Thoughts
Bob Morris
morris.bob at GMAIL.COM
Mon Feb 13 09:16:55 CET 2006
On 2/13/06, Bob Morris <morris.bob at gmail.com> wrote:
>
> OK. I understand. Now I need to know on which Wiki people are developing
> discussion of the requirments and availability of RDF tools. I'm aware only
> of ontology development tools and machine reasoning tools, and I need to
> educate myself about where are the tools and frameworks for building
> applications and, since the enterprise at hand is database intensive, for
> databinding, and for examples of systems built with those tools.
Thanks
Bob
On 2/13/06, Donald Hobern <dhobern at gbif.org> wrote:
> >
> > Bob,
> >
> >
> >
> > I'm sorry that the conclusions of the meeting still seem so unclear.
> > I'll try to summarise a few points of importance. Please come back with
> > your thoughts/exasperation on any or all of these.
> >
> >
> >
> > 1. The general conclusion of the meeting was that an RDF-based
> > model was desirable for content as well as description (recognising that in
> > most of our existing standards the distinction is blurred). However we
> > expect to use the next few months to clarify what will work for our needs
> > and I can still foresee several possible variant solutions if we are not
> > satisfied with a full RDF-based approach (e.g. RDF Dublin Core for
> > metadata and tighter formalization of how we provide the rest of the
> > information as data, including use of versions; or, metadata containing a
> > URL to retrieve our content data from a DiGIR/BioCASe/TAPIR provider etc.;
> > or, working with IBM to introduce a modification to the LSID specification;
> > etc.).
> > 2. We recognised that a recast of TDWG standards into an RDF-based
> > representation was not trivial, but a change at least somewhat like this
> > (from large document-based models to reusable data objects) is in any case
> > needed for many other reasons (better re-use, less churn from versioning;
> > simpler extensibility, etc.).
> > 3. The GUID workshop is not a totally isolated activity. The new
> > TDWG Architecture Group (TAG) will be meeting separately to consider how to
> > standardise our data modeling and integrate better with other standards
> > (such as WFS and RDF). It would be a major step forward for us to model our
> > standards in a framework that makes our OO-model explicit (rather than
> > relying on unstated implications of structure) and where it is also easy for
> > us to extend it with additional concepts/properties as required. I hope
> > that we can agree our actual approach through the TAG discussions.
> > <personalAside>For what it's worth, my own vision up to now had been for
> > something like UML modeling followed by simultaneous generation of OWL-Lite
> > and XML Schema definitions for each data class (the XML Schema
> > representation being regarded as a convenience tool for generating a
> > document that – I hope – would perfectly correspond to the more semantically
> > clear OWL-Lite document). The advantage of leap-frogging RDF to some form
> > of OWL is that we could have the semantic foundation to our models but still
> > retain something that has a familiar structure.</personalAside>
> > 4. It is important to note that the suggested prototype activities
> > are prefixed, "The *potential* prototypes…". Right now I would
> > expect several of these only to test out the assignment of LSIDs to data
> > objects and their use for retrieving the objects independently of full LSID
> > resolution or RDF mapping. I believe that the first real LSID-resolver test
> > is likely to be with Darwin Core (which is just about RDF-ready
> > immediately). We want to use the next few months to play around with LSIDs
> > in whatever areas we can. Part of the purpose is to allow us to understand
> > what software we need to develop before trying it on a larger scale. It
> > will be part of my job to find ways to get such software developed.
