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

Peter DeVries pete.devries at gmail.com
Tue May 12 20:48:27 CEST 2009

Hi Roger,
I was wondering if you needed any help?

I have using Protege. And most recently I have been trying to make my
ontology work with the other major ontologies and TDWG.

The items that I needed, that were not there originally, were a
SpeciesConceptID (different from the name) and the ability to play well
with the LinkedData community.

These two issues seem to have been resolved. :-)

- Pete

Also, Protege is free http://protege.stanford.edu/

On Tue, May 12, 2009 at 3:59 AM, 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
> -----------------------------------------------------
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Pete DeVries
Department of Entomology
University of Wisconsin - Madison
445 Russell Laboratories
1630 Linden Drive
Madison, WI 53706
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