[tdwg-content] FW: [STDTRK] Request for a Decision for Public Review of DarwinCore Draft Standard

John R. WIECZOREK tuco at berkeley.edu
Wed Aug 26 18:01:50 CEST 2009

Comments inline.

On Tue, Aug 25, 2009 at 6:20 PM, Donald Hobern<dhobern at gmail.com> wrote:
> Thanks, John.
> I must still be missing something on the definitions of Event, etc.  Where
> are the definitions you quote below?

They are modifications of the most recently published definitions as
an attempt to address the issues you raised. I wanted to see if the
new ones were adequate.

> http://rs.tdwg.org/dwc/terms/type-vocabulary/index.htm has definitions like
> the rather circular "A resource describing an occurrence" and the cryptic "A
> non-persistent, time-based occurrence" - which raises a whole new problem
> because (at least as I understand it) "occurrence" in this definition means
> something more general than "occurrence" as used for the Occurrence resource
> type.

The definition "A resource describing an occurrence" is a direct copy
of the definition of dcterms:Event (Dublin Core). Originally I did
nothing to change definitions of terms adopted from Dublin Core, but
as discussion has progressed, and precisely because Dublin Core is
purposely vague, I decided it would be useful to add "For Darwin Core,
..." to the definitions to describe how they are intended to be used
in biodiversity contexts. Though the new definitions are more
explicit, I don't believe they warrant new term refined from the
original Dublin Core terms. So again, the proposed definitions are:

dcterms: Event - "A non-persistent, time-based occurrence. For Darwin
Core, a resource describing an instance of the Location class."

Event (class) - "The category of information pertaining to an event
(an action that occurs at a place and during a period of time)."

dwctypes:Occurrence - "A resource describing an instance of the
Occurrence class."

Occurrence (class) - "The category of information pertaining to
evidence of an occurrence in nature, in a collection, or in a dataset
(specimen, observation, etc.)."

> As for the question whether examples or lengthier definitions would be good,
> I tend to think that in Dublin Core world, examples would only be a sample
> of possible uses within the range intended by a definition and that they may
> therefore help to steer people towards appropriate use but cannot introduce
> any constraints which could help us to tighten up cross-resource data
> integration.

Exactly, and that's what I was trying to do with Darwin Core terms -
to constrain their semantics only as far as possible given the range
of uses to which they may be put.

> The scientific name example is a clear case.  I have a feeling
> that the semantics for this element as it stands right now (spanning
> Occurrence and Checklist uses) imply a very general definition like "the
> scientific name which is connected with this item" with the nature of that
> connection unstated or at best covered by an implicit "it should be obvious
> in each case what we expect to see in this field".  I admit that abuses of
> this term to do things we don't expect seem unlikely - someone giving
> ScientificName="Homo sapiens" because that is the scientific name for the
> collector, or something.  However the laudable wish not to over-restrict the
> use of these terms does have the corollary that consumers of data always
> have to be aware that a provider may use the terms in semantically
> incompatible ways.  If we knew that Occurrence->ScientificName was defined
> to mean something like "the scientific name used for the most refined taxon
> concept to which the specimen or observation has been identified", and that
> Occurrence->DecimalLatitude and Occurrence->DecimalLongitude related to the
> site at which the observation was made or the specimen was collected, we
> would more or less have a contract that Occurrence records containing a
> ScientificName, Latitude and Longitude were explicit assertions that an
> individual of the given taxon concept had indeed been found at those
> coordinates.  If we have no assurance that the ScientificName relates to the
> identification of the specimen/observation, or that the coordinates relate
> to the observing/collecting site (rather than say the coordinates for the
> collection building), we always have some latent uncertainty about what is
> asserted.

Agreed. My original naive attempt to solve the problem was to assign
terms to domains (classes), but as Hilmar pointed out, that would have
inappropriate inference consequences. It also doesn't solve the
problem when a term could describe (be a property of) more than one
class. The other attempt to clarify the semantics was the
recommendation of the use of the dcterms:type term to define which
class (Occurrence, Location, etc.) a record represents. So, if the
dcterms:type was Occurrence, you could infer that the scientificName
in the record was for an Identification of an Occurrence because of
the natural relationship between Taxon, Identification, and
Occurrence. Those relationship can be made explicit with the TDWG
Ontology, but it wasn't Darwin Core's place, in my mind, to finish the
Ontology work. I think Darwin Core is safe without doing so, and will
not be adversely affected when the Ontology work is done as it will
only really affect the RDF.

Nevertheless, you are right, the uncertainty is there. But I think we
can avoid most problems simply by describing what a term would mean in
a given context. That's what I tried to do in the Definition for

"The taxon name (with date and authorship information if applicable).
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."

> Very best wishes,
> Donald

The same! Thanks for the commentary.


