[tdwg-tag] darwin core terms inside tdwg ontology

John R. WIECZOREK tuco at berkeley.edu
Sat May 2 05:42:42 CEST 2009

OK, so it took four days, not one or two, but it wasn't for lack of effort.

The version of DwC addressing the peer review comments are now on the
official site at http://rs.tdwg.org/dwc/index.htm and submitted to the
standards track.

If I didn't still have to pack to go to Argentina in the morning I
might be tempted to address some of the concerns that have arisen.
That'll have to wait. Have fun with it.

On Mon, Apr 27, 2009 at 6:25 PM, John R. WIECZOREK <tuco at berkeley.edu> wrote:
> Please note again that at this moment the resources Stan mentioned are
> not in sync because I am finishing the revision based on peer review.
> When that is done (in a day or two) they will be in sync, and that
> state will be versioned and sent as a package back to the editor.
> On Mon, Apr 27, 2009 at 6:22 PM, Blum, Stan <sblum at calacademy.org> wrote:
>> Please note, the most current draft of the DarwinCore is:
>>   here http://code.google.com/p/darwincore/ and
>>   here http://rs.tdwg.org/dwc/index.htm,
>>   not here
>> http://wiki.tdwg.org/twiki/bin/view/DarwinCore/DarwinCoreDraftStandard),
>> My primary concern with the latest draft is the absence of an explicit class
>> identifier (and an implicit class definition) that indicates what kind of
>> data object the sender is transmitting.  If an indexer/aggregator is
>> indexing multiple kinds of resources, as GBIF is, and a publisher provides a
>> record with these elements [ScientificName, ScientificNameAuthorship,
>> NamePublishedIn, and Country], how should the indexer interepret this
>> record?  Is it an organism occurrence record, an authoritative taxonomic
>> record (the country name indicating the entire known range of the taxon), or
>> part of a taxonomic checklist for that country?  The term/element
>> [BasisOfRecord] is the first step in narrowing the possible meanings, but
>> it's the only step and it appears not to be a required step.  (I interpret
>> the "Status: recommended" to mean that it's optional.)   At a minimum,
>> BasisOfRecord should be required.  It would still be possible to publish
>> garbage (at least hard to interpret records) because our tools don't
>> constrain structure, and there isn't (yet) any guidance controlling the
>> structures for different classes of objects.
>> The new GBIF Internet Publishing Toolkit (IPT) supports one-to-many
>> relationships among a series of flat tables and looks like it's going to
>> make it easier to transmit more complicated data than we were doing with
>> DiGIR and TAPIR.  In conjunction with this new expanded bag of elements we
>> could see a lot more complex data get published.  If I may use a skiing
>> metaphor, we've been on the bunny slopes (for beginners) up until now.  The
>> new DarwinCore looks like a nicely groomed black diamond slope, but we
>> haven't had any lessons or even watched anyone else do what we're going to
>> attempt.  I think we're going to end up in a heap at the bottom of the hill,
>> and the aggregators are going to have to sort it out.  ( Woohoo! Extreme
>> biodiversity informatics! )
>> Finally, I did not mean to say that the Ontology should not be ratified, as
>> in not supported; what I meant was that it should not be a standard because
>> we will want to change its contents without versioning the ontology as a
>> whole.  (Also, its not an application schema, so it can't be used directly
>> unless we venture into somewhat uncharted territory.)  Its role is to help
>> us keep our application schemas coordinated.
>> The earlier versions of the DarwinCore (or our protocols, or the way we used
>> them together) were too limiting (see Greg's comments); this version allows
>> terms to be combined in nonsensical ways.  It could make life very difficult
>> for data integrators.
>> I think the bottom line is that we URGENTLY need a similar concerted effort
>> to advance the TDWG (biodiversity informatics) ontology, and a companion set
>> of application schemas coming forward from the collections, marine biology,
>> paleo, observation, taxon-name-concept groups as soon as possible.
>> -Stan
>> -----Original Message-----
>> From: Chuck Miller [mailto:Chuck.Miller at mobot.org]
>> Sent: Monday, April 27, 2009 7:22 AM
>> To: Kevin Richards; Blum, Stan; Technical Architecture Group mailinglist;
>> exec at tdwg.org
>> Subject: RE: [tdwg-tag] darwin core terms inside tdwg ontology
>> Kevin,
>> I agree with you and Stan that the ontology is useful to all schemas.  It
>> seems to me that a “TDWG Ontology” is a totally new and different kind of
>> thing than all the data exchange standards of the prior 10 years – DwC, SDD,
>> TCS, etc.  But, it is a very useful and important new kind of thing that
>> should be part of the TDWG standards architecture. It challenges prior
>> thinking about the nature of TDWG standards to grasp what standardizing on
>> an ontology means.  But, I think it’s what is needed.
>> If TDWG standardized on one Ontology, then the vocabulary of all data
>> exchange could be standardized on it.  Then all TDWG standards could be
>> revised over time to comply to that vocabulary standard, including DwC.
>> Stan said: “ I'd like to hear the rationale for combining taxonomic
>> name/concept with organism occurrence.” An occurrence record generally has
>> an organism’s name associated with it in the real world. It is necessary and
>> inevitable that vocabulary about organism names will be used in an
>> occurrence data exchange schema like DwC. We have been stymied with this
>> idea for years. A standard Ontology/vocabulary for the elements of name
>> information needed to be associated with an occurrence, or a description, or
>> a taxon concept would go a long way toward solving this duality.  The
>> “standard vocabulary” would not be standardized within DwC but it would be
>> used in DwC.
>> Of course there is the problem of the hundreds of installations of DiGIR
>> that use DwC “classic” and are no doubt not going to change for a long
>> time.  I think they just have to be accepted and worked around going
>> forward.  It’s impractical to think of anything else.  But, the past should
>> not roadblock the future and we need to get moving toward that future.
>> Stan thinks that the Ontology is not appropriate for TDWG ratification.  Why
>> not?  Change has to start somewhere. Yes, other standards would probably be
>> in conflict if the Ontology were ratified, but I think we want to ultimately
>> have consistency across all the standards and that means there has to be
>> change going forward.  I think a ratified TDWG Ontology would provide the
>> foundation upon which to start building those changes.
>> Chuck
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