[tdwg-tag] RE: tdwg-tag Digest, Vol 22, Issue 2
Döring, Markus
m.doering at BGBM.org
Wed Oct 10 15:10:29 CEST 2007
Éamonn,
this was just a simplified example to illustrate the TAPIR problem.
It was not meant to be a new suggestion of any kind.
Although if you have read my last post in response to Gregor, I tend to think that we would be better off creating a basic set of 3 or 4 InfoItem classes which are more concise than having different options for expressing the same thing. If you look at the existing properties don't they boil down to 4 attributes?
associatedTaxon -> ORGANISM INTERACTION
category -> TAG
context
contextValue
contextOccurrence -> REGION
hasContent -> INFO
hasValue
Markus
-----Original Message-----
From: tdwg-tag-bounces at lists.tdwg.org on behalf of Eamonn O Tuama
Sent: Wed 10/10/2007 2:39 PM
To: tdwg-tag at lists.tdwg.org
Cc:
Subject: [tdwg-tag] RE: tdwg-tag Digest, Vol 22, Issue 2
Marcus,
I'm trying to relate your revised model below to the present description on
http://rs.tdwg.org/ontology/voc/SpeciesProfileModel.rdf .
You state -
"The problem we saw with TAPIR is that there are only 2 new concepts defined
by SPM - category and value. If you do not want to map anything more than
this in TAPIR models, you probably can produce SPM RDF. "
But what about the other properties defined for InfoItem - this is the full
list:
associatedTaxon
category
context
contextOccurrence
contextValue
hasContent
hasValue
Are you suggesting that we drop 'associatedTaxon', the three context
properties (context, contextOccurrence, contextValue) and the 'hasValue'
property (information about a taxon in the form of a controlled vocabulary
term), leaving just the 'category' and 'hasContent'. Is it possible to add
additional columns in your database to accommodate these fields or do we run
into trouble with TAPIR?
Éamonn
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Today's Topics:
1. Re: SPM Categories or Subclassing - again. (Gregor Hagedorn)
2. Re: SPM Categories or Subclassing - again. (D ? ring, Markus)
----------------------------------------------------------------------
Message: 1
Date: Mon, 8 Oct 2007 14:41:39 +0200
From: "Gregor Hagedorn" <g.m.hagedorn at gmail.com>
Subject: Re: [tdwg-tag] SPM Categories or Subclassing - again.
To: tdwg-tag at lists.tdwg.org
Message-ID:
<5ebbead70710080541l3cba340cyf2ebced50b4b9598 at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
In SDD we used what is here called the "tagging approach", i.e. for
descriptive concepts and characters we use
<Text ref="some.resource.org/123"><Content>Free form text</Content></Text>
In SDD, all element/attribute names refer to classes/attributes in UML or
Java, whereas the xml values are corresponding values. Expressing concepts
and characters as classes was considered impractical if the aim is generic
software (classes are creatable at runtime, but at a price) because the
number of characters is often very large.
My experience shows that the number of character in identification sets
varies between 50 and over 1000. Some studies in manual data integration (in
LIAS) convinced me that the number of "integratable" characters is often
less than imagined. A similar case study may also be the FRIDA data sets,
which limit the number of common characters (common to all plant families)
to 200, and from thereon use separate characters for each family.
Clearly, when limiting the approach to just "very high level concepts", both
class and value approaches are possible. The benefit of the SPM 0.2 approach
is that it does enable reasoning (as well as may simplify tapir usage).
However, as presented in Bratislava, I am doubtful that this limit holds. In
my experience the limit between free form text and categorical data tends be
diffuse rather than sharp and my intuition is that the SPM mechanism, being
extensible, will be extended.
I would like to note that the current TAG strategy is to provide both RDF
and xml schema. The schema approach to SPM, however, seems to be more and
more undesirable as the number of descriptive concepts grows.
I have a question for TAPIR:
Does TAPIR find it easier to search elements having specific attribute
values than elements having child elements with specific value:
<hasInformation>
<InfoItem
category="voc.x.org/DescriptiveConcepts/Size<http://some.resource.org/123>">
<....>
</InfoItem>
I might be useful to know. Although RDF allows this for literals, it seems
to require the rdf:resource="" step for categorical data, so this may or may
not help.
----------
PS: SDD calls the concepts "characters" based on the tradition and character
is clearly inappropriate. However, Category to me seems to express nothing
other than the type of the value. All contextValue and Value in SPM in
version 0.2 refer to categories. Can anyone suggest a better term? What is
the opposite of "value"?
I can think of "Class" (value = instance), or - but perhaps too much limited
to descriptions - "Feature" (also in GML). Anything else?
