Re: [Myexperiment-discuss] Upload any type of Workflow you want...

[Danius Michaelides]

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