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Re: Task proposal: Distributed self-publishing of experiments

From: AJ Chen <canovaj@gmail.com>
Date: Tue, 9 May 2006 17:07:06 -0700
Message-ID: <70055a110605091707m426a7b06r8ea73903c13f6bea@mail.gmail.com>
To: "Matthias Samwald" <samwald@gmx.at>
Cc: public-semweb-lifesci@w3.org
I appreciate all the comments. Let me first make myself clear so that I
won't get beaten up again! I'm trying to solve a specific problem or unmet
need here. When I don't see a satisfactory solution, I make a proposal. If
the feedback says there is a good solution existed already, then my job is
done. If only bits and pieces of a potential good solution are out there,
I'll refine the proposal to re-use the existing components.  Like all of
you, I don't have time to reinvent wheels.
So, what's the problem I'm trying to solve? One simple way to put it: There
is no search engine where one can search at the level of single experiment
and its components. I mean any experiment cross all research fields.  A few
concrete questions one may ask this search engine: What hypotheses people
have for this gene? What experiments have been done on this protein? What
tools/reagents/instrument/protocols have been used in characterize the
toxicity of this compound? What conclusions have been drawn about this new

The solution to this problem in my mind requires researchers to publish
their studies at the level of single experiment in a format (like RDF) that
a computer can understand the different parts of the experiment. It also
requires search engines to aggregate all these RDF data and provide search
by any part of the experiment. The third requirement is that the search
engine is not limited to a specific domain. I'm aware that a few search
engines for domain-specific experiments have already existed or are being
developed, and more will come. These are all important.  But I also see a
need for search engines that can search for any experiment cross all
research areas, enabling data sharing and integration across the board. Such
broad-based search engine lacks the specificity of domain-specific engines,
but it can be used by researchers in all fields and thus has the potential
advantage of scale.

Another way to look at why a general solution is useful is to ask this
question: Is there any tool that we can provide to the research community
that can let everyone benefit from the semantic web technology today?  The
answer must be a general-purpose tool, not domain-specific one like search
engine for microarray experiments.  In the end, users will be best served
with both general purpose and domain-specific tools.
 If anyone knows any ontology that is designed for publishing scientific
projects and experiments across all disciplines, please let me know. I have
been looking for them.


On 5/9/06, Matthias Samwald <samwald@gmx.at> wrote:
> >Deliverables:
> >Ontology for publishing projects and experiments. There are
> >some domain-specific ontologies, such as microarray experiment
> >ontology, already existed today.This task is intended to develop
> >a general purpose ontology for describing projects and
> >experiments in such a way that search and comparison of
> >components of experiments is possible.
> I don't think that it is necessary to develop a new ontology for the task
> you have proposed. It would be sufficient and already quite impressive to
> develop a system that harvests and aggregates existing ontologies AND the
> ontologies that are developed in the other Tasks. I think having souch a
> system would be of great benefit to the other tasks, because it would
> demonstrate one of the main advantages of the RDF standards. It would
> probably suffice to have a main portal that aggregates RDF from a fixed set
> of websites and allows to explore the aggregated RDF with something like
> OINK [1].
> On a sidenote, I would suggest that any RDF that is put online during the
> project should be submitted to Swoogle for faster indexing:
> http://swoogle.umbc.edu/index.php?option=com_swoogle_service&service=submit
> The Swoogle web-interface is not something that could be used for a
> demonstration of RDF to scientists, though. At the time, it is mainly useful
> for Semantic Web developers.
> kind regards,
> Matthias Samwald
> [1] http://www.lassila.org/blog/archive/2006/03/oink.html
Received on Wednesday, 10 May 2006 00:07:16 UTC

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