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

greg whitbread ghw at anbg.gov.au
Tue May 12 16:19:51 CEST 2009


We have been working up to a similar suggestion. The plan was to
implement in the the first instance using the TDWG wiki itself, if it
is up to it.  A page for each brick and mortar pages to build them
into the graph in different ways.  OWL DL files and Protege 4
compliance may be where we need to be, and perhaps individual effort
will be required initially to take these pages there, but there are
many working in this space with the will to contribute and we need to
accommodate them with a more collaborative approach to ontology
development and an appropriate level of accessibility.  Opening up the
process might just lead to some standardized TDWG standards.


2009/5/12 Bob Morris <morris.bob at gmail.com>:
> I think this is a good idea. However, I would be more specific about what
> compliance means. Perhaps the most future proof is something like: "The
> ontology must be valid OWL DL as determined by the Manchester owl Lint
> plugin to Protege 4."   Probably this is equivalent to requiring
> determination by the Manchester WonderWeb OWL validator.
> The biggest recurring problem I've had with identifying the OWL species of
> TDWG ontologies is that frameworks  try to resolve some of the legacy DC
> terms to the old versions of DC, many of which are not OWL DL for relatively
> simple reasons.  Try, e.g.
> http://rs.tdwg.org/ontology/voc/SpeciesProfileModel.rdf in WonderWeb, which
> quickly indicts some older DC that can easily be replaced with  the 2008
> versions.
> (It also finds some similar lint in TDWG owl files).
> Aside from that, I remain silent, in agreement with Gregor.
> On Tue, May 12, 2009 at 4:59 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
>> -----------------------------------------------------
>> _______________________________________________
>> 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
> UMASS-Boston
> ram at cs.umb.edu
> http://bdei.cs.umb.edu/
> http://www.cs.umb.edu/~ram
> http://www.cs.umb.edu/~ram/calendar.html
> phone (+1)617 287 6466
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Greg Whitbread
Australian National Botanic Gardens
Australian National Herbarium
+61 2 62509482
ghw at anbg.gov.au

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