping a: verbatim name -> dwc:scientificName / authorship->dwc:scientificNameAuthorship Mapping b: canonical name -> dwc:scientificName / authorship->dwc:scientificNameAuthorship / verbatim name -> dwc:verbatimScientificName 5. a mix of canonical and verbatim names in a single column Mapping a: verbatim name + canonical names -> dwc:scientificName Mapping b: verbatim name + canonical names -> dwc:verbatimScientificName Summary - with the current two terms are left with no choice but to support both canonical and verbatim names in a single term, which makes consuming these data difficult. We propose that a new term, dwc:verbatimScientificName carry the existing definition for dwc:scientificName and that dwc:scientificName follow the more accepted convention that is better represented by the definition for Canonical Name Best, David Remsen / Markus Döring
_______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
participants (2)
-
Peter DeVries -
Richard Pyle