Hi Bob,
Ah the problem may be OWL rather than RDF - I am a reluctant OWL - t'wit t'woo
If I take your 24 September 2008 example off the wiki
http://wiki.tdwg.org/twiki/bin/view/SPM/PlaziEOLProject
and change the part of taxon concept that starts like this:
<tc:TaxonConcept rdf:ID="_tc1">
into a taxon concept like this
<tc:TaxonConcept rdf:about="urn:lsid:biostuff.org:tc:123"> and remove the "etc.." from the bottom
then it validates just fine as RDF.
I could then add in some Dublin Core properties for urn:lsid:biostuff.org:tc:123 either embedded within the construct there or anywhere else in the file. I paste in the complete example below. It validates fine as RDF on the W3C validator.
Now your mileage may vary with OWL depending on the nature of the assertions you have loaded into your ontology. You would at least have to have a dc ontology (I don't believe there is an official one) and the ontology you have the tdwg namespaces mapped to would have to allow you to add properties. These things would have to be specific to your project and shouldn't be determined by the TDWG ontology - that is only there to give the minimal semantics and not specifics of what properties something should/should not have. (I regret having the vocabularies in OWL now. Almost wish there were plain text place holders for the URIs so that it was clear it is up to someone else to define precise semantics).
Does this help?
Roger
--------------8<-------------------------------------
<?xml version="1.0" encoding="UTF-8"?> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:spmi="http://rs.tdwg.org/ontology/voc/SPMInfoItems#" xmlns:spm="http://rs.tdwg.org/ontology/voc/SpeciesProfileModel#" xmlns:tn="http://rs.tdwg.org/ontology/voc/TaxonName#" xmlns:dc="http://dumplingCore.org/terms#" xmlns:tc="http://rs.tdwg.org/ontology/voc/TaxonConcept#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns="http://www.owl-ontologies.com/2008/7/1/Ontology1214964455.owl# " xml:base=""> <spm:SpeciesProfileModel rdf:ID="spm_1"> spm:hasInformation <spmi:Description rdf:ID="_Description_1_1"> spm:hasContent[[ soldier ]]. Very pale dirty yellow, head reddish yellow, mandibles dark red, teeth, scapes, anterior border of clypeus, and extreme anterior angles of cheeks black, clothed with very sparse outstanding longer and shorter yellow hairs and some fine very short decumbent yellow hairs. Sculpture consisting of very fine reticulations, a little stronger on head.Head large, triangular, considerably broader behind than in front, broadest a little before posterior angles, which are rounded and prominent, posterior border excised, slightly sinuate on each side; mandibles massive, strongly punctured and with transverse ridges, masticatory border armed with six large strong teeth, the apical one being the longest, curved and sharp, the next two longer and sharper than the last three; clypeus large, somewhat flat, carinate and slightly convex on disc, anterior border considerably produced in middle where it is somewhat crenulate, and five large punctures are present along the edge, and smaller punctures, rather wide apart, are scattered over the rest of the surface, posterior border excised in middle; frontal area very faintly defined; frontal carinas rather long, raised, with sharp edges, the rims or edges enclosing the antennal sockets are considerably raised and prominent; a very fine narrow longitudinal ridge takes the place of the frontal furrow and extends between the frontal carinae as far back as their extreme edges; eyes large, broad oval, rather flat, are situated rather high up before the middle of the sides of the head; antenna 12 - jointcd, scape long, thickened at apex, extending beyond the posterior border of head funiculus with all the joints elongate, first slightly shorter than the others, last joint long and pointed. Thorax longer than broad, broadest behind centre of sides of pronotum, somewhat slender behind; pronotum ample. convex, with a short neck, sides margined, considerably widened afterneck, posterior border semicircular; sutures between pro- and mesonotum, and meso- and epinotum fine but distinct; mesonotum longer than broad, shorter than pronotum, somewhat flat on disc, sides rather straight, epinotum longer than mesonotum, sides rather straight, angle between dorsal surface and declivity not marked, dorsal surface longer than declivity. Scale of petiole rather thick at base, anterior surface slightly convex, posterior surface slightly concave, upper surface narrow and forming a rather sharp, ridge; gaster oval, not very voluminous, pointed at apex. Legs fairly long; tibiae prismatic. Long. 18 mm.[[ worker ]] Of the same pale colour as the [[ soldier ]]. but only the extreme anterior angle of clypens and cheeks blackish; the mandibles are pale yellow with the teeth red. The sculpture and hairs are similar.Head long, narrow, broader in front than behind, broadest a little in front of sides of head, narrowed, rather sharply behind eyes to base; teeth to mandibles somewhat more slender and sharper, carinae on clypeus a little more pronounced; eyes more prominent. Thorax narrow and slender; pronotum more narrowed to apex. Scale of petiole of similar shape, but a little narrower; gaster and-legs of similar shape. Long. 10 - 12 mm.