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Re: Task proposal: Distributed self-publishing of experiments

From: AJ Chen <canovaj@gmail.com>
Date: Tue, 9 May 2006 23:20:33 -0700
Message-ID: <70055a110605092320p17f719cfx50026d9aa5748710@mail.gmail.com>
To: "Tim Clark" <tim_clark@harvard.edu>
Cc: public-semweb-lifesci@w3.org
Hi Tim,
Thanks. I thought you would understand exactly I'm talking about because my
proposed task is for the task force you had proposed. You gave a grant
picture, and my intention is to have a specific, well-defined task to get
the ball rolling. I'm hoping someone else will also see the value of this
and join the task.


On 5/9/06, Tim Clark <tim_clark@harvard.edu> wrote:
> AJ
> There isn't such a tool to my knowledge.  However you might like to look
> at what we're doing with SWAN, which encompasses exactly what you propose.
> We have focused on Alzheimer Research for pragmatic reasons and because we
> believe in working with the domain scientists close to us. We also believe
> in deploying immediately useful CONTENT, which we will do, and in getting
> traction on the ground with individual researchers, which we are working
> towards.  So that is how we are proceeding.
> But in our opinion all the concepts are generalizable.  And if people in
> the HCLS group would like to work with us to generalize them, we'll do it --
> which is why we proposed the Knowledge Lifecycle task group.  Anyone wanting
> to work on this stuff together, please feel free to contact me directly.
> Best
> Tim Clark
> On May 9, 2006, at 8:07 PM, AJ Chen wrote:
> 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 phenomenon?
> 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.
> Thanks,
> AJ
> 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 06:20:58 UTC

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