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
<tn:nomenclaturalCode rdf:resource="http://tdwg.org/2006/03/12/TaxonNames/botanical" />
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).
Regards
Rod
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 can.
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? Sally
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 resolve because we didn't have a policy at that time. The use if entity references was 'borrowed' from an example (probably Protege output) and 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 TDWG St Louis. It would be good to have face to face discussions about it and 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 it would require 6 independent schemas each with it's own target namespace. 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 this.
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 name
A property in MyClass would be: http://rs.tdwg.org/ontology/tdwg123_myProperty
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 nothing 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 documents.
It is radical which is why I thought it would be good to talk about it.
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.
Roger
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?
Sally
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 take 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 the fully qualified resource URI which looks like:
<tn:nomenclaturalCode rdf:resource="http://tdwg.org/2006/03/12/TaxonNames/botanical" />
-Steve
*** Sally Hinchcliffe *** Computer section, Royal Botanic Gardens, Kew *** tel: +44 (0)20 8332 5708 *** S.Hinchcliffe@rbgkew.org.uk
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--
Roger Hyam Technical Architect Taxonomic Databases Working Group
http://www.tdwg.org roger@tdwg.org
+44 1578 722782
*** Sally Hinchcliffe *** Computer section, Royal Botanic Gardens, Kew *** tel: +44 (0)20 8332 5708 *** S.Hinchcliffe@rbgkew.org.uk
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------------------------------------------------------------------------ ---------------------------------------- Professor Roderic D. M. Page Editor, Systematic Biology DEEB, IBLS Graham Kerr Building University of Glasgow Glasgow G12 8QP United Kingdom
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