> >
> >
> >
> > By the way, the GUID wiki is open for comments. You can add pages to
> > the wiki, or use the comments link at the bottom of the page (these are
> > WikkaWakka comments that are shown like a set of footnotes). As an
> > alternative I have added a new page for comments on this report:
> >
> >
> >
> > http://wiki.gbif.org/guidwiki/wikka.php?wakka=GUID1ReportComments
> >
> >
> >
> > Thanks as ever for your input,
> >
> >
> >
> > Donald
> >
> >
> > ---------------------------------------------------------------
> > Donald Hobern (dhobern at gbif.org)
> > Programme Officer for Data Access and Database Interoperability
> > Global Biodiversity Information Facility Secretariat
> > Universitetsparken 15, DK-2100 Copenhagen, Denmark
> > Tel: +45-35321483 Mobile: +45-28751483 Fax: +45-35321480
> > ---------------------------------------------------------------
> > ------------------------------
> >
> > *From:* Taxonomic Databases Working Group GUID Project [mailto:
> > TDWG-GUID at LISTSERV.NHM.KU.EDU] *On Behalf Of *Bob Morris
> > *Sent:* 13 February 2006 05:09
> > *To:* TDWG-GUID at LISTSERV.NHM.KU.EDU
> > *Subject:* Re: Thoughts
> >
> >
> >
> > I'm quite confused from the meeting reports whether there was some
> > argument accepted that LSID metadata in RDF should represent the \content/
> > of the current concerns of TDWG, including TCS, DC, ABCD, SDD, and the
> > impending new groups, or merely \describe/ the databases against which
> > answers are rendered in those content standards. For example, if a taxon
> > concept is given an LSID, is the metadata returned expected to be a
> > replacement for the current XML constrained by TCS? RDF certainly can
> > encode a taxon concept and address the relations it encodes, but I'm unaware
> > of applications of LSID metadata of objects in a database where the datum is
> > encoded, though in many cases RDF could rationally make a claim to do so. I
> > agree with Sally:Where's the robust, widely accepted killer app?
> >
> > I hate long email posts, and the present rules of the GUID wiki don't
> > yet permit comment, so I have posted something on the SDD Wiki. I'll move it
> > when the GUID wiki is open. http://wiki.cs.umb.edu/twiki/bin/view/SDD/RDFConsideredHarmful
> >
> >
> > Depending on the resolutiuon to my cofusion expressed in the first
> > paragraph, I am somewhere been vigorously opposed and neutral on RDF, for
> > reasons in the above linked RDFConsideredHarmful.
> >
> > I'm also amazed that a whole crew of volunteers seem to be persuaded (or
> > appointed) to drop everything they are doing and take on what may or may not
> > be a substantial piece of software engineering to in the next three months.
> > Either there were a lot of persuasive arguments that I couldn't see in what
> > I've been through so far in the report, or somewhere there is sitting an
> > LSID resolver package that just needs a little configuration. mod_LSID??? I
> > guess I'll learn which from Greg Riccardi. I sure hope it's the latter.
> >
> > Bob
> >
> > On 2/12/06, *Roderic Page* <r.page at bio.gla.ac.uk> wrote:
> >
> > For my take on McCool's articles see
> > http://iphylo.blogspot.com/2006/02/rob-mccool-on-rethinking-semantic-
> > web.html
> >
> >
> > Regards
> >
> > Rod
> >
> > On 11 Feb 2006, at 20:44, Bob Morris wrote:
> >
> > >
> > > Rethinking the semantic Web. Part I
> > > McCool, R.;
> > > Internet Computing, IEEE
> > > Volume 9, Issue 6, Nov.-Dec. 2005 Page(s):88, 86 - 87
> > > Abstract:
> > >
> > > The semantic Web is a compelling vision, in which the World Wide Web
> > > will include a notion of meaning in data and services. Intelligent
> > > agents will exchange information and rules for how to interact with
> > > that information, with or without human intervention; appointments
> > > will be automatically scheduled; and automated agents will select and
> > > invoke services. Information will be easy to find without depending
> > > solely on keywords. In part one of this column, the author propose
> > > several reasons that this vision hasn't yet been adopted despite
> > > substantial research funding in the US and European Union (EU). These
> > > reasons will provide the foundation for a new approach, which propose
> > > in part two.
> > >
> > > McCool is one of the architects of a number of RDF and RDF related
> > > systems. This doesn't bear very much on LSID vs. something else, but
> > > it does argue that RDF is burdened by its weight and hasn't achieved
> > > certain of its aims. A question arises about whether this has
> > > implications for other applications that have ontological overtones,
> > > including many of TDWGs.
