[tdwg-content] Occurrences, Organisms, and CollectionObjects: a review

"Markus Döring (GBIF)" mdoering at gbif.org
Tue Sep 13 18:59:12 CEST 2011

Hi Steve,
I agree this is a good thing to me more clear about what an occurrence actualize is and I would't disagree with the proposed 3 classes. Still there is a drastic change in semantics of an existing term Occurrence and I would feel more comfortable if we can tell those different usages apart. If thats via a namespace based versioning of (all?) darwin core terms, through the use of a different term name or sth else I don't know. 

Don't you think this an issue? Would you also change an owl ontology class definition in the same way and would't that be harmful to existing instances?


> With regards to Markus' concern about whether people will be able to know whether somebody is talking about a "new-style" Occurrence or an "old" Occurrence, I would assert that the "old" Occurrence didn't really have a clear meaning.  If you review the summary of the discussion on Occurrence, you can see that it was used to mean at least three different kinds of "things" by different people.  What John is actually doing with his proposal is to add clarity about what an Occurrence is where it didn't exist before.  I think that is a good thing.  If, by the "old" kind of Occurrence people are meaning that Occurrence is a fancier name for PreservedSpecimen (which I believe is how some people in the museum community are thinking of it), then I would say that such a characterization is incorrect (based on the apparent consensus) and that clarifying the incorrectness of that view is a really good thing.
> Steve
> Éamonn Ó Tuama (GBIF) wrote:
>> It would be good to hear from someone who is familiar with the work going on in the Observations Task Group and could explain how a generic model for observations/measurements (e.g. OBOE) might help sort out these issues. It seems to me that we are trying to build in an ad-hoc manner an increasingly complex model on top of DwC which is really just a glossary of terms. That does not seem like a good approach - but I'm no modeller :-) 
>> _Éamonn
>> -----Original Message-----
>> From: Dag Endresen (GBIF) [
>> mailto:dendresen at gbif.org
>> ] 
>> Sent: 13 September 2011 12:18
>> To: "Markus Döring (GBIF)"
>> Cc: 
>> tdwg-content at lists.tdwg.org
>> ; Éamonn Ó Tuama
>> Subject: Re: [tdwg-content] Occurrences, Organisms, and CollectionObjects: a review
>>  Hi Markus,
>>  I believe that the discussion here originates from the view that the 
>>  "CollectionObject"/"Sample" is a different thing from the "Organism" - 
>>  and that there can be a relationship between CollectionObjects/Samples 
>>  and Organisms that could be difficult to describe if these things are 
>>  identified as the same think (occurrenceID). Do you think that the 
>>  "Occurrence" would be seen as a thing different from the proposed 
>>  CollectionObject/Sample and Organism - or as a super-class that would 
>>  include CollectionObjects/Samples and Organisms? Would the semantics of 
>>  Occurrence change?
>>  I fully share your view that the Darwin Core Archive (DwC-A) would not 
>>  be suited to share the full complex relationship between entities - even 
>>  if persistent identifiers would be used. However if we start to describe 
>>  and include other things (core types) than only the taxon and 
>>  occurrences then perhaps the DwC-A could be a useful way to provide a 
>>  simple list of these entities? This could perhaps provide easier 
>>  indexing and discovery of these new entities?
>>  Dag
>>  On Tue, 13 Sep 2011 10:03:00 +0200, Markus Döring (GBIF) wrote:
>>> I have to say that the change in semantics to the Occurrence class
>>> makes me a bit nervous.
>>> Can someone try help fighting my fears?
>>> DarwinCore has no versioning of namespaces, so there is no way for a
>>> consumer to detect if its an old style Occurrence or a new one. I am
>>> currently parsing various RSS feeds and even though its a mess having
>>> to parse 10 different styles I am glad that at least the designers
>>> made sure they all have their own namespace! Also removing or 
>>> renaming
>>> terms might cause serious problems. Would discrete versions of dwc
>>> with their own namespace hurt?
>>> Another observation relates to dwc archives and its star schema. As
>>> an index to data that has been flattened there is no problem with 
>>> more
>>> classes and core row types, but if you want it as a way to transfer
>>> complete normalized data it will not work. But that never really was
>>> the intention and I simply wanted to stress that fact.
>>> Markus
>>> On Sep 9, 2011, at 4:52 PM, Steve Baskauf wrote:
>>>> Richard Pyle wrote:
>>>>> I'm also wondering if we necessarily need to "break" the 
>>>>> traditional view of
>>>>> the "Occurrence" class in order to implement Organism and 
>>>>> CollectionObject.
>>>>> As long as we keep in mind that DwC is a vocabulary of terms 
>>>>> focused on
>>>>> representing an exchange standard (rather than a full-blown 
>>>>> Ontology),
>>>>> perhaps Occurrence records can continue to be represented in the 
