Hi Everyone,
I am cross posting this to the TCS list and the TAG list because it is relevant to both but responses should fall neatly into things to do with nomenclature (for the TCS list) and things to do with technology - for the TAG list. The bit about avowed serializations of RDF below are TAG relevant.
The move towards using LSIDs and the implied use of RDF for metadata has lead to the question: "Can we do TCS is RDF?". I have put together a package of files to encode the TaxonName part of TCS as an RDF vocabulary. It is not 100% complete but could form the basis of a solution.
You can download it here: http://biodiv.hyam.net/schemas/TCS_RDF/tcs_rdf_examples.zip
For the impatient you can see a summary of the vocabulary here: http://biodiv.hyam.net/schemas/TCS_RDF/TaxonNames.html
and an example xml document here: http://biodiv.hyam.net/schemas/TCS_RDF/instance.xml
It has actually been quite easy (though time consuming) to represent the semantics in the TCS XML Schema as RDF. Generally elements within the TaxonName element have become properties of the TaxonName class with some minor name changes. Several other classes were needed to represent NomenclaturalNotes and Typification events. The only difficult part was with Typification. A nomenclatural type is both a property of a name and, if it is a lectotype, a separate object that merely references a type and a name. The result is a compromise in an object that can be embedded as a property. I use instances for controlled vocabularies that may be controversial or may not.
What is lost in only using RDFS is control over validation. It is not possible to specify that certain combinations of properties are permissible and certain not. There are two approaches to adding more 'validation':
OWL Ontologies
An OWL ontology could be built that makes assertions about the items in the RDF ontology. It would be possible to use necessary and sufficient properties to assert that instances of TaxonName are valid members of an OWL class for BotanicalSubspeciesName for example. In fact far more control could be introduced in this way than is present in the current XML Schema. What is important to note is that any such OWL ontology could be separate from the common vocabulary suggested here. Different users could develop their own ontologies for their own purposes. This is a good thing as it is probably impossible to come up with a single, agreed ontology that handles the full complexity of the domain.
I would argue strongly that we should not build a single central ontology that summarizes all we know about nomenclature - we couldn't do it within my lifetime :)
Avowed Serializations
Because RDF can be serialized as XML it is possible for an XML document to both validate against an XML Schema AND be valid RDF. This may be a useful generic solution so I'll explain it here in an attempt to make it accessible to those not familiar with the technology.
The same RDF data can be serialized in XML in many ways and different code libraries will do it differently though all code libraries can read the serializations produced by others. It is possible to pick one of the ways of serializing a particular set of RDF data and design a XML Schema to validate the resulting structure. I am stuck for a way to describe this so I am going to use the term 'avowed serialization' (Avowed means 'openly declared') as opposed to 'arbitrary serialization'. This is the approach taken by the prismstandard.org http://www.prismstandard.orggroup for their standard and it gives a number of benefits as a bridging technology:
1. Publishing applications that are not RDF aware (even simple scripts) can produce regular XML Schema validated XML documents that just happen to also be RDF compliant. 2. Consuming applications can assume that all data is just RDF and not worry about the particular XML Schema used. These are the applications that are likely to have to merge different kinds of data from different suppliers so they benefit most from treating it like RDF. 3. Because it is regular structured XML it can be transformed using XSLT into other document formats such as 'legacy' non-RDF compliant structures - if required.
There is one direction that data would not flow without some effort. The same data published in an arbitrary serialization rather than the avowed one could be transformed, probably via several XSLT steps, into the avowed serialization and therefore made available to legacy applications using 3 above. This may not be worth the bother or may be useful. Some of the code involved would be generic to all transformations so may not be too great. It would certainly be possible for restricted data sets.
To demonstrate this instance.xml is included in the package along with avowed.xsd and two supporting files. instance.xml will validate against avowed.xsd and parse correctly in the w3c RDF parser.
I have not provided XSLT to convert instance.xml to the TCS standard format though I believe it could be done quite easily if required. Converting arbitrary documents from the current TCS to the structure represented in avowed.xsd would be more tricky but feasible and certainly possible for restricted uses of the schema that are typical from individual data suppliers.
Contents
This is what the files in this package are:
README.txt = this file TaxonNames.rdfs = An RDF vocabulary that represents TCS TaxonNames object. TaxonNames.html = Documentation from TaxonNames.rdfs - much more readable. instance.xml = an example of an XML document that is RDF compliant use of the vocabulary and XML Schema compliant. avowed.xsd = XML Schema that instance.xml validates against. dc.xsd = XML Schema that is used by avowed.xsd. taxonnames.xsd = XML Schema that is used by avowed.xsd. rdf2html.css = the style formatting for TaxonNames.html rdfs2html.xsl = XSLT style sheet to generate docs from TaxonNames.rdfs tcs_1.01.xsd = the TCS XML Schema for reference.
Needs for other Vocabularies
What is obvious looking at the vocabulary for TaxonNames here is that we need vocabularies for people, teams of people, literature and specimens as soon as possible.
Need for conventions
In order for all exchanged objects to be discoverable in a reasonable way we need to have conventions on the use of rdfs:label for Classes and Properties and dc:title for instances.
The namespaces used in these examples are fantasy as we have not finalized them yet.
Minor changes in TCS
There are a few points where I have intentionally not followed TCS 1.01 (there are probably others where it is accidental).
* basionym is a direct pointer to a TaxonName rather than a NomenclaturalNote. I couldn't see why it was a nomenclatural note in the 1.01 version as it is a simple pointer to a name. * changed name of genus element to genusEpithet property. The contents of the element are not to be used alone and are not a genus name in themselves (uninomial should be used in this case) so genusEpithet is more appropriate - even if it is not common English usage. * Addition of referenceTo property. The vocabulary may be used to mark up an occurrence of a name that is not a publishing of a new name. In these cases the thing being marked up is actually a pointer to another object, either a TaxonName issued by a nomenclator or a TaxonConcept. In these cases we need to have a reference field. Here is an example (assuming namespace) <TaxonName referenceTo="urn:lsid:example.com:myconcepts:1234"><genusEpithet>Bellis</genusEpithet><specificEpithet>perennis</specificEpithet></TaxonName> This could possibly appear in a XHTML document for example.
Comments Please
All this amounts to a complex suggestion of how things could be done. i.e. we develop central vocabularies that go no further than RDFS but permit exchange and validation of data using avowed serializations and OWL ontologies.
What do you think?
Roger