[tdwg-tag] Where to put LSIDs on tdwg ontology objects

Bob Morris morris.bob at gmail.com
Mon Oct 6 16:49:47 CEST 2008


I don't regret that you put the ontologies in OWL. I only regret that
you regret it.  :-)

FWIW, it seems to be an open secret that the "official" dc rdf/xml
http://purl.org/dc/elements/1.1/ is not owl-valid, and there is one at
Stanford that is OWL DL.
http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl

What this discussion has clarified for me is that the problem we are
wrestling with is better stated as  "where to put a GUID in such a way
that the object can be referenced  elsewhere in the RDF document and
in a way that allows the object's properties to be retrieved"  rather
than simply as "where to put a GUID".  What I seem to believe, and
what worries me if correct, is that, even in RDF, never mind OWL,  the
semantics of rdf:id by design clearly allows this, and the semantics
of rdf:about clearly forbids it. That's because rdf:about requires an
absolute URI (which is the very reason one would use it to hang a GUID
on).

Bob



On Mon, Oct 6, 2008 at 9:30 AM, Roger Hyam <rogerhyam at mac.com> wrote:
> 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:title>Camponotus (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 at 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 at 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 at lists.tdwg.org
>
> http://lists.tdwg.org/mailman/listinfo/tdwg-tag
>
> -------------------------------------------------------------
>
> Roger Hyam
>
> Roger at 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 at 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 at 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 at 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 at 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



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