</spm:hasContent> </spmi:Description> </spm:hasInformation> spm:aboutTaxon <tc:TaxonConcept rdf:about="urn:lsid:biostuff.org:tc:123"> <dc:rights rdf:resource="http://creativecommons.org/some/license/ example" /> dc:titleCamponotus (Tanaemyrmex) gerberti</dc:title> <tc:nameString xml:lang="en">Camponotus (Tanaemyrmex) gerberti</tc:nameString> <tc:hasInformation rdf:resource="urn:lsid:biosci.ohio-state.edu:osuc_concepts:135414 "/> tc:hasName <tn:TaxonName rdf:ID="_tn1"> <tn:rankString xml:lang="en">Species</ tn:rankString> </tn:TaxonName> </tc:hasName> </tc:TaxonConcept> </spm:aboutTaxon> </spm:SpeciesProfileModel> <spm:SpeciesProfileModel rdf:ID="spm_2"> spm:hasInformation <spmi:Description rdf:ID="_Description_2_1"> spm:hasContent Very like trispinosus but without the two shorter spines on the mesonotum. The sculpture is different, and the species is also a little darker in colour. [[ worker ]]. Head: the sculpture is quite different; the disc is smooth and shining, from the outer part of the smooth surface at sides semicircular carinae run on each side along the cheeks, and from the posterior part a few weaker carinae extend towards base of head, the space between these and the posterior border of head being smooth and shining.Thorax: the ridges on the pronotum are considerably less marked; the mesonotum is smooth and shining and there are no spines present. The ridges on the sides of the thorax are less marked; the dorsal surface and the declivity of the epinotum are smooth and shining.The spines on the pronotum are slightly longer and stronger, and those of the epinotum, being of a different shape, being slightly shorter, and projecting outwards then inwards in an even curve. Long. 5 mm.</spm:hasContent> </spmi:Description> </spm:hasInformation> spm:aboutTaxon <tc:TaxonConcept rdf:ID="_tc2"> <tc:nameString xml:lang="en">Dodous bispinosus</ tc:nameString> <tc:hasInformation rdf:resource="urn:lsid:biosci.ohio-state.edu:osuc_concepts:143647 "/> tc:hasName <tn:TaxonName rdf:ID="_tn2"> <tn:rankString xml:lang="en">Species</ tn:rankString> </tn:TaxonName> </tc:hasName> </tc:TaxonConcept> </spm:aboutTaxon> </spm:SpeciesProfileModel> <spm:SpeciesProfileModel rdf:ID="spm_3"> spm:aboutTaxon <tc:TaxonConcept rdf:ID="_tc3"> <tc:nameString xml:lang="en">Solenopsis mameti Donisthorpe</tc:nameString> <tc:hasInformation rdf:resource="urn:lsid:biosci.ohio-state.edu:osuc_concepts:36308 "/> tc:hasName <tn:TaxonName rdf:ID="_tn3"> <tn:rankString xml:lang="en">Species</ tn:rankString> </tn:TaxonName> </tc:hasName> </tc:TaxonConcept> </spm:aboutTaxon> </spm:SpeciesProfileModel> <spm:SpeciesProfileModel rdf:ID="spm_4"> spm:hasInformation <spmi:Description rdf:ID="_Description_4_1"> spm:hasContent[[ worker ]]. Black, rather shining, mandibles, antennae and legs dirty pale yellow, the petiole brighter yellow. Sculpture: head and gaster finely reticulate, thorax more distinctly so, clothed with fine golden pubescence, which is more pronounced on gaster and a few short outstanding hairs, more being present on gaster.Head oval, somewhat narrower in front than behind, broadest a little behind eyes, posterior angles rounded,. posterior border excised in middle; mandibles moderately long, triangular apical tooth sharp and curved, masticatory border armed with a number of small sharp teeth, the second and fourth being longer than the third; clypeus fairly large, anterior border excised in middle, posterior border extending in a point between the frontal carinae; frontal area small but distinct; frontal carinae short, low, fairly wide apart, parallel; eyes large, round, rather prominent, situated in front of sides of head; antennal 12 - jointed, scape long, extending beyond posterior border of head, funiculus with first joint longer than third, second joint the shortest, rest of joints gradually increasing in length and breadth, last joint as long as the two preceding taken together. Thorax with a neck, longer than broad, constricted in middle, broadest at humeral angles; pronotum large, transverse, convex, anterior border margined, posterior border semicircular encircling mesonotum; mesonotum shorter and narrower than pronotum, a little longer than broad, slightly convex; sutures between pro- and mesonotum and meso- and epinotum well marked, especially the latter; epinotum with angle between dorsal surface and declivity well marked, declivity abrupt, somewhat flat, considerably longer than dorsal surface. Petiole narrow, flat, slightly longer than broad, scale entirely rudimentary; gaster oval, overhanging the petiole, pointed at apex, fifth segment extending a little beyond the fourth, cloacial opening terminal. Long. 2.5 mm.</spm:hasContent> </spmi:Description> </spm:hasInformation> spm:aboutTaxon <tc:TaxonConcept rdf:ID="_tc4"> <tc:nameString xml:lang="en">Technomyrmex primroseae</ tc:nameString> <tc:hasInformation rdf:resource="urn:lsid:biosci.ohio-state.edu:osuc_concepts:36839 "/> tc:hasName <tn:TaxonName rdf:ID="_tn4"> <tn:rankString xml:lang="en">Species</ tn:rankString> </tn:TaxonName> </tc:hasName> </tc:TaxonConcept> </spm:aboutTaxon> </spm:SpeciesProfileModel> </rdf:RDF>
On 6 Oct 2008, at 13:46, Bob Morris wrote:
On Mon, Oct 6, 2008 at 6:30 AM, Roger Hyam rogerhyam@mac.com wrote:
I am not sure I understand the problem. In RDF any non-literal can be represented as a URI or a local id and can therefore be the subject of an assertion (triplet). How can there not be a place to hang something? You can hang anything anywhere!
