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

To: "[ontolog-forum]" <ontolog-forum@xxxxxxxxxxxxxxxx>
From: Wacek Kusnierczyk <Waclaw.Marcin.Kusnierczyk@xxxxxxxxxxx>
Date: Tue, 28 Aug 2007 14:37:27 +0200
Message-id: <46D41707.4010200@xxxxxxxxxxx>
> 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.    (01)

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):    (02)

[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?    (03)

Carole Goble wrote:
 > no
 > there is a commercial version and a new version as part of ComparaGrid    (04)

Robert Stevens wrote:
I think there are  a whole range of reasons why TAMBIS  only really ever 
worked at the level of research prototype:    (05)

    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.    (06)

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