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

Roger Hyam rogerhyam at mac.com
Mon Oct 6 15:30:25 CEST 2008

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


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?



<?xml version="1.0" encoding="UTF-8"?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns="http://www.owl-ontologies.com/2008/7/1/Ontology1214964455.owl# 
    <spm:SpeciesProfileModel rdf:ID="spm_1">
            <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>
            <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)  
                <tc:hasInformation rdf:resource="urn:lsid:biosci.ohio-state.edu:osuc_concepts:135414 
                    <tn:TaxonName rdf:ID="_tn1">
                        <tn:rankString xml:lang="en">Species</ 
    <spm:SpeciesProfileModel rdf:ID="spm_2">
            <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>
            <tc:TaxonConcept rdf:ID="_tc2">
                <tc:nameString xml:lang="en">Dodous bispinosus</ 
                <tc:hasInformation rdf:resource="urn:lsid:biosci.ohio-state.edu:osuc_concepts:143647 
                    <tn:TaxonName rdf:ID="_tn2">
                        <tn:rankString xml:lang="en">Species</ 
    <spm:SpeciesProfileModel rdf:ID="spm_3">
            <tc:TaxonConcept rdf:ID="_tc3">
                <tc:nameString xml:lang="en">Solenopsis mameti  
                <tc:hasInformation rdf:resource="urn:lsid:biosci.ohio-state.edu:osuc_concepts:36308 
                    <tn:TaxonName rdf:ID="_tn3">
                        <tn:rankString xml:lang="en">Species</ 
    <spm:SpeciesProfileModel rdf:ID="spm_4">
            <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>
            <tc:TaxonConcept rdf:ID="_tc4">
                <tc:nameString xml:lang="en">Technomyrmex primroseae</ 
                <tc:hasInformation rdf:resource="urn:lsid:biosci.ohio-state.edu:osuc_concepts:36839 
                    <tn:TaxonName rdf:ID="_tn4">
                        <tn:rankString xml:lang="en">Species</ 

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
Royal Botanic Garden Edinburgh
20A Inverleith Row, Edinburgh, EH3 5LR, UK
Tel: +44 131 552 7171 ext 3015
Fax: +44 131 248 2901

Roger Hyam
Roger at 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

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