On 2/13/06, Bob Morris <morris.bob@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@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@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@LISTSERV.NHM.KU.EDU] On Behalf Of Bob Morris
Sent: 13 February 2006 05:09
To: TDWG-GUID@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@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@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@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/
>> > 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@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@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/
Find out what we know about a species at http://ispecies.org




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