>>>>> traditional
>>>>> way as "flat" content, but the Organism and CollectionObject 
>>>>> classes allow
>>>>> us to present data in a somewhat more "normalized" way in those
>>>>> circumstances that call for it (e.g. tracking individuals or groups 
>>>>> over
>>>>> time [Organism], or managing fossil rocks with multiple taxa
>>>>> [CollectionObject] -- to name just two).
>>>> I've been thinking about this issue of "backward compatibility" with
>>>> respect to Occurrences if the CollectionObject/Sample/Token/whatever
>>>> class is adopted.  I really don't think it is going to be as big of 
>>>> a
>>>> deal as people are making it out to be.
>>>> It seems to me that the main problems arise in two areas: when one 
>>>> wants
>>>> to be clear about typing and when one wants to express relationships 
>>>> in
>>>> a system where it is possible to do through semantics (like RDF).  
>>>> In
>>>> that kind of circumstance, it's bad (oh yeh, I forgot - the term is
>>>> "naughty") to say  something like
>>>> resourceA hasOccurrence resourceB
>>>> when resourceB isn't actually an Occurrence.   "Wrong" typing also
>>>> happens all the time because the classes don't exist (yet) to do the
>>>> typing correctly.  As a case in point, in the Morphbank system, I 
>>>> have
>>>> multiple images of the same tree.  In that system the tree is typed 
>>>> as a
>>>> "specimen".  That is totally wrong because the tree isn't a 
>>>> specimen,
>>>> but what else is it going to be typed as?  There isn't (yet) an
>>>> appropriate class to put it in.
>>>> Although these two problems (wrong typing and using a term with the
>>>> wrong kind of object which are actually different manifestations of 
>>>> the
>>>> same class-based problem) are naughty, realistically very few people 
>>>> are
>>>> actually using a system that is "semantic-aware" (e.g. serving and
>>>> consuming RDF) so right now making those mistakes doesn't really 
>>>> "break"
>>>> anything.  Most data providers are using traditional databases or 
>>>> even
>>>> Excel spreadsheets where the DwC terms are just column headings with 
>>>> no
>>>> real "meaning" other than what the data managers intend for them to
>>>> mean.  So if a manager has a table where each line contains a record 
>>>> for
>>>> a specimen and has a column heading for a column entitled
>>>> "dwc:catalogNumber", there isn't really anything other than an idea 
>>>> in
>>>> the manager's head that the catalogNumber is a property of a 
>>>> specimen or
>>>> Occurence or CollectionObject.  If each line in the database table 
>>>> is
>>>> "flat" such that one specimen=one CollectionObject=one Occurrence, 
>>>> all
>>>> that is required to make catalogNumber be a property of a
>>>> CollectionObject instead of an Occurrence is a different way of 
>>>> thinking
>>>> in the managers mind because there are really no semantics embedded 
>>>> in
>>>> the table.  We are already doing this kind of mental gymnastics with
>>>> existing classes like dwc:Identification .  If our hypothetical 
>>>> database
>>>> manager has a column heading that says "dwc:identifiedBy" in the
>>>> specimen table, that is really a property of dwc:Identification, not
>>>> dwc:Occurrence but again that is a distinction that is only going to 
>>>> be
>>>> made in the manager's mind.  Making the distinction really only 
>>>> becomes
>>>> an issue when the database stops being "flat" for a particular
>>>> relationship, e.g. if the database wants to allow multiple
>>>> Identifications per specimen record.  Then the database structure 
>>>> must
>>>> be changed accordingly to accommodate that "normalization".
>>>> What we have here at the present moment is a situation where data
>>>> providers don't have any way to have anything but "flat" records 
>>>> where 1
>>>> specimen=1 Occurrence=1 Organism.  By adding the Organism and
>>>> CollectionObject classes, we allow people who need or want to have 
>>>> less
>>>> "flat" (=more "normalized") databases to have something to call the
>>>> entities that are represented by the new tables they create to 
>>>> handle
>>>> 1:many relationships instead of 1:1 relationships.  Anybody who only
>>>> cares about 1:1 relationships really doesn't need to worry about the
>>>> fact that the new class exists, just as people currently don't have 
>>>> to
>>>> worry about the Identification class if they only allow one
>>>> Identification per specimen in their database.
>>>> So I guess what I'm saying is that if a database manager has a table
>>>> labeled Occurrence, they really don't have to freak out if we now 
>>>> tell
>>>> them that their table actually should be labeled CollectionObject as
>>>> long as there is only one CollectionObject per Occurrence.  They 
>>>> didn't
>>>> freak out before when we told them that they should call their table
>>>> "Occurrence" instead of "Observation" or "Specimen" in 2009, did 
>>>> they?
>>>> I think what I'm saying here is what Rich was trying to say in the
>>>> paragraph I quoted, but I'm not sure.
>>>> Steve
>>>> --
>>>> 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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