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

Roderic Page r.page at bio.gla.ac.uk
Tue May 12 17:22:32 CEST 2009

I like to keep things simple, and like to play ball outside our  
community. Wonderful blog post by Benjamin Good hints at this (http://i9606.blogspot.com/2009/05/cwa-at-ymca.html 
  ), I suspect we may be guilty of over-engineering things a bit (that  
said, I really appreciate the effort that's gone into this so far).

However, what I find more pressing than OWL + Protege, etc. would be  
tools to validate metadata that's already in the wild. For example,  
Zoobank has minted a LSID, urn:lsid:zoobank.org:pub:20B00870-7416-4583-ADE0-4302E5571B66 
, that includes the triple:

tpub:url "doi: 10.3897/zookeys.10.157"

Now, "doi: 10.3897/zookeys.10.157" (note the space between "doi:" and  
the start of the identifier) isn't, by any criterion, a URL.  
Furthermore, there's actually a term in the vocabulary tpub:doi that  
could be used for the DOI (but I'd argue we should use prism:doi). But  
we also need to be careful how we write them (note the extraneous  
space in the example above). And don't get me started on what can end  
up in date fields.

Without some tools to quickly check the metadata that is being  
produced, I suspect we are going to get a bit of a mess. A tool such  
as http://feedvalidator.org would be a great help.



On 12 May 2009, at 15:22, Jim Croft 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
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Roderic Page
Professor of Taxonomy
Graham Kerr Building
University of Glasgow
Glasgow G12 8QQ, UK

Email: r.page at bio.gla.ac.uk
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