> -----Original Message-----
> From: gtuco.btuco at gmail.com [mailto:gtuco.btuco at gmail.com] On Behalf Of John
> Sent: Wednesday, 26 August 2009 10:52 AM
> To: Donald Hobern
> Cc: tdwg-content at lists.tdwg.org
> Subject: Re: [tdwg-content] FW: [STDTRK] Request for a Decision for Public
> Review of DarwinCore Draft Standard
> Finally getting around to some older messages in an effort to finish
> up the public review of Darwin Core.  Comments inline.
> On Sun, Jul 26, 2009 at 6:03 PM, Donald Hobern<dhobern at gmail.com> wrote:
>> At Gail's request, I'm forwarding some discussion between Renato and
> myself
>> on the Darwin Core draft
>> Thanks,
>> Donald
>> Renato,
>> You are quite right - domains and ranges may cause us more problems.  At
>> very least it may be sensible for these to be things which get asserted
>> within other OWL files used within specific projects to govern their own
>> application models and inference rules.
> Domains have been removed for all terms. A new attribute
> "organizedInClass" is used for term organizational maintenance.
>> In the end my concerns are really around the need for more clarity on the
>> way that the dcTerms:type values are to be used and how this relates to
> past
>> use of Darwin Core.  I'm not sure I ultimately disagree with any of the
>> decisions made.  However I still cannot find any actual definition for the
>> Occurrence and Event cases to explain what situations they are intended to
>> cover.  Unless we take the time to define the intended scope for all our
>> terms and property values, it is hard to predict whether data from
> multiple
>> sources can be expected to be suitable for combination.
> I agree that there a great challenge for the new Darwin Core will be
> to make sure that publishers and consumers do not mix apples with
> oranges, unless their particular use case warrants doing so.
> What is missing from the explanations at
> http://rs.tdwg.org/dwc/terms/type-vocabulary/index.htm? Or from the
> definitions:
> Event - The category of information pertaining to an event (an action
> that occurs at a place and during a period of time).
> Occurrence - The category of information pertaining to evidence of an
> occurrence in nature, in a collection, or in a dataset (specimen,
> observation, etc.).
> dcmitype:Event - A non-persistent, time-based occurrence. For Darwin
> Core, a resource describing an instance of the Location class.
> dwctype:Occurrence - A resource describing an instance of the Occurrence
> class.
>> The scientific name case is one example.  I would like an explicit
> statement
>> that it means nothing more than "the name of a taxon (somehow) associated
>> with this record" rather like a Dublin Core subject.  If, e.g. in the case
>> of an Occurrence record, it is meant to be a statement that a taxon was
>> actually recorded at the location on the given date, we may need to be
> more
>> explicit.  I'm still not comfortable with leaving these things unstated.
> Would clarity be best served by examples? Or by lengthier definitions?
> I have adopted the Dublin Core tendency toward brevity wherever
> possible, not pretending to know the scope of usage of a term in the
> long run. We have the supplementary wiki at our disposal to clarify as
> much as necessary. It has only just begun to be filled with useful
> material that I happened to feel qualified to provide based on my
> experience. I think we could do a lot more with it, and not affect the
> standard while doing so.
>> I must however emphasise that I am very happy to see how much work has
> gone
>> into this revision and the level of forethought in addressing many
> important
>> issues.
> Much appreciated, sincerely.
> John
>> Donald
>> -----Original Message-----
>> From: renato at cria.org.br [mailto:renato at cria.org.br]
>> Sent: Friday, 24 July 2009 7:04 AM
>> Subject: RE: [STDTRK] Request for a Decision for Public Review of
> DarwinCore
>> Draft Standard
>> Hi Donald,
>> Scientific name is precisely the kind of term that I feel should be
>> generic. There's an ancient search interface at CRIA that illustrates the
>> use case "give me everything you have related with this scientific name":
>> http://names.cria.org.br/index?lang=en
>> (check all checkboxes at the bottom of the page)
>> In SPARQL I think the query would simply look like:
>> SELECT ?x
>> WHERE { ?x  <http://rs.tdwg.org/ont/scientificName>  "some name" }
>> instead of repeating the same condition for every possible combination of
>> domain#property.
>> Most id properties (collectionID, locationID, etc.) should also probably
>> be "domainless" since they can appear in objects from many different
>> classes.
>> Best Regards,
>> --
>> Renato
>>> Looking at what is in the DwC document, I think my concerns are with
>>> plans to use DwC for checklist data rather than the DwC proposal itself,
>>> but the problem issue may be in there somewhere.  Here are some comments
> I
>>> sent earlier:
>>> I need to take some time and provide some comments on the use of Darwin
>>> Core for non-occurrence data.  In general I believe we need to be moving
>>> towards simple class properties with tightly defined explanations of the
>>> expected content and format.  This use of DwC seems to me to be a
>>> significant dilution of the semantic content of these properties.  If DwC
>>> is an object property just for a taxon occurrence, the explanation of
>>> dwc:ScientificName would be something like "The scientific name assigned
>>> to the taxon to which the recorded organism was identified".  If we
> extend
>>> it to cover taxon occurrences, checklist entries and all the other things
>>> that people seem to have in mind, the explanation would reduce to "The
>>> scientific name which is associated with this record".  In practice few
>>> people will be stumbled, but I really don't like it.  It would be so easy
>>> just to have chk:ScientificName as well as dwc:ScientificName and to keep
>>> the semantics explicit. This becomes particularly problematic when we
>>> play with RDFS and OWL. We could choose to define the
> "dwc:ScientificName"
>>> property to have a domain restricted to TaxonOccurrence, allowing a
>>> reasoner > to infer that objects with this property can be treated as
>>> TaxonOccurrence records.  With the diluted dwc:ScientificName all we can
>>> infer is that the object is a
>>> ThingWithSomethingToDoWithTheBiologicalDomain.
>>> Donald
>> --
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