> > >
> > > The second columm is in the January issue of the same journal.
> > >
> > >
> > >
> > >
> > > On 2/10/06, Sally Hinchcliffe < S.Hinchcliffe at kew.org> wrote:Hi Rod,
> > >> Your comment facility is down or I would have added this to the blog
> > >> ...
> > >> I think that most of the talk re serving XML from LSIDs was by way of
> >
> > >> an upgrade path rather than as a final goal. As you say (rightly or
> > >> wrongly) the community has put a lot of effort into XML schemas and
> > >> it worried me (and others) that tying LSIDs to RDF might mean that
> > >> the LSID baby got thrown out with the RDF bathwater as the community
> > >> rejected it wholesale. But I was persuaded this wouldn't happen and
> > >> now I face some scepticism here at Kew about the benefits of RDF so a
> >
> > >> killer app would be good...
> > >>
> > >> On the meeting itself, yes it was frustrating (and interesting and
> > >> useful as well) and it struck me on my return that we might have got
> > >> further had we had some professional (and neutral) facilitators - not
> >
> > >> to say that the chairs didn't do a good job getting us all to a
> > >> decision in the end, but that we are all (me included) so parti pris
> > >> and bound up in the subject that herding cats didn't even come close
> > >> ... For the next meeting the decisions will be harder and more
> > >> concrete and there will be a lot to decide. It might help having
> > >> people who know how to facilitate useful debate and close off some of
> >
> > >> the blind alleys and circular pathways we have a tendency to wander
> > >> into
> > >> Sally
> > >>
> > >>
> > >>
> > >> > For those at the workshop, it was great to meet you and to discuss
> > >> > GUIDs. I've posted a personal view on proceedings on one of my
> > >> blogs:
> > >> > http://iphylo.blogspot.com/2006/02/globally-unique-identifiers.html
> >
> > >> .
> > >> > Comments are welcome.
> > >> >
> > >> > Regards
> > >> >
> > >> > Rod
> > >> >
> > >> >
> > >>
> > ----------------------------------------------------------------------
> > >> --
> > >> > ----------------------------------------
> > >> > Professor Roderic D. M. Page
> > >> > Editor, Systematic Biology
> > >> > DEEB, IBLS
> > >> > Graham Kerr Building
> > >> > University of Glasgow
> > >> > Glasgow G12 8QP
> > >> > United Kingdom
> > >> >
> > >> > Phone:+44 141 330 4778
> > >> > Fax:+44 141 330 2792
> > >> > email: r.page at bio.gla.ac.uk
> > >> > web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
> > >> > reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html
> > >> >
> > >> > Subscribe to Systematic Biology through the Society of Systematic
> > >> > Biologists Website: http://systematicbiology.org
> > >> > Search for taxon names at
> > >> http://darwin.zoology.gla.ac.uk/~rpage/portal/<http://darwin.zoology.gla.ac.uk/%7Erpage/portal/>
> > >> > Find out what we know about a species at http://ispecies.org
> > >>
> > >> *** Sally Hinchcliffe
> > >> *** Computer section, Royal Botanic Gardens, Kew
> > >> *** tel: +44 (0)20 8332 5708
> > >> *** S.Hinchcliffe at rbgkew.org.uk
> > >>
> > ------------------------------------------------------------------------
> > ----------------------------------------
> > Professor Roderic D. M. Page
> > Editor, Systematic Biology
> > DEEB, IBLS
> > Graham Kerr Building
> > University of Glasgow
> > Glasgow G12 8QP
> > United Kingdom
> >
> > Phone: +44 141 330 4778
> > Fax: +44 141 330 2792
> > email: r.page at bio.gla.ac.uk
> > web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
> > reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html
> >
> > Subscribe to Systematic Biology through the Society of Systematic
> > Biologists Website: http://systematicbiology.org
> > Search for taxon names at http://darwin.zoology.gla.ac.uk/~rpage/portal/<http://darwin.zoology.gla.ac.uk/%7Erpage/portal/>
> > Find out what we know about a species at http://ispecies.org
> >
> >
> >
> >
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