[tdwg-content] What is dwc:basisOfRecord for?
Steve Baskauf
steve.baskauf at vanderbilt.edu
Tue Nov 2 04:52:59 CET 2010
I'm having problems with this in several ways, but I think the main one
at the moment is saying that PreservedSpecimen is a rdfs:subClassOf
Occurrence. If we do that, then we say that all instances of
PreservedSpecimen are also instances of Occurrence. Based on the
discussion that took place in the thread about what is an Occurrence, I
thought the consensus was that the Occurrence was a separate resource
from the token that documents it. If that is true, then it does not
make sense to say that a PreservedSpecimen is an Occurrence. Rather, in
RDF I would say:
<rdf:Description rdf:about="http://something.org/12345#occurrence">
<rdf:type rdf:resource="http://rs.tdwg.org/dwc/dwctype/Occurrence"/>
... other properties of the Occurrence such as dwc:recordedBy ...
</rdf:Description>
<rdf:Description rdf:about="http://something.org/12345#specimen">
<rdf:type
rdf:resource="http://rs.tdwg.org/dwc/dwctype/PreservedSpecimen"/>
... other properties of the specimen such as dwc:preparations ...
</rdf:Description>
If it is NOT true that an Occurrence is a separate resource from the
token, then do we want to say:
<rdf:Description rdf:about="http://something.org/12345">
<rdf:type rdf:resource="http://rs.tdwg.org/dwc/dwctype/Occurrence"/>
<rdf:type
rdf:resource="http://rs.tdwg.org/dwc/dwctype/PreservedSpecimen"/>
... other properties of the Occurrence such as dwc:recordedBy ...
... other properties of the specimen such as dwc:preparations ...
</rdf:Description>
?
If we go by this approach, (as you seem to suggest by
Why not? Nothing in Darwin Core says that you can't create a schema in
which an Occurrence is supported by multiple "tokens", each with its own
basisOfRecord. Of course, Simple Darwin Core doesn't support that, and
maybe that's where these perceptions of inadequacy come from.
) then that suggests to me that we could say that an Occurrence which is
documented by both a specimen and an image would be described as:
<rdf:Description rdf:about="http://something.org/12345">
<rdf:type rdf:resource="http://rs.tdwg.org/dwc/dwctype/Occurrence"/>
<rdf:type
rdf:resource="http://rs.tdwg.org/dwc/dwctype/PreservedSpecimen"/>
<rdf:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/>
... other properties of the Occurrence such as dwc:recordedBy ...
... other properties of the specimen such as dwc:preparations ...
... other properties of the image such as dcterms:rights,
mrtg:caption, etc. ...
</rdf:Description>
and you get odd statements like saying that occurrences have copyrights,
images have preparations, etc.
Ugh. It gets even worse. I just looked at
http://darwincore.googlecode.com/svn/trunk/rdf/dwctype.rdf which I guess
is the official RDF description of the dwctypes. According to it, not
only is PreservedSpecimen a subclass of Occurrence, but Occurrence is a
subclass of http://purl.org/dc/dcmitype/Event . That means that not
only is an instance of PreservedSpecimen an instance of Occurrence, but
it is also by inference an instance of Event, (even if we don't
explicitly state that using rdf:type). Thus the resource I've
represented in RDF above is all at once an event, an occurrence, a
specimen, and an image. That really mixes up entities that we seemed to
be considering separate things in that thread. I guess if this kind of
subclassing is in the RDF, that's the way it is. But I don't like it.
This was all just starting to make sense to me when I had decided that
it was best to go against what I said in the Biodiversity Informatics
paper and separate Occurrences from their tokens. Maybe this separation
only matters if one is trying to clearly define what is a property of
what as in RDF and doesn't matter in databases where you don't really
have to be clear about the subject of properties. But it seems to me
like it's overloading the dwctypes to say that they should both serve as
the way to define they type of a thing (i.e. the class to which the
thing belongs) and to indicate the relationship that some thing has to
something else (i.e. hasASpecimen, hasAnImage, hasAnObservation, etc.)
as one is apparently doing with basisOfRecord. I guess if one objects
to this kind of overloading, one could just use the URIs of the DwC
classes themselves as values for rdf:type rather than using the dwctype
URIs. The RDF there doesn't seem to have any kind of subclassing (but
there is the problem of typing PhysicalSpecimen which is not a generic
DwC class).
By the way, we don't have one DwCType for every DwC (or borrowed Dublin
Core) Class as you said. There are no types for Identification, Event,
and GeologicalContext
Thanks for the explanation - I'll keep trying to understand.
Steve
John Wieczorek wrote: [some pieces cut out to paste above]
> Sorry for the delay. Just back from Tanzania.
