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Re: Role of RDFa in OWL classes, Systems that create URI's classes but allow regular humans to add information about those classes, alternative classifications

From: Peter DeVries <pete.devries@gmail.com>
Date: Wed, 25 Jan 2012 16:38:37 -0500
Message-ID: <CAE0MQeF2JnWbqdn5amS=D3owrdW_CQKDZjbq7rTsfWNL=fmToQ@mail.gmail.com>
To: Niklas Lindström <lindstream@gmail.com>, Bernard Vatant <bernard.vatant@mondeca.com>
Cc: public-lod@w3.org
Hi Niklas,

I was not able to be as ambitious as you and unable to update all my
markup, but I did make this HTML5 RDFa example to see if I am understanding
things correctly.

Background:

Since the scientific name consist of the genus and specific epithet e.g *Puma
concolor*, the name for the species can change overtime.

This greats lots of problems because Felis concolor => Puma concolor  or

Culex triseriatus => Aedes triseriatus => Ochlerotatus triseriatus.

So that was why I started creating LOD resources like
http://lod.taxonconcept.org/ses/iuCXz.html (
http://lod.taxonconcept.org/ses/iuCXz.rdf)

In Sig.ma http://bit.ly/yLatne

Species have original published descriptions (some of which are quite old
and not always very descriptive.)

However, I would still like to link to them when possible, since they form
the basis of the what we mean by this species.

In addition, there is usually a "type" specimen identified that serves as
the specimen to which the original name is connected.

I am thinking of using *dcterms:references *to link from the original
description to the URI for the type specimen

Since the original species description is a separate part of the species
concept itself, and something I would like to make statements about,  I
create a separate related URI for it.

http://lod.taxonconcept.org/ses/iuCXz#OriginalDescription

I marked up an HTML5 RDFa page that shows Thomas Says original description
text and links it to the original description URI.

http://lod.taxonconcept.org/odes/thomas_say_1823_culex.html

You run it through this parser

You can run it through this parser
http://www.w3.org/2007/08/pyRdfa/Shadow.html

The RDFa markup  links the text in the description to the URI for the
original description of the species (a portion shown below)

4. C. triseriatus. Anterior margin of the wings fuscous; tergum with white
spots on each side. Inhabits Pennsylvania. Body brown; atethidium
livid-brown; thorax with white hair each side; pleura with two spots of
white hair; feet pale, covered with dusky hair; thighs naked, blackish
above near the tip; tergum with a triangular white spot at the base of each
segment on each side; each of these spots extends upon the venter in the
form of a band, interrupted each side of the middle; thus forming three
spots on each scries upon that part, the middle ones of which are almost
connected into a longitudinal line. Length one-fifth of an inch. V The
white spots contrast strongly with the brown colour of the abdomen.
</dc:description>
</rdf:Description>

Now this shows up in my KB when you view the original description for that
species (which isPartOf the species description)

http://lsd.taxonconcept.org/describe/?url=http%3A%2F%2Flod.taxonconcept.org%2Fses%2FiuCXz%23OriginalDescription
(if
this gets broken in you email try)

bit.ly http://bit.ly/yWV3Tg

So in theory, the information in old and often hard to find original
descriptions can be incorporated into the RDF linked to the TaxonConcept
species URI.

I woud be interested in what people think of this, also I have updated my
ontology slightly adding in *txn:hasCitation *for linking between species
and the uniprot URI's for pubmed articles.

I wil be following up shortly on a new thread about my draft ontology for
Mammals.

