[tdwg-content] Heretics and illuminati, oh my! [SEC=UNCLASSIFIED]

Steve Baskauf steve.baskauf at vanderbilt.edu
Fri May 6 12:59:29 CEST 2011

Thanks for this helpful suggestion, Paul.  I have a question related to 
what you said.  As a general practice, DSW "imported" class terms from 
DwC to use as the basic classes in the ontology.  This seemed like a 
relatively "safe" thing to do, since the RDF definitions of the class 
terms in DwC don't really say anything restrictive about how they are 
used.  We then basically tried to describe (using properties) how those 
classes were connected and put in some restrictions intended to prevent 
people from calling apples oranges (range/domain restrictions coupled 
with disjoin declarations).  However, we went beyond that in the Taxon 
class.  We declared that dwc:Taxon was equivalent to tc:Taxon (Taxon in 
the TDWG ontology, which is declared within the TDWG ontology to be the 
same thing as tc:TaxonConcept).  Our motivation was to try to add some 
clarity to what exactly the dwc:Taxon class was (that wasn't exactly 
clear to us) and also to avoid having to try to describe the properties 
of the Taxon class since they were already described (to some extent) 
within the TDWG ontology.  However, from what you have said below, it 
sounds like it might have been a better idea to have declared the 
equivalency of dwc:Taxon and tc:Taxon outside of the main ontology 
document to allow further development of the Taxon class within DSW 
without causing a conflict with the description of Taxon within the TDWG 

I guess the wisdom of doing this partially depends on the future of the 
TDWG ontology, which is not within our (Cam and my) hands.  We didn't 
really want to get into describing Taxon (not our area of specialty) and 
the tc:Taxon class and terms were in use by some people (you, for 
example).  But if the TDWG ontology is permanently "frozen" (a.k.a. 
abandoned), then maybe tying Taxon to it was not wise.  I would be 
interested in your opinion on this. 


Paul Murray wrote:
> On 05/05/2011, at 1:13 PM, Steve Baskauf wrote:
>> Peter DeVries wrote:
>>> I also don't seem to understand why if someone can find some missing 
>>> utility in existing vocabularies, and mints one starting with txn, 
>>> it is seen by some as an act of heresy, while the minting a new 
>>> vocabulary starting with dsw is not.
> I might jump in and make a technical point about OWL/RDF here.
> One of the strengths of OWL is that you can define equivalencies 
> between your own vocabulary and someone else's. You can declare that 
> your own "Taxon" notion is narrower or broader than some other notion 
> of taxon. The power of this is that if someone attempts to reason over 
> some well-known vocabulary and you define semantic relationships, 
> their rules will also reason over your dataset - as far as is possible.
> However, what you can do, and what I think would be a very sensible 
> thing to do, is to keep your vocabulary terms and your semantic 
> equivalencies in separate ontology documents. 
> For instance:
> Lets say you have a predicate "isVoucherFor", and it's quite obvious 
> that it is pretty much the same thing 
> as http://rs.tdwg.org/ontology/voc/Specimen#isVoucherFor, but slightly 
> more specific. For instance, your "isVoucherFor" might apply only to 
> specimens that are RegisteredSpecimens in your vocabulary. It has a 
> range declaration on it. In this case, it seems obvious that your 
> isVoucherFor is a subproperty of the tdwg isVoucherFor. 
> I'm suggesting suggest that the declaration of your 'isVoucherFor' 
> probably should include your range specifier (it's part of the way 
> your vocabulary works), but the declaration of the subproperty 
> relationship should be put in some other file/ontology, which would 
> import both your vocabulary and the TDWG vocabulary (or DwC 
> vocabulary, in this case). Any RDF files containing data should 
> probably import your vocabulary but not the equaivalency semantics.
> This allows you to "plug in" sets of equivalencies. A sparql query can 
> drag in some data using your vocabulary, and can separately drag in 
> your rules. Or not. That way:
> * if the other vocabulary changes in ways that break things, you can 
> define new equivalencies without disturbing an existing ruleset that 
> people might be using
> * people who want to use your terms but have their own ideas as to 
> what the equivalencies are can do their own reasoning
> * if someone's data uses your terms but using the equivalencies 
> results in inconsistencies, a querent can plug in a stripped-down set 
> of semantics and reason over that
> * the act of simply reading and processing your data does not cause 
> the other vocabulary to be dragged into the engine
> The ongoing problem is management: what rules are applicable? What 
> rule sets are there? The TDWG site itself (or any webserver anywhere) 
> can serve as an aggregator for bioinformatic RDF/OWL semantics simply 
> by hosting empty ontologies that import others . Thus 
> "Old-tdwg-and-DwC.owl", "DwC-and-taxonconcept(lax).owl", 
> "rulesets-that-pertain-to-occurence.owl", 
> "absolutely-everything-ever.owl", and so on.
> The work , of course, is in thrashing out the equivalencies - an 
> ongoing job.
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Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences

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