>
> The basisOfRecord is meant to classify the content of the resource
> (record) as specifically as possible, in the sense of how the
> contributor of the resource intended for it to be used. The value of
> the basisOfRecord should be based on the most specific Class (a
> DwCtype) of information the resource (record) represents. Thus, if an
> Occurrence record was supported by a PreservedSpecimen as evidence,
> then the record containing the specimen information should have
> PreservedSpecimen as the basisOfRecord. It's still an Occurrence,
> because PreservedSpecimen is a formal refinement of an Occurrence in
> the RDF sense of <rdfs:subClassOf
> rdf:resource="http://rs.tdwg.org/dwc/dwctype/Occurrence"/>. So, your
> example record should have PreservedSpecimen as its basisOfRecord, and
> that means it is an Occurrence record, because all PreservedSpecimen
> records are.
>
> Why have the Occurrence type? For consistency. We have one DwCType for
> every DwC (or borrowed Dublin Core) Class. Yet, we are much more
> interested in the peculiarities of Occurrences than we are in
> different types of, say, Events, because of the implications for their
> use. So we have gone to the effort to create several subclasses of
> Occurrence based on demonstrated requirements.
>
> Why have a basisOfRecord at all? To assist the data consumer to know
> the ways in which the resource (record) might be used. Without the
> basisOfRecord term, the detailed content of the records would have to
> be assessed to assert what the record was about.
>
> Steve said,
> "But realistically, any such table that includes multiple token types
> isn't going to work very well."
>
> and,
>
> "basisOfRecord also has no use for Occurrences that have several
> tokens. Which of the several tokens are we saying is the "basis" of
> the record?"
>
> Why not? Nothing in Darwin Core says that you can't create a schema in
> which an Occurrence is supported by multiple "tokens", each with its
> own basisOfRecord. Of course, Simple Darwin Core doesn't support that,
> and maybe that's where these perceptions of inadequacy come from.
>
>
> On Wed, Oct 27, 2010 at 10:34 AM, Steve Baskauf
> <steve.baskauf at vanderbilt.edu <mailto:steve.baskauf at vanderbilt.edu>>
> wrote:
>
> occurrenceID
> recordedBy
> other Occurrence terms
> preparations
> other specimen-related terms
> basisOfRecord
> http://herbarium.org/12345
> Joe Curator
> ...
> pressed and dried
> ...
> ???
>
>
> OK, above is an example of a database record that I would consider
> typical. The manager has flattened the general model we have been
> discussing to merge the Occurrence resource with the token
> resource since in his/her database no occurrence has any token
> other than a single specimen. So what is the value for
> basisOfRecord: Occurrence or PreservedSpecimen? What I'm getting
> at here is that there seems to be ambiguity as to whether we
> intend for basisOfRecord to represent the type of the record
> (which in this case I would say is Occurrence) or the type of the
> token on which the record is based (which in this case is
> PreservedSpecimen). In that lengthy discussion that happened last
> October, there was discussion of having the proposed recordClass
> represent the type of the overall record (Occurrence, Event,
> Location, etc.) and basisOfRecord representing the type of the
> token or evidence on which an Occurrence record is based
> (PreservedSpecimen). I'm not sure what is intended now.
>
> I see this lack of clarity as being a consequence of the general
> blurring of the distinction between the Occurrence and the
> "token". I feel like there is a general consensus that we need to
> tighten up our definitions regarding Occurrences and their
> evidence even if some people will prefer to continue using the
> "flattened" approach to Occurrences and their tokens illustrated
> above (which they are entitled to do). I don't have a problem
> with the various types that you've listed below. The problem is
> that I don't think the definition of basisOfRecord makes clear how
> it (basisOfRecord) should apply - the definition just says "the
> specific nature of the data record" and that the controlled
> vocabulary of the Darwin Core Type Vocabulary should be used.
> Since the Type Vocabulary includes all of the classes (Event,
> Location, Occurrence, etc.) in addition to the types of "tokens",
> I believe that some users might think that making a statement like
> basisOfRecord="Event"
> is correct. If we intend for basisOfRecord to ONLY apply to
> Occurrences, and for basisOfRecord to ONLY have as valid values
> the types that apply to tokens (i.e. PreservedSpecimen,
> LivingSpecimen, HumanObservation), then we should say so
> explicitly in the definition. If we do not say this, then we end
> up with the kind of ambiguity that I illustrated above.
> basisOfRecord ends up getting "overloaded" to represent general
> classes of records and also to represent the types of tokens.
>
> In addition, I'm not entirely convinced that basisOfRecord
> actually has any use at all. It seems to be intended for
> situations such as I've illustrated above where a database table
> has rows that could contain occurrences documented with different
> types of tokens. Ostensibly, basisOfRecord is needed to tell us
> the type of the token. But realistically, any such table that
> includes multiple token types isn't going to work very well. For
> example, if the table includes Occurrences that are documented by
> specimens, images, and no token/memories (i.e. HumanObservations),
> then it's going to have a bunch of columns that are empty for any
> particular record. The specimens rows won't have anything in the
> image term columns, the images won't have anything in the specimen
> term columns, and the human observations won't have anything in
> either the specimen or image term columns. I think most database
> managers would just include the terms that apply to all
> Occurrences in the Occurrence table and then use identifiers to
> link separate tables for the metadata terms that are specific to
> the various types of tokens. basisOfRecord also has no use for
> Occurrences that have several tokens. Which of the several tokens
> are we saying is the "basis" of the record?