Respectfully,

- Pete


2012/1/13 Niklas Lindström <lindstream@gmail.com>

> Hello Pete!
>
> On Thu, Jan 12, 2012 at 10:08 PM, Peter DeVries <pete.devries@gmail.com>
> wrote:
> > Hi All,
> >
> > I is is my understanding that if we want to setup a web resource that
> > defines owl classes you can't use RDFa markup.
> >
> > For instance, if I wanted to mint an owl class for the taxon group
> Mammalia,
> > I would need to do that in one of the following ways.
> >
> > 1) An OWL ontology created with something like Protege
> > 2) A RDF file like http://lod.taxonconcept.org/ses/v6n7p.rdf
> > 3) Using one of the various systems like Virtuoso, OpenStructs etc.
> >
> > This would be different that defining an instance of the class Taxon for
> the
> > Mammalia in RDFa
> >
> > I thought I would just put this to the list to check if my understanding
> of
> > this is correct.
>
> As Gregg said, RDFa can mark up basically any RDF. I wonder though if
> something specific has given you the impression that this is not the
> case? Admittedly, in RDFa 1.0 there is e.g. no shorthand for
> expressing RDF lists (meaning in 1.0 you'd have to use rdf:first,
> rdf:next pairs, etc.).  However, (as Gregg also mentioned) RDFa 1.1
> has a facility for this (the attribute 'inlist'), along with lots of
> other great modifications to improve ease of use and power of
> expression. (Among them making RDFa fit better in HTML5 (non-XML),
> e.g. by not relying on the use of xmlns.)
>
> Regarding describing classes and such in RDFa, it is so that you're
> referring to the various philosophical complications of HttpRange-14,
> the meaning of URI fragments in various media types or similar? If so,
> I hope that this recent elaboration [1] by the TAG might be of help on
> the topic in relation to RDFa.
>
> In part for fun (since I'm intrigued by the data and domain you work
> with) and in part to exercise RDFa 1.1 a bit, I created the following
> example of your data, to give you an idea of how it can look like
> embedded in HTML(5) using RDFa:
>
>    https://gist.github.com/1609388
>
> Please note that I made this fairly quickly (semi-automatically with
> some Vim macros), and that I didn't work on the presentation (at least
> some CSS could make it more palatable visually). I did take some care
> in expressing all of your data, and I took the liberty of adding some
> language and datatype information as I saw fit (albeit guessing on the
> Latin). I also tried to use judiciously varied forms of elements and
> attribute combinations, to give you a more substantive feel for how
> things can be expressed. (Granted, that does make the markup a bit
> dense; but it was quite rich data to begin with.) Also, I used some
> semantically unstable HTML5 constructs, such as the <time> element
> (though I also added an explicit datatype, which might be superfluous
> in the future) and some uses of <link> and <meta> in the body.
>
> RDFa 1.1. is now on the verge of Last Call [2]. We very much
> appreciate anyone interested to review and give us feedback on it (the
> planned timeline is described in [3])!
>
> (Also note that due to the additions and changes in RDFa 1.1 you must
> use an RDFa 1.1 aware parser, such as [4].)
>
> Best regards,
> Niklas
> --
> <http://neverspace.net/>
>
> [PS. Had I more time I'd elaborate on some ideas of how you might
> reduce the number of explicit triples by relying on inference, and
> possibly by distinguishing also the information resource describing
> the class from its two format representations. Alas, that'd be a much
> more involved and open-ended discussion. And I am sure that you are
> aware of much of this deeper stuff, as evidenced by the rest of your
> mail. So for now I leave this topic by recommending a look at the
> (optional) vocabulary expansion part of RDFa 1.1 [5], which I hope is
> of interest for anyone using RDF (regardless of format). Also, these
> aspects are orthogonal to serialization (though in some respects
> editing and consumption are important common denominators).]
>
> [1]: http://lists.w3.org/Archives/Public/public-rdfa-wg/2011Dec/0055.html
> [2]: http://lists.w3.org/Archives/Public/public-rdfa-wg/2011Dec/0057.html
> [3]: http://lists.w3.org/Archives/Public/public-rdfa-wg/2012Jan/0003.html
> [4]: http://www.w3.org/2007/08/pyRdfa/Shadow.html
> [5]: http://www.w3.org/TR/rdfa-core/#s_vocab_expansion
>
>
> > One option would be to write some custom application in Ruby on Rails
> but I
> > thought I would ask the list about other alternatives and what their
> > experiences are with them.
> >
> > In the future we are looking into creating a system where various clades
> > like Mammalia, Felidae etc. are defined and allows less technical
> editors to
> > add and edit attributes that help define those groups.
> >
> > One thing to note is that various groups recognize different taxonomic
> > clades so the species entailed within one family on DBpedia is often
> > different than
> > the species entailed in the Uniprot Taxonomy.
> >
> > What we would like is to allow different groups to assign a given species
> > concept to different classifications depending on their analysis needs.
> >
> > We have been able to do something like this with Protege but I think it
> > would be better to do this in a more user friendly way.
> >
> > We have also been thinking of defining subproperties for skos:broader and
> > skos:narrower that could be used to link the taxonomic levels together.
> >
> > :broaderTaxon and narrowerTaxon
> >
> > This would make it clearer that the link is to a broader or narrower
> taxon.
> >
> > In the past one of the leaders in the LOD community suggested creating a
> > separate predicate for these kinds of relations and I am thinking if
> these
> > subproperties would address that suggestion without creating to much
> > complication.
> >
> > Respectfully,
> >
> > - Pete
> >
> > P.S. I am currently in Woods Hole MA working the the Eol.org and
> > GlobalNames.org. I hope to have a new RDF dump soon that includes links
> > between my taxa and the related EoL pages. In the past, this links was
> > incomplete. I will update the list when the new RDF dump is available.
> >
> >
> ------------------------------------------------------------------------------------
> > Pete DeVries
> > Department of Entomology
> > University of Wisconsin - Madison
> > 445 Russell Laboratories
> > 1630 Linden Drive
> > Madison, WI 53706
> > Email: pdevries@wisc.edu
> > TaxonConcept  &  GeoSpecies Knowledge Bases
> > A Semantic Web, Linked Open Data  Project
> >
> --------------------------------------------------------------------------------------
>



-- 
------------------------------------------------------------------------------------
Pete DeVries
Department of Entomology
University of Wisconsin - Madison
445 Russell Laboratories
1630 Linden Drive
Madison, WI 53706
Email: pdevries@wisc.edu
TaxonConcept <http://www.taxonconcept.org/>  &
GeoSpecies<http://about.geospecies.org/> Knowledge
Bases
A Semantic Web, Linked Open Data <http://linkeddata.org/>  Project
--------------------------------------------------------------------------------------
Received on Wednesday, 25 January 2012 21:39:07 UTC

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