[tdwg-tag] darwin core terms inside tdwg ontology

David Remsen dremsen at mbl.edu
Mon Apr 27 23:04:43 CEST 2009

Paul - I'll post some examples as soon as I can (I'm in a GBIF Science  
Committee meeting the next two days) that illustrate how we can use  
the DwC terms to create simple schemas for representing rich taxonomic  
data.  Markus and I have modelled complex zoological and botanical  
taxonomies using it for testing the GBIF IPT and it works.  I'll get  
these examples served in the next day or so.  It includes some Euro 
+Med Plants data and a Smithsonian taxonomic bulletin on Cetacean  
taxonomy (zoological + botanical examples).   It covers all of the  
components of taxonomic opinion to which you refer and more.  It can  
represent all that I know are contained in Index Fungorum and Species  
Fungorum unless you are hiding a lot more, which you may well be.    
The only thing it doesn't do well are the explicit concept-to-concept  
assertions enabled by TCS but I have other strategies for achieving  
that.   There are some homonym cases as well which I'm not sure we do  
well but which Markus thinks we can so I need to dig in there a bit.

If you have some sample taxonomic or nomenclatural data that you think  
will break it I would be happy to take it for a ride within the DwC- 
with-extensions approach that is employed within the IPT and see if it  
can't be effectively addressed.   I don't mind being wrong about it so  
long so as I or someone else can provide some clues as where to go  
from here.


On Apr 27, 2009, at 4:20 PM, Paul Kirk wrote:

> I tend to agree with David ... but only to a point.
> Are we not discussing the equivalent here of database  
> normalization ... where two diametrically opposite opinions hold -  
> fully normalized and it don't work (performance issue) or fully de- 
> normalized and it don't work (integrity issues - accepting that a  
> well designed UI can protect database content (and integrity) from  
> the user)? Here we have DwC-with-extensions on the one hand and  
> something like TCS/CDM? on the other. By taxonomic information I  
> assume we mean that a taxonomic opinion on a name has been expressed  
> (usually by a person). If so, the requirements are fairly basic -  
> name with nomenclatorLSID, status, who, when and where. It gets  
> complex, and it's what I do not think DwC supports, when everything  
> in a complex taxonomic opinion (homotypic names, heterotypic names,  
> misapplications, pro-parte synonyms etc) is placed in one 'object' -  
> the equivalent of recursive joins to go back to a database analogy.
> In haste,
> Paul
> From: tdwg-tag-bounces at lists.tdwg.org [mailto:tdwg-tag-bounces at lists.tdwg.org 
> ] On Behalf Of David Remsen
> Sent: 27 April 2009 14:47
> To: Kevin Richards
> Cc: Technical Architecture Group mailing list; exec at tdwg.org
> Subject: Re: [tdwg-tag] darwin core terms inside tdwg ontology
> Kevin,   Can you tell me what the limitations are on being able to  
> exchange taxonomic information with the DwC terms?  As far as I can  
> tell, you can exchange fairly complex taxonomic information short of  
> concept-to-concept relations and I find the DwC-with-extensions  
> approach we are using to exchanging information tied to taxa (not  
> instances of taxa) to be a nice and practical compromise between  
> complexity and practicality.   My understanding is that the IPT can  
> output TCS/RDF for those who want it.   I am personally very happy  
> to see the DwC taxon terms added.  Finally I can provide format  
> specifications that biologists can understand.
> David Remsen
> On Apr 25, 2009, at 9:52 AM, Kevin Richards wrote:
>> I see the ontology as a model of ALL (hopefully, eventually all)  
>> the data in our domain of biodiversity informatics.
>> I would love to see it as a standard (at the least it might give it  
>> a bit more clout).
>> I agree that the ontology is useful to tie other TDWG schemas  
>> together, using it as a core/master model.  I would be happy to see  
>> it used for ALL tasks within TDWG, but I understand the usefulnes  
>> of the more specific schemas/standards - horses for courses.
>> If I understand Stan here, I agree with him about the dubious use  
>> of DwC for representing Taxon Concepts/Names.  As far as I know, it  
>> was really intended as a transfer standard for observation  
>> records??  It contains very limited taxon information!  It really  
>> is not a overly difficult job to use a more suitable schema/ 
>> ontology.  I think the popularity of Darwin Core is due to its  
>> simplicity - and I wonder if what Roger is proposing will help with  
>> this - ie an XML implementation of the ontology as well as an RDF  
>> version.  This will allow people to create very simple XML  
>> documents with reasonably simple/flat data, eg an xml document of  
>> TaxonName entities, with perhaps 6 or 7 or so key fields - even  
>> simpler than DwC.   :-)
>> Kevin
>> From: tdwg-tag-bounces at lists.tdwg.org [tdwg-tag-bounces at lists.tdwg.org 
>> ] On Behalf Of Blum, Stan [sblum at calacademy.org]
>> Sent: Saturday, 25 April 2009 6:12 a.m.
>> To: Technical Architecture Group mailing list; exec at tdwg.org
>> Subject: Re: [tdwg-tag] darwin core terms inside tdwg ontology
>> From: tdwg-tag-bounces at lists.tdwg.org on behalf of John R. WIECZOREK
>> Sent: Fri 2009-04-24 8:58 AM
>> To: Roger Hyam
>> Cc: Technical Architecture Group mailing list
>> Subject: Re: [tdwg-tag] darwin core terms inside tdwg ontology
>> Anything I should do on the DwC side in anticipation of harmony?
>> http://rs.tdwg.org/dwc/terms/index.htm#theterms
>> ===========================================================
>> John,
>> At some point, all or (most) of the DarwinCore terms need to be  
>> added to the TDWG ontology.
>> But having said that, I also need to say that I'm uncomfortable with:
>> 1) The current state of the TDWG ontology (primarily the naming  
>> conventions; lets just use terms names), and our understanding of  
>> the role it plays in TDWG and how it will be managed (entry of  
>> terms, integration of terms into the conceptual [is-a / has-a]  
>> relationships to other terms); and
>> 2) the fact that the new DarwinCore straddles or overlaps the roles  
>> of an ontology and an application schema.
>> I understood the past TAG roadmaps to indicate that we were  
>> adopting an approach in which the TDWG Ontology would be a  
>> repository for data concepts that are present in (or implied by)  
>> TDWG standards; and that real data transmission would be  
>> accomplished with application schemas.  The ontology itself would  
>> not be a standard, but would be a tool that helps integrate  
>> standards.  I thought our standards would be created to function as  
>> application schemas or components of application schemas (as in the  
>> DwC and its extensions).  I am now pretty confused.  I'd like to  
>> hear the rationale for combining taxonomic name/concept with  
>> organism occurrence.  I haven't gone over all the existing docs, so  
>> apologies if I've missed that, but I think it's confusing   that a  
>> (new) DarwinCore record could be either a taxonomic name or an  
>> organism occurrence, or maybe something else.  Maybe I'm too  
>> attached to object orientation and just don't GET the semantic web,  
>> but it feels to me like we are stepping into squishy ground.
>> Also, I the the DCMI maintenance procedures are also more  
>> appropriately applied to the ontology than a TDWG standard.  The  
>> existing process for ratifying TDWG standards and the procedure in  
>> the DwC seem to be pretty explicitly in conflict; one can change  
>> the other cannot (without becoming another thing).
>> Is anyone else having these same trepidations?  I don't think I've  
>> been as much of a Rip Van Winkle as Jim Croft, but I clearly missed  
>> some important shifts.
>> -Stan
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