>
> So again, my basic question is not so much about the various types
> and subtypes to which we can refer, but specifically how the
> basisOfRecord term is to be used.
>
> Steve
>
> Blum, Stan wrote:
>> Steve,
>>
>> I'm wasn't involved in those final discussions of dwc:basisOfRecord and the
>> type vocabulary, but I don't see a difficulty. The Dublin Core type
>> vocabulary includes the following:
>>
>> Collection
>> Dataset
>> Event
>> Image
>> InteractiveResource
>> MovingImage
>> PhysicalObject
>> Service
>> Software
>> Sound
>> StillImage
>> Text
>>
>> The Darwin Core types extend that with the three additional types, and with
>> Occurrence being further subtyped with those different kinds of Occurrences.
>>
>> Location
>> Taxon
>> Occurrence
>> PreservedSpecimen
>> FossilSpecimen
>> LivingSpecimen
>> HumanObservation
>> MachineObservation
>> NomenclaturalChecklist
>>
>> Data publishers/providers should categorize their Occurrence data as one of
>> those subtypes (or perhaps another subtype that wasn't included in that
>> list). It's up to the consumer to decide which kind of Occurrence subtypes
>> are appropriate for a particular use.
>>
>> Could you give examples of the inconsistent use of values in basisOfRecord ?
>>
>> Also note, John W. is traveling at the moment. Markus might be able to
>> provide additional thoughts.
>>
>> -Stan
>>
>>
>>
>>
>> On 10/25/10 10:34 PM, "Steve Baskauf" <steve.baskauf at vanderbilt.edu> <mailto:steve.baskauf at vanderbilt.edu> wrote:
>>
>>
>>> OK, I know that this sounds like a stupid question, but I really want
>>> somebody who was involved in the development and maintenance of the
>>> current DwC standard to tell me how the term dwc:basisOfRecord is
>>> supposed to be used (not what it IS - I've seen the definition at
>>> http://rs.tdwg.org/dwc/terms/index.htm#basisOfRecord)? I would like for
>>> the answer of this question to be separated from the issue of what the
>>> Darwin Core type vocabulary
>>> (http://rs.tdwg.org/dwc/terms/type-vocabulary/index.htm) is for.
>>>
>>> I re-read the lengthy thread starting with
>>> http://lists.tdwg.org/pipermail/tdwg-content/2009-October/000301.html
>>> which talked a lot about basisOfRecord and its relationship to other
>>> ways of typing things. I don't want to re-plough that ground again, but
>>> I couldn't find the post that stated what the final decision was. I
>>> remember that there was a decision to NOT create the recordClass term
>>> which was the subject of much discussion.
>>>
>>> I guess my confusion at this point is with the inclusion of both
>>> "Occurrence" and "PreservedSpecimen" in the same list. Let's say that I
>>> have a flat database where I include metadata about the Occurrence (such
>>> as dwc:recordedBy) and the specimen (such as dwc:preparations) in the
>>> same line. What is the basisOfRecord for that line? I would guess that
>>> the "basis of the record" was the specimen. But the line in the record
>>> also represents an Occurrence. It seems like there is a lack of clarity
>>> as to whether basisOfRecord is supposed to indicate the type of the
>>> record (which would be an Occurrence record) or whether it's supposed to
>>> indicate the kind of evidence on which the record is based (which would
>>> be PreservedSpecimen). There have been various times where I've seen a
>>> database record that includes basisOfRecord and it seems to be
>>> inconsistently applied.
>>>
>>> I can see how the Darwin Core type vocabulary could be useful - it
>>> pretty much lays out useful values that one could give for rdfs:type.
>>> But basisOfRecord as a term is confusing me.
>>>
>>> Steve
>>>
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>>
>>
>
> --
> Steven J. Baskauf, Ph.D., Senior Lecturer
> Vanderbilt University Dept. of Biological Sciences
>
> postal mail address:
> VU Station B 351634
> Nashville, TN 37235-1634, U.S.A.
>
> delivery address:
> 2125 Stevenson Center
> 1161 21st Ave., S.
> Nashville, TN 37235
>
> office: 2128 Stevenson Center
> phone: (615) 343-4582, fax: (615) 343-6707
> http://bioimages.vanderbilt.edu
>
>
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--
Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences
postal mail address:
VU Station B 351634
Nashville, TN 37235-1634, U.S.A.
delivery address:
2125 Stevenson Center
1161 21st Ave., S.
Nashville, TN 37235
office: 2128 Stevenson Center
phone: (615) 343-4582, fax: (615) 343-6707
http://bioimages.vanderbilt.edu
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