W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > April 2006

Re: Ontology editor + why RDF?

From: Tony Hammond <t.hammond@nature.com>
Date: Tue, 11 Apr 2006 12:15:31 +0100
To: "Waard, Anita de A (ELS-AMS)" <A.dewaard@elsevier.com>, <public-semweb-lifesci@w3.org>
Message-ID: <C0614E63.C043%t.hammond@nature.com>
  > So my question is: if (content and indexing) offerings are commercial
and 
  > proprietary, does it make them less "semantic"? Does interoperability
  > require openness?

Interesting question from Anita. Surely this is directly akin to the general
subject of computer internetworking. Local internets can be very productive
(and protective) within local enterprises, but to really max out their
utility one¹s going to get best effect from joining up all those little
dots, i.e. fusing these separate computing islands into the global Internet.
Same deal with info spaces. Small difference there between ³openness² and
³public², both being interoperable ­ which I guess translates to ³working
together² - just a question of how much ³togetherness² there is.

Local solutions are always such a bore. Tools such as Piggy Bank and Solvent
do a great deal to help out but ultimately may not scale as well as we might
like. Maybe off topic here but thought I would take the opportunity to talk
about a proof of concept that Nature Publishing Group presented at last
week¹s BioIT World Life Sciences Conference in Boston, see

http://www.lifesciencesexpo.com/dev/26/events/26BOS06A/conference/tracksessi
ons//QMONYA04PW75

OTMI is NPG¹s suggestion for how to support text mining and metadata
discovery for access controlled content. The idea behind OMTI (which is an
acronym for ³Open Text Mining Interface²) emerged from a need to offer text
mining researchers a way of accessing our content. The suggestion is to do
some pre-processing on the full text ourselves, and offer the results of
that in an XML file published alongside the article and freely available for
download.

The XML file identifies the article it's for and gives some basic
bibliographic information, which means that OTMI files also serve as a
source of structured metadata about the article. Each OTMI file has a
pointer to it in the HTML for both the abstract and full text pages. The
OTMI XML itself is simply an Atom Entry document with some extensions.

See

http://www.nature.com/nature/journal/v440/n7083/otmi/otmi-440413a.xml

for an example.

Like I said, just an early proof of concept for discussion. We are very
aware of improvements that could be applied, but would be more than happy to
receive any feedback.

Cheers,

Tony



On 10/4/06 10:50, "Waard, Anita de A (ELS-AMS)" <A.dewaard@elsevier.com>
wrote:10/4/06 10:50

> 
> 
> In this discussion, I would be intersted in separating:
> 
> A. WHO does what (and do they charge for it):
> - Who owns and distributes content (free for all vs. sold for a fee)
> - Who owns and distributes thesauri/ontologies (,,)
> - Who connects thesauri/ontologies to a) text (indexing) and b) other
> thesauri (thesaurus mapping) (,,)
> 
> B. HOW do they do this:
> - Using open (free) technology vs. using commercially available technology
> And 
> - Using interoperable formats vs. using proprietary formats.
> 
> My understanding was/is that the semantic web is specifically about doing B:
> using openly avilable technologies and interoperable formats, to access and
> link enriched content through thesauri/ontologies.
> 
> It seems in these discussions some items from list A. are getting added as
> well e.g.: 
> [Jim Myers] 
>> > the public (at least domain specialists) should be able to specify models
> and 
>> > publish information conforming to them without help from knowledge
>> > engineers or software developers
> and 
> [Jim Hendler] 
>> > One thing I'd love to see would be some interoperability between the
> products of 
>> > various publishers by linking their thesauri/vocabulary/ontologies.
> 
> Interestingly enough, the use cases that I have seen where semantic web
> technologies are actually being used in large-scale practice are not on the
> 'open' web, but instead inside large organisations: Siemens, large
> hospitals, some major pharma conpanies. There, interoperability is key, but
> the content and the thesauri are usually not free (either in the sense of
> 'without cost' or in the sense of 'available to all') nor is the
> annotation/indexing done by 'the general public'. Rather, specialists
> (knowledge engineers and software developers) set up a system that uses
> RDF/OWL for accessing and linking internal, commercial sources - sometimes
> to the outside world, but sometimes specifically to internal proprietary
> sources. 
> Also, linking taxonomies is done in various commmercial products.
> 
> So my question is: if (content and indexing) offerings are commercial and
> proprietary, does it make them less "semantic"? Does interoperability
> require openness?
> 
> Anita de Waard 
> Advanced Technology Group
> Elsevier, Amsterdam
> a.dewaard@elsevier.com
> Content and Knowledge Engineering
> University of Utrecht
> http://www.cs.uu.nl/people/anita
> 



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Received on Tuesday, 11 April 2006 11:15:39 UTC

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