[tdwg-tag] darwin core terms inside tdwg ontology

Roger Hyam rogerhyam at mac.com
Mon Apr 27 16:06:12 CEST 2009

I am posting this for Bryan as his message seems to have bounced. I  
leave our comments in as they are informative re identifiers.


Begin forwarded message:

> From: "P. Bryan Heidorn" <pheidorn at illinois.edu>
> Date: 27 April 2009 14:36:31 BST
> To: Roger Hyam <roger at hyam.net>
> Subject: Re: Auto-discard notification
> No, I did not know it bounced. Can you forward for me while I figure  
> it out? Univ of Illinois changed its domain which might be the  
> problem... case in point for the need for stable identifiers that  
> are not university domain names!
> Thanks,
> Bryan
> -- 
> --------------------------------------------------------------------
>    P. Bryan Heidorn
>   Graduate School of Library and Information Science
>   University of Illinois at Urbana-Champaign
>   pheidorn at illinois.edu
>   http://www.uiuc.edu/goto/heidorn
> On Apr 27, 2009, at 4:36 AM, Roger Hyam wrote:
>> Hi Bryan,
>> Did you know this one bounced? Did it get through eventually?
>> Roger
>> Begin forwarded message:
>>> From: tdwg-tag-bounces at lists.tdwg.org
>>> Date: 25 April 2009 15:04:03 BST
>>> To: tdwg-tag-owner at lists.tdwg.org
>>> Subject: Auto-discard notification
>>> The attached message has been automatically discarded.
>>> From: "P. Bryan Heidorn" <pheidorn at illinois.edu>
>>> Date: 25 April 2009 15:03:33 BST
>>> To: Technical Architecture Group mailing list <tdwg-tag at lists.tdwg.org 
>>> >
>>> Cc: Stan Blum <sblum at calacademy.org>, exec at tdwg.org, Kevin  
>>> Richards <RichardsK at landcareresearch.co.nz>
>>> Subject: Re: [tdwg-tag] darwin core terms inside tdwg ontology
>>> Some taxon concept/name is always part of a Darwin Core record and  
>>> in the loose constraints of DwC that can just be a name string but  
>>> (typing back to the dreaded LSID/GUID argument) it could be a term  
>>> that is "defined" within the broader taxon concept world. This can  
>>> of course be _optional_ and when used might just be a string plus  
>>> a reference to the other standard where it is defined. So you can  
>>> just say "Quercus alba" or say Quercus alba plus a taxonomic  
>>> identifier that would lead to the particular concept of Quercus  
>>> alba you mean in this case with relationships to synonyms,  
>>> historical usage etc, but none of those relationships are in the  
>>> DwC record.
>>> A user of a collection of such records could then decide if the  
>>> string "Quercus alba" is a sufficient qualifier for the task at  
>>> hand or if a particular circumscription resolved by the taxonomic  
>>> reference is required. For example, if you are really interested  
>>> in all oaks you could build a parser that reads the records and  
>>> decides that the word "Quercus" means oak or you could choose to  
>>> use the taxonomic LSID/QUID to have the computer go to a taxonomic  
>>> resolution service that would be able to answer if or if not this  
>>> is a Quercus.
>>> The same type of mechanism could be used for locality.
>>> Any of this requires just an optional side element on fields  
>>> identifying two things. It need not be a globally accepted  
>>> standard if there are two components. One component that is an  
>>> identifier and another identifying the resolution context. That  
>>> context could be the "Backwoods Arboretum Shop and Taxonomic  
>>> Authority Database (BASTARD)"  that defines everything by its  
>>> historical woodworking use or the context can be a  TDWG approved  
>>> taxonomic resolution service respected by systematists (but not  
>>> necessarily wood workers or conservationists).
>>> --------------------------------------------------------------------
>>> P. Bryan Heidorn, Program Director
>>> Division of Biological Infrastructure Rm. 615 N
>>> National Science Foundation
>>> 4201 Wilson Blvd.
>>> Arlington VA 22230
>>> (703) 292-8470
>>> pheidorn at nsf.gov
>>> On Apr 25, 2009, at 2:52 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.  
>>>> 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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