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RE: Tools

From: Gordon Segersten <gordon@landcglobal.com>
Date: Sun, 16 Oct 2005 20:16:19 -0500
To: "'Phillip Lord'" <Phillip.Lord@newcastle.ac.uk>, "'Eric Miller'" <em@w3.org>, "'public-semweb-lifesci'" <public-semweb-lifesci@w3.org>
Message-ID: <007401c5d2b8$61621340$6501a8c0@LANDCGLOBAL>

Another option is LinKFactory from Language and Computing
www.landcglobal.com. LinKFactory has already been used to develop large
medical ontologies (one using SNOMED CT as a core for the DoD's Military
Health System) and also to federate the Gene Ontology and SwissProt with a
large medical ontology.  Large pharma is starting to take notice.
Additionally, there are many automated and auto-assist features, plus it
scales and is true multi-user.


-----Original Message-----
From: public-semweb-lifesci-request@w3.org
[mailto:public-semweb-lifesci-request@w3.org] On Behalf Of Phillip Lord
Sent: Sunday, October 16, 2005 2:50 PM
To: Eric Miller; public-semweb-lifesci
Subject: RE: Tools

It's probably worth looking at the tools that the bio-ontology community are

already using, whether based on semantic web technologies or not. The 
obvious example is OBO-Edit. The main characteristics that this has compared
with protege, for example, are speed. You can add new terms and navigate
around the very quickly. 
Of course, it's using a simpler formalism than protege, but obo-edit is very



From: public-semweb-lifesci-request@w3.org on behalf of Eric Miller
Sent: Fri 14/10/2005 17:33
To: public-semweb-lifesci
Subject: Tools

On Oct 12, 2005, at 5:04 PM, helen.chen@agfa.com wrote:

> Hi, Robert
> Two points I would like to make here:
> Point 1: tools, I could not agree with you more.
> I am a new "farmer" ploughing the fields - developing ontologies in 
> Healthcare, for semantic webized clinical pathways [1] or radiation 
> protection guidelines [2].  Ontologies will be produced at an 
> increasingly speed and volume, much the same way data being 
> generated today. Although you can preach to physicians "best 
> practice" in developing ontologies, I have no doubt that we will 
> have to interact with ontologies as diversify as the data we are 
> facing today. As a ontology developer, I am eagerly looking for 
> tools to make my life easier.

Helen's point is a very good one.

At the risk of stating what may or may not be obvious to all, there 
are several *general* tools that are focused on helping people create 
ontologies that may be useful.  In no particular order ...

Protege - http://protege.stanford.edu/ is an ontology editor that now 
has an OWL plugin http://protege.stanford.edu/plugins/owl/

SWOOP - http://protege.stanford.edu/ is a OWL Ontology Editor. There 
has been various discussions on this thread on "normalizing" (which 
I'm not quite sure I understand), but if its the same notion as 
modularizing / re-factoring / partitioning, the "partition" function 
SWOOP provides may be of use to some. I also particularly find the 
debugging capabilities very useful.

Altova's SemanticWorks - http://www.altova.com/
products_semanticworks.html is a new new RDF/OWL editor from the 
folks that built XMLSpy. Altova has provided complementary licenses 
for their tools to W3C members working in the area of Semantic Web. - 
(member only)

and the list goes on...

I think a useful question *this* group might consider is "are these 
general tools directly useful by the HCLS domain, or is something 
more specific helpful". To elaborate on this further and ground this 
in specific suggestions, one area of work I could see occurring in 
the HCLSIG might be to form a "Tools Task-force". This task force (as 
a start) might take the DOAP [1] descriptions of tools being 
described in the Semantic Web Best Practices and Deployment working 
group [2] (and elsewhere) and annotate these with characteristics 
more relevant to the HCLS community. Annotations might include 
associating tags that are more specific and of particular interest to 
the HCLS domain, usage and implementation experiences, how these 
tools are being used in production, what worked what didn't. etc.

Thoughts? Anyone want to take a crack at what specific 
characteristics might be useful to folks in this community and draft 
a proposal for such a task force?

[1] http://usefulinc.com/doap
[2] http://esw.w3.org/mt/esw/archives/cat_applications_and_demos.html

eric miller                              http://www.w3.org/people/em/
semantic web activity lead               http://www.w3.org/2001/sw/
w3c world wide web consortium            http://www.w3.org/
Received on Monday, 17 October 2005 01:16:57 UTC

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