December 2010 - tdwg-content

An individual identified to a higher group like Order, is still an instance of a species - just a species that is currently unspecified
by Peter DeVries 25 Sep '11

25 Sep '11

What I would recommend is that you treat a specimen that is identified to an order (Perciformes) with something like the following. Species => Order Perciformes species undetermined. The individual is still an instance of a species, however that species has yet to be determined. What would work best is to have some standard way of writing the green string above. This would allow the occurrences that are of individuals identified only to the Order Perciformes, to be interpreted as a species that falls somewhere within the Order Perciformes. - Pete --------------------------------------------------------------- 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/> ------------------------------------------------------------

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Animal Camera Trap data and Darwin Core: Thoughts?
by Pilsk, Suzanne 23 Dec '10

23 Dec '10

Dear TDWG group, I am working with some folks on building an animal camera trap data repository. We are seriously looking at Darwin Core as the basis of the metadata model for the information regarding these images and animals caught on camera. Do you know of any Camera Trapping or other similar style data collection program that is using Darwin Core? Do you have any suggestions on the pro's and con's of using Darwin Core for such a project? Feel free to email me directly. Thank you, Suzanne Suzanne C. Pilsk Head, Metadata Unit Smithsonian Institution Libraries Connecting. Ideas. Information. You. 10th & Constitution Avenues, NW, NH2207 MRC 154, P.O. Box 37012 Washington, DC 20013-7012 v. 202.633.1646 PilskS(a)si.edu<mailto:PilskS@si.edu> P Please consider the environment before printing this email.

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proposed term: dwc:verbatimScientificName
by David Remsen (GBIF) 13 Dec '10

13 Dec '10

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

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ECN 2010 "Biodiversity Informatics on the Semantic Web" Talk available on SlideShare
by Peter DeVries 13 Dec '10

13 Dec '10

I just uploaded my talk to slideshare. http://www.slideshare.net/pjdwi/biodiversity-informatics-on-the-semantic-web I added some of the things I ad-libbed or were not clear from the slides themselves - so the text should be easy to follow. - Pete --------------------------------------------------------------- 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/> ------------------------------------------------------------

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Invitation to connect on LinkedIn
by Peter DeVries 13 Dec '10

13 Dec '10

LinkedIn ------------ I'd like to add you to my professional network on LinkedIn. - Peter Peter DeVries Ph.D. Dissertator at Department of Entomology, University of Wisconsin Madison, Wisconsin Area Confirm that you know Peter DeVries https://www.linkedin.com/e/-pnstdp-ghnv035t-1d/isd/2020277116/PfDV2eoc/ -- (c) 2010, LinkedIn Corporation

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Re: [tdwg-content] proposed term: dwc:verbatimScientificName
by Peter DeVries 09 Dec '10

09 Dec '10

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(a)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(a)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(a)lists.tdwg.org [mailto: > tdwg-content-bounces(a)lists.tdwg.org] *On Behalf Of *David Remsen (GBIF) > *Sent:* Wednesday, December 08, 2010 6:10 AM > *To:* tdwg-content(a)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(a)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/> > ------------------------------------------------------------ > -- --------------------------------------------------------------- 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/> ------------------------------------------------------------

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