> But there is an inheritance hierarchy that I don't know how to
> handle using W3C's specifications alone. A genus has properties
> values (e. g.flower/petals/color = 'white' ) that MUST be inherited
> by the species in this genus. The properties values of a genus CAN
> be overriden by some species in this genus.
I have no insight on the way it would be handled in XML, but I
believe we must consider that (a) inheritance goes up and down, and
(b) information may be original or …
[View More]virtual.
The genus description is nothing more than the consensus description
of all species placed in that genus. This is true regardless, whether
it is done by computer or a scientist. The type species (the species
to which the genus name is bound) will carry more wheight, some
people may wheigh it very strongly.
Thus
currently placed in GenusX
Species1=101 \
Species2=10U > synthesized ("summary function") description of GenusX
Species3=10U /
results in a description GenusX=[101)
(1 = a state applies, 0 = does not apply, U = unknown, not yet
observed)
Some information, e.g. anatomical or electron microscopy is usually
only obtained from one or few species and then assumed to be true for
all species in the Genus. Thus, information that was passed up, is
now passed down again to species where this has not been studied.
Care must be taken that the information is recognized as being passed
down, it can NOT be simply copied as if it would indeed have been
studied there.
Species1=10 1
Species2=10[1]
Species3=10[1]
Square brackets shall here indicate that the information has been
passed down.
It will often happen that Species3 is transferred to a different
Genus, because the assumption that it belongs to GenusX turned out to
be false. The GenusX description must now be revised, and information
that was passed up from Species3 to GenusX and down to Species1/2
must be removed.
This is a continous dynamic process in science, and must be modeled
on the computer.
However, the Genus description is not necessarily entirely dynamic.
In many cases it will be necessary to copy information from
publication, thus the Genus description may be physical and original
data, in contrast to the virtual descriptions obtained by automatic
synthesis processes.
Gregor
----------------------------------------------------------
Gregor Hagedorn G.Hagedorn(a)bba.de
Institute for Plant Virology, Microbiology, and Biosafety
Federal Research Center for Agriculture and Forestry (BBA)
Koenigin-Luise-Str. 19 Tel: +49-30-8304-2220
14195 Berlin, Germany Fax: +49-30-8304-2203
Often wrong but never in doubt!
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Jean-Marc Vanel wrote under the Subject:
RDF Schema design pb: inheritance of properties
(Subject renamed, because this post refers to
issues secondary to the original post)
> There is a containment hierarchy (e. g. a flower contains petals)
which
> raises no problems in XML.
I would like to challenge this assumption, which seems to be
generally accepted in the discussion here.
It is true: Morphological structures may have containment
hierarchies, but I believe that these depent …
[View More]strongly on the
viewpoint of the author or user.
EXAMPLE 1: The peduncle (stalk of a flower) is usually assumed to be
part of the flower, but anatomically it is clearly a part of the stem
(in contrast to the petiole, stalk of a leaf!).
EXAMPLE 2: Stuff can be in-between: The inflorescence contains part
of stem, part of leaves, and all flowers. Which leaves are part of
inflorescens and thus called bracts, and which aren't is often a
matter of taste, school, country...
Thus: there are multiple concurrent or competing hierarchies, which
may overlap.
EXAMPLE 3: Further, other, non-morphological
hierarchies/classifications exist. These may be much more relevant
for many purposes, and may be the primary outline used in a natural
language description. For example, structures can be classified by
function (sexual/asexual propagation), observation method (naked
eye/light microsc./electron microscopy, physiological/molecular etc.
EXAMPLE 3 (leaving morphology altogether): Gene sequences can be
classified as transscribed/non-transscribed, Protein-coding/rRNA
coding/non-coding, intron/exon, regulatory/structural,
conserved/variable/hypervariable etc. Most of these classifications
overlap.
*** Call for more examples: Can anybody come up with more good
examples (perhaps from animals) as to why a fixed hierarchy in the
form of a feature path may be unpractical?
> Info. for computer men: biology has a hierarchic classification of
> species whose 4 lowest levels are:
> order
> family
> genus
> species
Sorry this is a gross misrepresentation. Info from a biologist:
(incomplete list, reflecting botanical code, and devised with fungi
in mind). Number of ranks is a matter of taste, some people like to
supra and sub [and hyper+hypo? :-) ] everything:
CODE Description
fsp. forma specialis nov. -- nomenclatorially facultative
subfm. subforma nov. -- subform nomenclatorially obligatory
fm. forma nov. -- form nomenclatorially obligatory
subvar. subvarietas nov. -- sub-variety nomenclat. obligatory
var. varietas nov. variety nomenclatorially obligatory
ssp. subspecies nov. subspecies priority mandatory
sp. species nov. -- species priority mandatory
subser. subseries nov. -- subseries priority mandatory
ser. series nov. -- section priority mandatory
subsect. subsectio nov. -- subsection priority mandatory
sect. sectio nov. -- section priority mandatory
subgen. subgenus nov. -- subgenus priority mandatory
gen. genus nov. -- genus priority mandatory
subtrib. subtribus nov. -- subtribus priority mandatory
trib. tribus nov. -- tribus priority mandatory
subfam. subfamilia nov. -- subfamily priority mandatory
fam. familia nov. -- family priority mandatory
superfam. superfamilia nov. -- super-family priority mandatory
subord. subordo nov. -- suborder priority facultative
ord. ordo nov. -- order priority facultative
superord. superordo nov. -- superorder priority facultative
subclass. subclassis nov. -- subclass priority facultative
class. classis nov. -- class priority facultative
subdiv. subdivisio nov. -- subdivision priority facultative
div. divisio nov. -- division priority facultative
subreg. subregnum novum. -- sub-regnum priority facultative
reg. regnum novum. -- regnum priority facultative
Gregor
----------------------------------------------------------
Gregor Hagedorn G.Hagedorn(a)bba.de
Institute for Plant Virology, Microbiology, and Biosafety
Federal Research Center for Agriculture and Forestry (BBA)
Koenigin-Luise-Str. 19 Tel: +49-30-8304-2220
14195 Berlin, Germany Fax: +49-30-8304-2203
Often wrong but never in doubt!
