[tdwg-tag] Re-organisation of TDWG Ontology: Danger silence will == acquiescence!

Bob Morris morris.bob at gmail.com
Tue May 12 18:29:09 CEST 2009

I'm not too alarmed that domain specialists might not be able to use the
tools that create ontologies, if as you say, they can appropriately provide
the input about the domain to those defining the ontology, and can use
simple tools for critiquing the result.  To make an analogy:  OWL ontologies
are analogous to the formal specification of a programming language, say
Java. OWL instances documents, e.g. the representation of a specimen record,
are analagous to programs in the programming language, say Java programs.
You don't need to know how to be a compiler writer, or even be able to read
a document like
http://java.sun.com/docs/books/jls/third_edition/html/syntax.html#18.1 to be
able to write Java programs.  What you need are good tools, such as
compilers, libraries, API documentation,  integrated development

Rod put it more simply than I (he usually does---maybe everybody usually
does): "Without some tools to quickly check the metadata that is being
produced, I suspect we are going to get a bit of a mess. " Or, as I tried to
say: Domain specialists should be most concerned about the utility and
correctness of instance documents, not formal specifications.


On Tue, May 12, 2009 at 10:22 AM, Jim Croft <jim.croft at gmail.com> wrote:

> As an aside, there is a technological aspect this approach which is
> symptomatic of where TDWG finds itself at the moment.  Unless a
> taxonomist speaks fluent OWL and owns and can drive a copy of Protege,
> they will not able to participate, effectively excluding most
> taxonomists on the planet.  (on second thought, this might actually be
> a good thing...)
> How do we propose to engage those who work daily with the 'bricks and
> mortar' of taxonomy but who are just not equipped to understand what
> is being done with and presented by the technology?  Or has the fabric
> of taxonomy now finally become too important and to complicated to be
> left to taxonomists?
> Perhaps a translation of the ontologies into a non technical format
> that taxonomists could read and comment on might be a way get greater
> engagement from a wider range of taxonomists?  Given the opportunity
> and the means, they might be able to offer significant narrative for
> the vocabularies.  Or maybe not...
> In the absence of a workable alternative to what is being proposed, I
> too must offer silence...
> jim
> On Tue, May 12, 2009 at 6:59 PM, Roger Hyam <rogerhyam at mac.com> wrote:
> > Hi All,
> > I need to do some work on the Taxon Name and Taxon Concept vocabularies
> and
> > believe I have come up with a good way of organising the TDWG ontology
> space
> > (everything within http:/rs.tdwg.org/ontology).
> > The following are the changes I suggest:
> >
> > All files should be OWL DL compliant
> > All files should be openable in Protege 4 (I believe this is now good
> enough
> > to use for editing these small ontologies)
> > We take a highly structured modular approach I call this the Bricks and
> > Mortar design pattern
> >
> > Some files are 'Bricks' and as such import or reference no other files,
> > classes or individuals. e.g. TaxonName does not mention a higher 'Name'
> > object in the class hierarchy.
> > Other files are 'Mortar'. These files import Bricks and stipulate
> > relationships between things. Because we are using OWL it is easy to
> define
> > things like the class hierarchy or the range of a property in a separate
> > file to the file the original class or property was defined in.
> > This pattern gives us maximum re-usability as the same Brick could be
> used
> > in different ways. It does not bind us to any one implementation of one
> > object.
> > An example of the usage pattern would be to define TaxonName,
> TaxonConcept,
> > Rank, NomenclaturalCode as separate bricks that don't reference each
> other
> > at all then create a TCS ontology that imports these 4 bricks and defines
> > their relationships.
> >
> > We move to some other method of presenting the ontologies on line -
> possibly
> > the OWLDoc plug-in for Protege. This would lose us the branded look we
> have
> > at the moment but would be more flexible and consistent in the long run.
> >
> > As I need to do this for the TaxonName TaxonConcept vocabularies I
> volunteer
> > to do manage the space this year if people are happy going down this
> route.
> > From the point of view of deployed systems (the nomenclators) there may
> be a
> > need for a namespace change on some properties but I would review what is
> in
> > use and this would be trivial - if necessary at all.
> > What do you think? I will take silence as acquiescence on the grounds
> that
> > any movement is better than none -  though I don't suppose I will get
> round
> > to doing anything about changes till after e-Biosphere in June.
> > All the best,
> > Roger
> >
> > -----------------------------------------------------
> >  Roger Hyam - Project Officer WP4
> >  Pan European Species Infrastructure
> >  +44 75 90 60 80 16
> > -----------------------------------------------------
> >
> >
> >
> >
> > _______________________________________________
> > tdwg-tag mailing list
> > tdwg-tag at lists.tdwg.org
> > http://lists.tdwg.org/mailman/listinfo/tdwg-tag
> >
> >
> --
> _________________
> Jim Croft ~ jim.croft at gmail.com ~ +61-2-62509499 ~
> http://www.google.com/profiles/jim.croft
> "Words, as is well known, are the great foes of reality."
> - Joseph Conrad, author (1857-1924)
> "I know that you believe that you understood what you think I said,
> but I am not sure you realize that what you heard is not what I meant."
>  - attributed to Robert McCloskey, US State Department spokesman
> _______________________________________________
> tdwg-tag mailing list
> tdwg-tag at lists.tdwg.org
> http://lists.tdwg.org/mailman/listinfo/tdwg-tag

Robert A. Morris
Professor of Computer Science
ram at cs.umb.edu
http://www.cs.umb.edu/~ram <http://www.cs.umb.edu/%7Eram>
phone (+1)617 287 6466
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.tdwg.org/pipermail/tdwg-tag/attachments/20090512/d14e2039/attachment.html 

More information about the tdwg-tag mailing list