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Re: SKOS question: car models and make

From: Michael F Uschold <uschold@gmail.com>
Date: Tue, 7 May 2013 18:37:57 -0700
Message-ID: <CADfiEMMF7jLXBW4gQvPseenGroQW8njNTXWpuuU=ATujLj4QtA@mail.gmail.com>
To: Andrea Splendiani <andrea.splendiani@iscb.org>
Cc: Jeremy J Carroll <jjc@syapse.com>, "semantic-web@w3.org" <semantic-web@w3.org>
This is a can of worms.  First be clear on your purpose for the thesaurus.
 That will impact modeling chiloices. It it good to be clear that u care
about term, not concepts. But u shoulfd know what kinds of things the term
refer to, indiv things? Topics? Tags? Categories. Etc

On Tuesday, May 7, 2013, Andrea Splendiani wrote:

> Hi,
>
> Perhaps I am misunderstanding this. SKOS goes a bit into modeling, though
> in a very loose way.
> Perhaps you can use skos:Collection for listings "vocabularies" of genes
> and alleles. But if you start with scheme,narrower and broader, than there
> is some sort of "modeling" of what generalization is. SKOS scheme without
> narrower/broader seems to me a bit of a degenerate case (maybe this is a
> misunderstanding from me).
>
> So you consider skos as a language to represent vocabularies only ?
>
> best,
> Andrea
>
> Il giorno 07/mag/2013, alle ore 18:52, Jeremy J Carroll <jjc@syapse.com<javascript:_e({}, 'cvml', 'jjc@syapse.com');>
> >
>  ha scritto:
>
> I think for this part of the work, I am really only worrying about the
> terms, and not what the concepts mean .
>
>
> So that the two vocals allow you to decorate some other thing with a name
> from a gene vocab and a name from an allele vocab where they actually go
> together , and the problem of whether this actually makes any sense in
> terms of the gene and the allele and the species and whatever, is
> orthogonal to the vocabulary problem. That sounds a bit naive writing it .
> otoh - it divides the problem up helpfully: a vocabulary problem, and a
> modeling problem
>
>
> Jeremy J Carroll
> Principal Architect
> Syapse, Inc.
>
>
>
> On May 7, 2013, at 4:48 AM, Andrea Splendiani <andrea.splendiani@iscb.org<javascript:_e({}, 'cvml', 'andrea.splendiani@iscb.org');>>
> wrote:
>
> Hi,
>
> Not an expert of SKOS either.
> I think you will need an ex-SKOS property to characterize the link between
> genes and alleles. So having two schemes + property seems a good choice.
> I would consider collections rather than schemes. At least for genes, you
> have a flat space characterized by belonging to the same organism. But this
> may be different in your specific use case.
> One thing I would pay some attention at is your definition of alleles and
> genes.
> A gene is a bit semantically polymorphic. You can see it as a unit of
> genetic information which you may inherit (pretty much in line with the
> conceptualization behind alleles), but you can also see it as a nucleotide
> sequence. Then imagine you talk about meta-genomics, alleles are not
> strictly related to genes anymore.
> By the way, I'm not even sure that the term allele makes sense for simpler
> organisms (say, a virus).
>
> If you are dealing with humans, alleles and genes are more coherent, but
> still depending on how you see the gene, the relation between one and the
> other may vary.
>
> Getting back to Steven, rather than considering it a meronymy relation, I
> would consider a functional interpretation in terms of parameters/values.
> So an allele would be linked to a gene by something sounding like
> "hasValue".
> In any case, all these properties are out of SKOS. If you strictly need
> SKOS, than probably narrower is the only possible relation (with some great
> level of information loss and distortion).
>
> best,
> Andrea
>
>
> Il giorno 06/mag/2013, alle ore 22:54, Jeremy J Carroll <jjc@syapse.com<javascript:_e({}, 'cvml', 'jjc@syapse.com');>>
> ha scritto:
>
>
>
> I am trying to model some vocabularies to do with genes and alleles in
> SKOS.
>
> For the sake of a wider audience, I can reformulate the question in terms
> of cars.
>
> If I go to, e.g.
> http://www.fueleconomy.gov/feg/findacar.shtml
> and enter a year in the form (e.g. 2008)
>
> then I get a menu which is a choice from a vocabulary of makes, and I can
> make a selection (e.g. Volkswagen or Honda)
>
> then I can choose a model (e.g. New Beetle Convertible or Accord )
>
> Notice that it is an error if the UI presents Accord as an option for
> Volkswagen
>
> How should I model this with SKOS?
>
> With a naive mapping to SKOS from what we currently have, I would get
> different concept schemes for makes (genes) as opposed to models (alleles),
> and a property on each model (allele) showing the related (gene).
>
> What is the 'right way' to do this?
>
>
> Jeremy J Carroll
> Principal Architect
> Syapse, Inc.
>
>
>
>
>
>
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Received on Wednesday, 8 May 2013 01:38:32 UTC

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