[View Less]
> But there is an inheritance hierarchy that I don't know how to handle
> using W3C's specifications alone. A genus has properties values
> (e. g. flower/petals/color = 'white' ) that MUST be inherited by the
> species in this genus. The properties values of a genus CAN be
> overriden by some species in this genus.
I believe RDF handles this, see below.
> It seems that the "refines" property in XML Schema would bring the
> desired semantics, together with the "Schema …
[View More]Information Set
> Contribution: augmentations to instance information sets which follow as
> a consequence of schema-validation". But the uncomplete state of the W3C
> document makes me unshure.
Hmm, I'm not 100% sure either, but my feeling is that RDF is better
suited to this task than Schema.
As I understand things - we're looking to produce a generic schema for
capturing character data. In this case, "refines" could be used to extend
the schema to include attributes/elements from other disciplines.
RDF allows you to describe 'resources' independent of the structure
of the schema they conform to, and allows things like sub-classing.
> I don't see anything clearly specified in RDF and RDF Schema for
> inheritance of properties.
>>>From the RDF Schema spec : http://www.w3.org/TR/PR-rdf-schema/
"Classes themselves are often organised in a hierarchical fashion,
for example the class 'dog' might be considered a sub-class of 'animal'
which is a sub-class of 'organism' etc., meaning that any resource which is
of rdf:type 'dog' is ipso facto also of rdf:type 'animal' and so on. This
specification describes a property, rdfs:subClassOf, to denote such
relationships
between classes."
...and (describing subClassOf)...
"If class A is a sub-class of some broader class B, and B is a sub-class of
C,
then A is also implicitly a sub-class of C. Consequently, resources that are
instances of class A will also be instances of C, since A is a sub-set of
both B and C"
...and (describing subPropertyOf)...
"If the property biologicalFather is a sub-property of the broader
property biologicalParent, and if Fred is the biologicalFather of John, then
it is implied that Fred is also the biologicalParent of John."
I think these portions of the spec apply to the sort of 'inheritance' you
require - or am I missing a subtle difference here? If you wish to
provide default values for properties then I think this needs to be
addressed at an application level.
> Info. for computer men: biology has a hierarchic classification of
> species whose 4 lowest levels are: order family genus species
Heres an RDF example of this structure (I've kept it to the
lower 4 levels of the classification, ignoring Kingdom, Phylum, Class,
etc.).
<rdf:Description ID="Order">
<rdf:type
resource="http://www.w3.org/TR/1999/PR-rdf-schema-19990303#Class"/>
<rdfs:subClassOf rdf:resource="http://www.foo.com/taxonomy-schema#Class"/>
</rdf:Description>
<rdf:Description ID="Family">
<rdf:type
resource="http://www.w3.org/TR/1999/PR-rdf-schema-19990303#Class"/>
<rdfs:subClassOf rdf:resource="#Order"/>
</rdf:Description>
<rdf:Description ID="Genus">
<rdf:type
resource="http://www.w3.org/TR/1999/PR-rdf-schema-19990303#Class"/>
<rdfs:subClassOf rdf:resource="#Family"/>
</rdf:Description>
<rdf:Description ID="Species">
<rdf:type
resource="http://www.w3.org/TR/1999/PR-rdf-schema-19990303#Class"/>
<rdfs:subClassOf rdf:resource="#Genus"/>
</rdf:Description>
Here we can declare Chrysanthemum to be a subclass of species, forgive
me for not knowing the latin name...
<rdf:Description ID="Chrysanthemum">
<rdf:type
resource="http://www.w3.org/TR/1999/PR-rdf-schema-19990303#Class"/>
<rdfs:subClassOf rdf:resource="#Species" />
</rdf:Description>
However, and this is where I'm still wrestling with RDF to an extent,
there are other ways to achieve this. For example, we may not need Genus and
Species
classes - instead modelling the Chrysanthemum genus as a class, and species
as subclasses.
Note that RDF does allow a resource to be a subclass of more than one class.
I can see a lot of work ahead in this area, and there seems to be a wealth
of
different ways to model the same ideas. I'm at present digging through the
literature to come up with some decent examples. (I hope the above was
vaguely
useful).
Cheers,
L.
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