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

Roger Hyam rogerhyam at mac.com
Thu May 14 14:37:37 CEST 2009


There is a difference between namespace re-use and importing of  
ontologies. When it comes to inference it depends on whether your  
inference engine goes off and pulls in the ontologies associated with  
the namespace or whether you override it in some way.

For good data provenance you need a crystal ball. Only after the event  
do you know what information should have been recorded in order to  
enable you to answer that all important question that has only now  
occurred to you. If we only knew how tall the photographer was we  
could .....  Which version of which software library compiled on which  
architecture was used to compress this image? Without a crystal ball  
you have to record everything just incase and I figure the law of  
diminishing returns kicks in pretty quickly.


On 12 May 2009, at 15:28, Bob Morris wrote:

> Sometimes DC works and sometimes it doesn't.  See http://www.keytonature.eu/wiki/MRTG_Schema_v0.7 
>  where we spent and continue to spend a lot of effort to sort out  
> (in the case of multimedia resources) what does and doesn't.   I  
> hope people will join that discussion.  At the simplest level, what  
> we do is use DC (and other standards) URI's for the URI of the term  
> we are adopting.  Some DC remains very vague and sloppy, even in the  
> 2008 revision.  The current "controversy" on the MRTG wiki is  
> whether too much complexity gets introduced by trying to provide for  
> data provenance. To me, this is an issue very important for science  
> data, but only somewhat so in the communities classically served by  
> DC---the cultural artifacts community possibly being the biggest  
> exception.
> Bob
> On Tue, May 12, 2009 at 10:17 AM, Roderic Page  
> <r.page at bio.gla.ac.uk> wrote:
> Dear Roger,
> This is probably off topic (and maybe I missed something), but it  
> really worries me that much of the TDWG vocabulary is unique to  
> TDWG. Journal publishers are busy pumping out Dublin Core and PRISM  
> (sometimes with FOAF). I'm trying to link this to records  
> nomenclators pump out. I seem to recall some statement that where  
> possible TDWG would reuse existing vocabularies, but I don't see  
> this happening. In the meantime, I'm busy mapping our idiosyncratic  
> vocabulary to that used by publishers.
> Regards
> Rod
> On 12 May 2009, at 09:59, Roger Hyam 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
> ---------------------------------------------------------
> Roderic Page
> Professor of Taxonomy
> Graham Kerr Building
> University of Glasgow
> Glasgow G12 8QQ, UK
> Email: r.page at bio.gla.ac.uk
> Tel: +44 141 330 4778
> Fax: +44 141 330 2792
> AIM: rodpage1962 at aim.com
> Facebook: http://www.facebook.com/profile.php?id=1112517192
> Twitter: http://twitter.com/rdmpage
> Blog: http://iphylo.blogspot.com
> Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
> _______________________________________________
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> -- 
> 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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Roger Hyam
Roger at BiodiversityCollectionsIndex.org
Royal Botanic Garden Edinburgh
20A Inverleith Row, Edinburgh, EH3 5LR, UK
Tel: +44 131 552 7171 ext 3015
Fax: +44 131 248 2901

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