Umm, I may be confused but (a)I think It is not the URI about which we need to make assertions, but rather the triple which has that URI as object of rdf:about in Ben's suggestion. (b)I thought you cannot reify a triple by using rdf:about, but must use a relative URI defined by rdf:id
Yes you can hang anything anywhere, but if you do, it seems not that hard to slip out of OWL, let alone OWL DL, or in our case, to slip out of being a valid SPM instance, such as in our initial attempt to use a URI as the object of hasInformation.
Are we talking here about XML Schema validated XML representation of RDF?
Terry and I are talking about triples. We generate XML/RDF but we test our results with RDF and OWL validators.
Roger
On 5 Oct 2008, at 17:10, Bob Morris wrote:
In our GBIF/EOL/Plazi SPM project, Terry Catapano and I have formed the conclusion (I hope wrong...) that there is not any place on several lsidvoc objects to hang an lsid (or any other GUID) asserted to identify that object. For example, we don't see any place to put one on a TaxonConcept or on a PublicationCitation. In the October 1 example at http://wiki.tdwg.org/twiki/bin/view/SPM/PlaziEOLProject we have a placeholder hack using
<tc:TaxonConcept rdf:ID="_tc2"> <tc:nameString xml:lang="en">Dodous bispinosus</tc:nameString> tc:hasInformation rdf:resource="urn:lsid:biosci.ohio-state.edu:osuc_concepts:143647"/ ... </tc:TaxonConcept>
but this is not valid in the tdwg ontology because hasInformation requires an InfoItem as its object.
We use other objects that face this problem, e.g. TaxonName, and I guess it is quite a broad issue (or not an issue at all if we are wrong).
Can someone recommend a valid way to address this, either for these three objects, or preferably, in general? If so, thanks in advance. If we are right, how about adding an InfoItem class named GUID, that includes an enumeration of the usual suspects, suitably typed.
Bob
Robert A. Morris Professor of Computer Science UMASS-Boston ram@cs.umb.edu http://bdei.cs.umb.edu/ http://www.cs.umb.edu/~ram http://www.cs.umb.edu/~ram/calendar.html phone (+1)617 287 6466 _______________________________________________ tdwg-tag mailing list tdwg-tag@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-tag
Roger Hyam Roger@BiodiversityCollectionsIndex.org http://www.BiodiversityCollectionsIndex.org
Royal Botanic Garden Edinburgh 20A Inverleith Row, Edinburgh, EH3 5LR, UK Tel: +44 131 552 7171 ext 3015 Fax: +44 131 248 2901 http://www.rbge.org.uk/
-- Robert A. Morris Professor of Computer Science UMASS-Boston ram@cs.umb.edu http://bdei.cs.umb.edu/ http://www.cs.umb.edu/~ram http://www.cs.umb.edu/~ram/calendar.html phone (+1)617 287 6466
------------------------------------------------------------- Roger Hyam Roger@BiodiversityCollectionsIndex.org http://www.BiodiversityCollectionsIndex.org ------------------------------------------------------------- Royal Botanic Garden Edinburgh 20A Inverleith Row, Edinburgh, EH3 5LR, UK Tel: +44 131 552 7171 ext 3015 Fax: +44 131 248 2901 http://www.rbge.org.uk/ -------------------------------------------------------------
------------------------------------------------------------- Roger Hyam Roger@BiodiversityCollectionsIndex.org http://www.BiodiversityCollectionsIndex.org ------------------------------------------------------------- Royal Botanic Garden Edinburgh 20A Inverleith Row, Edinburgh, EH3 5LR, UK Tel: +44 131 552 7171 ext 3015 Fax: +44 131 248 2901 http://www.rbge.org.uk/ -------------------------------------------------------------