myexperiment-discuss
[Top][All Lists]
Advanced
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [Myexperiment-discuss] Was: Upload.., Became: RDF solubility query

From: M. Scott Marshall
Subject: Re: [Myexperiment-discuss] Was: Upload.., Became: RDF solubility query
Date: Wed, 05 Nov 2008 17:39:42 +0100
User-agent: Thunderbird 2.0.0.17 (Windows/20080914) 
Hi Jean-Claude,
You've touched on an important issue - interfaces that will support the querying of RDF and OWL seem to be crucial to making Semantic Web accessible to users in general and domain scientists specifically.
I'm not sure if this is what you had in mind but part of the AIDA Toolkit[1] contains web services that provide query access to Sesame 1.2, an RDF repository (we're looking into doing the same for Sesame 2, which provides SPARQL support and named graphs). You will find workflows that make use of our services on myExperiment if you look for Marco Roos or BioAID. We also have applications that are built from the same web services but run on web browser ([2]AJAX) or a java application called [3]VBrowser.
What environment did you have in mind for the "user friendly" query interface? We have a SerQL query interface built into the VBrowser with ideas to make it more "user friendly" but maybe you mean an interaction service in Taverna that is tailored to the solubility data? As far as interoperable user interfaces go, I am very interested in XForms (which is a W3C MVC approach that is much more powerful than just 'forms'). I have seen an impressive demonstration of XForms from Mark Birbeck of webBackplane: 

XForms links:
http://www.picnicnetwork.org/page/22312/en
http://webbackplane.com/technology
http://www.w3.org/2007/Talks/11-15-steven-soc/

-Scott

[1]http://www.adaptivedisclosure.org/aida
[2]http://aida.science.uva.nl:8888/search/
[3]http://www.vl-e.nl/vbrowser/

--
M. Scott Marshall
tel. +31 (0) 20 525 7522
http://staff.science.uva.nl/~marshall
http://adaptivedisclosure.org

Jean-Claude Bradley wrote:

Danius - thanks!  That's really cool -and the correct answer :)

It looks like maybe with a few tweaks we could use RDF as a database
Are there "user friendly" interfaces out there to run queries?  Or maybe
someone can write an interface that does something simple like what is the
solubility of -dropdown menu of solutes- in -dropdown menu of solvents-
A big obstacle for getting people (at least the people I talk to) to use RDF
is it is hard to show a concrete example of a use.  You've convinced me with
this example but to convince my friends a little dropdown interface to play
with would seal the deal I think.

Jean-Claude

On Tue, Nov 4, 2008 at 12:07 PM, Danius Michaelides <address@hidden>wrote:


On Fri, 31 Oct 2008, Jean-Claude Bradley wrote:

 Jeremy - Pierre has converted our solubility measurements to RDF triples -

does that make it easier to use Taverna workflows and myExperiment to ask
questions like - "what are the compounds that have a solubility of 2-3
molar
in methanol?"

http://usefulchem.blogspot.com/2008/10/rdf-triples-for-open-notebook-science.html



To check the RDF out, I loaded it into Jena and used SPARQL to answer
your question:

PREFIX chem: <http://usefulchem.blogspot.com/ontology/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
SELECT ?compound
WHERE { ?r rdf:type chem:Result .
 ?r chem:solute ?compound .
 ?r chem:solvent <compound:methanol> .
 ?r chem:concentration ?conc .
 FILTER ((?conc >= 2) && (?conc <=3))
}

Which gave:
-------------------------
| compound              |
=========================
| <compound:o_vanillin> |
-------------------------

I did, however, have to change the rdf:datatype="chem:Molar" to
 rdf:datatype="&xsd;decimal"
(together with the entity definition for xsd) inorder to get the filtering
to work, as "chem:Molar" isnt correct syntax.

Danius



 On Fri, Oct 31, 2008 at 12:17 PM, Frey J.G. <address@hidden> wrote:

 We are thinking this way but not perhaps leaving it up to the user in

that
we will try and make the links automated.  But this keeps plans and
instances separated as they are different types of 'thing' but ones which
should be closely linked.
Jeremy



On 31/10/2008 15:55, "Jean-Claude Bradley" <address@hidden
wrote:

Jeremy - so basically the recording of the instances are separate from
myExperiment and up to the user - and this will always be the case?

Jean-Claude

On Thu, Oct 30, 2008 at 6:25 PM, Frey J.G. <address@hidden> wrote:
In our idea of MyExperiment meets the Blog, the plans/protocols are made
available via MyExperiment but the results of applying them are
stored/shared via the Blog & ELN systems, all of course cross-linked
Jeremy


On 30/10/2008 21:10, "Jean-Claude Bradley" <address@hidden
wrote:

Dave - is there a way to store instances of the execution of a protocol?
 For example this is an instance of a general protocol that was repeated
with different chemicals and times
http://usefulchem.wikispaces.com/RESULT0001

On Mon, Oct 27, 2008 at 7:12 PM, David De Roure <address@hidden>
wrote:
Hi Giovanni

You can share anything - Makefiles, matlab scripts, R scripts, whatever.
One of the things that makes myExperiment a "virtual research
environment"
rather than a social networking site is that it has support for the
particular research objects that people are using - we've focused on
workflows and experiment plans just now. So at present there's no special
support for makefiles (eg how to visualise them, search them, tag them or
execute them), though in fact this is something the team has discussed as
we
have long recognised the relationship between makefiles and workflows.
 If
there is a demand for makefile support we would be pleased to work with
people to develop this.

Thanks

-- Dave

-----Original Message-----
From: Giovanni Marco Dall'Olio [mailto:address@hidden
Sent: 27 October 2008 22:58
To: David De Roure
Cc: myexperiment
Subject: Re: [Myexperiment-discuss] Upload any type of Workflow you
want...

On Thu, Oct 23, 2008 at 12:39 AM, David De Roure <address@hidden>
wrote:


The myExperiment team is very pleased to announce that myExperiment can


now


store any type of workflow, not just Taverna ones.  This means that you


can


upload any file as a workflow which can then be shared, discovered,
downloaded, tagged, rated, commented on, added to packs and so on.


great :)

 If you would like to get involved in providing extended support for

other
types of workflows then please contact us. We are keen to work with you


in


getting myExperiment to support as many other workflows types as


possible.

sorry if this question has already been asked... does myExperiment
support makefiles or automated builds-like systems?




Thanks again for all your support!



The myExperiment Team



http://www.myexperiment.org/announcements/20

_______________________________________________
Myexperiment-discuss mailing list
address@hidden
http://lists.nongnu.org/mailman/listinfo/myexperiment-discuss





--
-----------------------------------------------------------

My Blog on Bioinformatics (italian): http://bioinfoblog.it

_______________________________________________
Myexperiment-discuss mailing list
address@hidden
http://lists.nongnu.org/mailman/listinfo/myexperiment-discuss












--
Jean-Claude Bradley, Ph. D.
E-Learning Coordinator for the College of Arts and Sciences
Associate Professor of Chemistry
Drexel University

http://drexel-coas-elearning.blogspot.com
http://drexel-coas-talks-mp3-podcast.blogspot.com/
http://usefulchem.blogspot.com






------------------------------------------------------------------------

_______________________________________________
Myexperiment-discuss mailing list
address@hidden
http://lists.nongnu.org/mailman/listinfo/myexperiment-discuss
reply via email to
[Prev in Thread] Current Thread [Next in Thread]