[tdwg-tag] literal enumerated values in TCS-RDF
r.page at bio.gla.ac.uk
Mon Oct 2 15:21:19 CEST 2006
From an RDF perspective, I would vote for referring to the botanical
code (or any other code) using a URI, not a literal, and not a name
space reference (such as "tn:botanical) which, as Steve pointed out,
RDF parsers can't handle.
By referencing a URI, the semantics are clear (I can fetch whatever the
URI points to and figure out what it means).
In other words, something like
as Steve proposed (so long as the URI is actually resolvable, which is
another difference between XML schema and RDF --- in RDF the name
spaces must be resolvable).
I haven't really followed what Roger proposes, but IMHO anything
motivated by an attempt to salvage the use of XML schema is bound to
end in tears. It's a hack (anything that exposes internal identifiers
of a class has got to be hack, surely).
On 2 Oct 2006, at 13:52, Sally Hinchcliffe wrote:
> I'm trying to nail down a final spec for the IPNI LSID server if I
> Steve Perry raised the point, over on the tdwg-guid mailing list,
> that the following bit of output from the IPNI server was an error:
> <tn:nomenclaturalCode rdf:resource="&tn;#botanical" />
> This syntax has been used in a number of places - for the value for
> the nomenclaturalCode, for the nomenclaturalNote noteType (eg.
> basedOn) and for the typeOfTyp (eg. holo) - basically wherever there
> was an enumeration in the original schema.
> Roger's response is below - but I'm not quite clear how that will
> work in terms of replacing the syntax Steve found was failing. I'm
> not sure from Roger's email whether he really meant we should use
> numeric ids for all literal enumerated values, or whether those were
> merely place holders - but if so it would seem to make the resulting
> rdf willfully unreadable.
> Roger - can you explain with a more concrete example?
>> Hi Everyone,
>> In the not very comforting words of software vendors these are "known
>> issues" and will be resolved in the next release ;)
>> But seriously.The namespaces in the TCS names vocabulary do not
>> because we didn't have a policy at that time. The use if entity
>> references was 'borrowed' from an example (probably Protege output)
>> I wouldn't mind doing away with it.
>> I have been thinking long and hard about the namespace issues in the
>> last few weeks and believe I have a solution that I will propose at
>> St Louis. It would be good to have face to face discussions about it
>> make a decision there.
>> To briefly summarize: The issue is getting a namespace convention that
>> will work across technologies. Suppose we want to serve data in a
>> technology that "isn't very good at namespaces". As an example - if we
>> were to have separate namespaces for TaxonNames, TaxonConcepts,
>> Specimens, Metadata, GeospatialStuff, Collections and we wanted to
>> validate a document using XML Schema that contained all these things
>> would require 6 independent schemas each with it's own target
>> If you have ever tried to debug something like this you will know what
>> total madness it is. We can't just abandon XML Schema because it would
>> rule out not only our existing technologies but GML and probably
>> others... It may also be desirable to express our ontology in things
>> that aren't even XML.
>> The only solution I can think is that for the TDWG Ontology we should
>> have a single formal namespace of: http://rs.tdwg.org/ontology/
>> Within the ontology we have a convention for concepts that goes like
>> A class would be: http://rs.tdwg.org/ontology/tdwg123_MyClass
>> where 123 is the internal id of the class and MyClass is the class
>> A property in MyClass would be:
>> where 123 is the *class* id not the property id and myProperty is the
>> property name.
>> An instance would be http://rs.tdwg.org/ontology/tdwg123_789
>> where 123 is the *class* id and 789 is the instance id (there is
>> stable about an instance that we could use as an identifier unless we
>> force a label property and make it immutable).
>> In a way this is using the part before the _ as a pseudo namespace.
>> I think this hits the balance between something that is technology
>> independent and something that will produce reasonably human readable
>> It is radical which is why I thought it would be good to talk about
>> Any one got an alternative?
>> We have to have a solution for this by the end of the St Louis meeting
>> as it is critical path for ontology work.
>> Most grateful for you patience and any thoughts you have.
>> Sally Hinchcliffe wrote:
>>> Hi Steve /all
>>> We took that syntax straight from Roger's RDF/TCS examples. I think
>>> Roger was going to do more work on tidying up those sorts of loose
>>> ends. I have to admit that my knowledge of RDF and particularly RDFS
>>> is pretty superficial
>>> We can switch to either the shorter format or the safer fully
>>> qualified URI - what do people think would be better?
>>>> By the way, the IPNI example you cite has an error:
>>>> <tn:nomenclaturalCode rdf:resource="&tn;#botanical" />
>>>> Many RDF/XML parsers will see &tn; as an entity which cannot be
>>>> resolved. Since I don't have a copy of the ontology (and
>>>> http://tdwg.org/2006/03/12/TaxonNames does not resolve), I can only
>>>> a guess that it should look something like:
>>>> <tn:nomenclaturalCode rdf:resource="tn:botanical" />
>>>> However, using XML namespace prefixes in resource references inside
>>>> RDF/XML documents tends to cause problems because not all RDF/XML
>>>> parsers are smart enough to dereference the namespace prefix and
>>>> build a
>>>> fully-qualified resource URI. A safer form of the above would be
>>>> fully qualified resource URI which looks like:
>>>> rdf:resource="http://tdwg.org/2006/03/12/TaxonNames/botanical" />
>>> *** Sally Hinchcliffe
>>> *** Computer section, Royal Botanic Gardens, Kew
>>> *** tel: +44 (0)20 8332 5708
>>> *** S.Hinchcliffe at rbgkew.org.uk
>>> TDWG-GUID mailing list
>>> TDWG-GUID at mailman.nhm.ku.edu
>> Roger Hyam
>> Technical Architect
>> Taxonomic Databases Working Group
>> roger at tdwg.org
>> +44 1578 722782
> *** Sally Hinchcliffe
> *** Computer section, Royal Botanic Gardens, Kew
> *** tel: +44 (0)20 8332 5708
> *** S.Hinchcliffe at rbgkew.org.uk
> tdwg-tag mailing list
> tdwg-tag at lists.tdwg.org
Professor Roderic D. M. Page
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