Gregor
-----------------------------------------------------
Gregor Hagedorn (G.M.Hagedorn at gmail.com)
Institute for Plant Virology, Microbiology, and Biosafety
Federal Research Center for Agriculture and Forestry (BBA)
Kvnigin-Luise-Str. 19 Tel: +49-30-8304-2220
14195 Berlin, Germany Fax: +49-30-8304-2203
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Message: 2
Date: Mon, 08 Oct 2007 16:39:16 +0200
From: "D ? ring, Markus" <m.doering at BGBM.org>
Subject: Re: [tdwg-tag] SPM Categories or Subclassing - again.
To: Donald Hobern <dhobern at gbif.org>, Roger Hyam <roger at tdwg.org>
Cc: "Kohlbecker, Andreas" <a.kohlbecker at BGBM.org>,
tdwg-tag at lists.tdwg.org
Message-ID: <C3300DB4.76C3%m.doering at BGBM.org>
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Donald, Roger,
The problem we saw with TAPIR is that there are only 2 new concepts defined
by SPM - category and value. If you do not want to map anything more than
this in TAPIR models, you probably can produce SPM RDF. But if you want to
only map the descriptions or distributions you are in trouble.
Imagine a simple database table with 3 columns: taxon, category and value.
You could map them to 3 concepts namely SPM/taxon, SPM/category and
SPM/value. You can then create an output model similar to this one here:
<outputModel
<structure>
<schema location="http://rs.tdwg.org/tapir/rs/SPM.xsd"/>
</structure>
<indexingElement path="/SpeciesProfileModel/hasInformation/InfoItem"/>
<mapping>
<node path="/SpeciesProfileModel/aboutTaxon/@rdf:resource">
<concept id="SPM/taxon"/>
</node>
<node
path="/SpeciesProfileModel/hasInformation/InfoItem/category/@rdf:resource">
<concept id="SPM/category"/>
</node>
<node path="/SpeciesProfileModel/hasInformation/InfoItem/value">
<concept id="SPM/value"/>
</node>
</mapping>
</outputModel>
With current provider implementations you will get a new SpeciesProfileModel
element for every record in your database, i.e. repeating taxa for every
InfoItem. This is valid SPM and you can actually search on it too with TAPIR
like Donald wanted to. So here you go. You would just need to know (and
understand) what categories this provider is using. You can get those
through an inventory instead of the capabilities, not a real problem.
If someone has a table with a taxon and a colum for description, one for
economic use and one for something else they would have to transform it into
a simple 3 column table.
My understanding of SPM in the beginning was just that I thought an initial
broad vocabulary should be part of SPM. I still think this is very much
needed, otherwise you all "mashup" will be done by the human enduser who is
presented with a nice long list of facts, sorted alphabetically.
Personally I am reluctant which approach to take. The tagging seems more
flexible, so yes, lets go for it!
But I cant see why OWL classes are not suited for defining a reusable,
external vocabulary. Isn't this what they are made for and what GO and all
the other ontologies use them for rather than just defining data exchange
formats? At least the tagging approach would free us from imposing a certain
definition language. I guess some can use SKOS, some OWL and some others
just RDFS. And of course there will be many different semantic definitions
in all those languages.
Markus
"Donald Hobern" wrote on 08.10.2007 13:53 Uhr:
> Roger,
>
> Your analysis (and the four points) seem perfectly correct to me. I
prefer a
> plain tagging approach and am particularly dubious about the long term
> benefits of subclasses which represent multiple inheritance because this
would
> seem to place a greater burden on consumers.
>
> However I am not so sure that the tagging approach does prevent the use of
> TAPIR. Surely the user is expected to be searching for InfoItems and each
> InfoItem will include a relative path "./category/@rdf:resource" which
could
> be searchable. In other words you could search for InfoItems where the
> concept identified by "./category/@rdf:resource" has the value
> "some.resource.org/123". Won't that work? Won't it return any InfoItem
which
> has any combination of category elements provided at least one is
identified
> to the given resource?
>
> Of course searching for InfoItems like this may prevent us from using
search
> elements outside the scope of the InfoItem - would this stop us from using
a
> ScientificName specified against the SpeciesProfileModel element? In
other
> words, would it be better to move the aboutTaxon down to the InfoItem?
>
> Donald
>
> Roger Hyam wrote:
>> Hi All,
>>
>> I'd like to re-ignite a debate we had over the summer in the light of
what
>> was discussed at Bratislava and things I am thinking about now.
>>
>> The original way the Species Profile Model was structure was to have
>> something like the attached UML diagram tagging.png
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> We didn't define a class "Category" but just left it as being any valid
URI
>> in the RDF style of doing things.
