[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
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/
-------------------------------------------------------------
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