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Re: [ontolog-forum] What's happened to TAMBIS, BACIIS and similar inform

To: "[ontolog-forum]" <ontolog-forum@xxxxxxxxxxxxxxxx>
From: Claudio Cardone <c.cardone@xxxxxxxxxxxxxxxx>
Date: Wed, 29 Aug 2007 10:02:47 +0200
Message-id: <46D52827.1040005@xxxxxxxxxxxxxxxx>
Really thank you for your help and your precious details about the 
conversation you had, this  helps my work very much.
I hope to find similar informations about the other systems I've mentioned.    (01)

Claudio    (02)

Wacek Kusnierczyk ha scritto:    (03)

>>In these days I'm trying to understand which information integration
>>systems (ontology-based) are currently available. In many papers I've
>>read about TAMBIS, but since the 2000 up to now I can't understand
>>what's happened: no official papers, no updated website, no mentions
>>among the past projects of the Manchester University
>>(http://img.cs.man.ac.uk/). This article
>>says that it's available at http://img.cs.man.ac.uk/tambis, but nothing
>>is there.
>I have recently asked Robert Stevens about TAMBIS;  here are some 
>excerpts from our communication (cc:-ing both Carole and Robert for 
>further comments if needed, and for the record):
>[WK] I have a historical question:  has the TAMBIS system ever been used 
>in a practical setup -- has it been accessed and used for scientific 
>purposes by people outside of the development team?
>Carole Goble wrote:
> > no
> > there is a commercial version and a new version as part of ComparaGrid
>Robert Stevens wrote:
>I think there are  a whole range of reasons why TAMBIS  only really ever 
>worked at the level of research prototype:
>    1.  We could ask good questions, but the underlying resources 
>couldnt answer them. The ontological model we used enabled us to ask 
>precise, well formed queries where only ones biological valid according 
>to our model were able to be constructred. The resources simply were not 
>able to answer them. Things are not a whole lot better now in many 
>respects. At least a translation in to something nasty like RDF would 
>enable me to use some kind of query language and this would be an 
>    2.  Our ontological model could have been a lot better. We know more 
>now. We conflated descriptions of biology and descriptions of 
>bioinformatics. Similar discussions are going on in the HCLS at  the 
>moment. Im not sure that a cleaner model would have made any practical 
>difference to questions, but maintenance, extension, etc. would have 
>been easier.
>    3. We modelled too close to the resources.   A little more distance 
>from the resource would have allowed easier extension etc.
>    4. Starting now, wed use pre-existing ontologies. The main part of 
>the TAMBIS ontology were SequenceComponent, biologcalFunction, 
>biologicalProcess, CellularComponent, Species and some stuff on protein 
>structure. Sound familiar? Today, Id just import the GO, So, and 
>others. This would give me access to many resources marked up with 
>ontologies and thus better querying.
>    5. web services would have been lovely. We wrapped and scraped  Web 
>pages. WS would have given more solid programmatic  acess and again made 
>querying easier.
>    6. Choice of middleware and  target for query re-writing is also 
>more interesting these days. One can of course think of RDF and 
>re-writing to an RDF query language. Ive also thought of re-writing to 
>Taverna workflows.
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