>>
>> Markus and several others pointed out that this would not work with TAPIR
>> very well as all the InfoItems will look the same. Something like this:
>>
>> <SpeciesProfileModel>
>> <hasInformation>
>> <InfoItem>
>> <category rdf:resource="some.resource.org/123" />
>> <....>
>> </InfoItem>
>> </hasInformation>
>> <hasInformation>
>> <InfoItem>
>> <category rdf:resource="some.resource.org/124" />
>> <....>
>> </InfoItem>
>> </hasInformation>
>> <hasInformation>
>> <InfoItem>
>> <category rdf:resource="some.resource.org/125" />
>> <....>
>> </InfoItem>
>> </hasInformation>
>> </SpeciesProfileModel>
>>
>> The xpaths to the data represented by <...> would all be the same.
>>
>> They suggested something like the next diagram:
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Where info item is subclassed. This allows RDF to be serialized like
this:
>>
>> <SpeciesProfileModel>
>> <hasInformation>
>> <Ecology>
>> <....>
>> </Ecology >
>> </hasInformation>
>> <hasInformation>
>> <Behaviour>
>> <....>
>> </Behaviour>
>> </hasInformation>
>> <hasInformation>
>> <BehaviouralEcology>
>> <....>
>> </BehaviouralEcology>
>> </hasInformation>
>> </SpeciesProfileModel>
>>
>> The xpaths to the <...> are all different and the model becomes TAPIR
>> friendly.
>>
>> At the time I wasn't too bothered either way because I saw this as an
>> artifact of serialization. The same thing could be written.
>>
>> <SpeciesProfileModel>
>> <hasInformation>
>> <InfoItem>
>> <rdf:type rdf:resource="some.resource.org/Ecology" />
>> <....>
>> </InfoItem>
>> </hasInformation>
>> <hasInformation>
>> <InfoItem>
>> <rdf:type rdf:resource="some.resource.org/Behaviour" />
>> <....>
>> </InfoItem>
>> </hasInformation>
>> <hasInformation>
>> <InfoItem>
>> <rdf:type rdf:resource="some.resource.org/BehaviouralEcology"
/>
>> <....>
>> </InfoItem>
>> </hasInformation>
>> </SpeciesProfileModel>
>>
>> With more or less that same meaning and looking just like a tagging
example.
>>
>> This was a mistake on my part because of course it isn't the same meaning
>> just a similar serialization - an RDF type really needs to point to a
class
>> and can't point to any old vocabulary that it could if it was treated
like a
>> tag.
>>
>> I have just added the category property back into InfoItem for discussion
>> purposes.
>>
>> I am concerned about going down the subclassing route for a few reasons.
>>
>> 1) Building a class hierarchy is difficult. The discussions we had in
>> Bratislava highlighted this. The examples put together in the current
>> vocabulary sparked a debate as to how things should be organized. There
are
>> issues with the diamond problem in multiple inheritance - if
contradictory
>> semantics occur in multiple inheritance routes to a class which has
priority?
>> If we don't have multiple inheritance how do we have InfoItems that are
about
>> both Ecology and Behaviour for example or any other two subjects such as
>> Dispersal and Asexual reproduction.
>>
>> 2) If a class hierarchy is required for analysis/inference it can be
>> superimposed on a tag based transfer protocol using OWL necessary and
>> sufficient properties. In fact this is arguably a better way of
approaching
>> the situation than building a class hierarchy a priori.
>>
>> 3) The motivation for going down the subclassing route is largely so it
will
>> work with the transport protocol - which sets alarm bells ringing for me.
>>
>> 4) It precludes us from using something like SKOS to build our
categories.
>>
>> "SKOS or Simple Knowledge Organisation System is a family of formal
languages
>> designed for representation of thesauri, classification schemes,
taxonomies,
>> subject-heading systems, or any other type of structured controlled
>> vocabulary. SKOS is built upon RDF and RDFS, and its main objective is to
>> enable easy publication of controlled structured vocabularies for the
>> Semantic Web. SKOS is currently developed within the W3C framework."
>> (http://en.wikipedia.org/wiki/SKOS)
>>
>> I would really like to be able to say to "domain experts" that they
"just"
>> need to build a SKOS vocabulary for the terms used in their domain and
then
>> use the URIs of these terms for tagging information that is passed
between
>> providers than specify that they need to construct a more formal ontology
of
>> classes. I appreciate that one could argue that SKOS terms are like
classes
>> but they form part of a structure that is specifically designed for
having
>> the debates that TDWG needs to have around the vocabulary part of the
>> standards (rather than the exchange parts).
>>
>> I would be grateful for peoples thoughts and criticisms.
>>
>> All the best,
>>
>> Roger
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> tdwg-tag mailing list
>> tdwg-tag at lists.tdwg.org
>> http://lists.tdwg.org/mailman/listinfo/tdwg-tag
>>
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