[tdwg-tag] darwin core terms inside tdwg ontology

John R. WIECZOREK tuco at berkeley.edu
Tue Apr 28 03:25:54 CEST 2009

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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