W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > May 2007

Re: Adding addition resources to the accruing in the NeuroCommons

From: Alan Ruttenberg <alanruttenberg@gmail.com>
Date: Thu, 31 May 2007 03:28:42 -0400
Message-Id: <E2712E62-007E-436E-BE08-8FEB69C90E70@gmail.com>
To: Eric Neumann <eneumann@teranode.com>, wilbanks@creativecommons.org, Jonathan Rees <jar@mumble.net>, William Bug <William.Bug@drexelmed.edu>, public-semweb-lifesci hcls <public-semweb-lifesci@w3.org>, Rob Williams <s2g2@mycingular.blackberry.net>, MaryAnn Martone <maryann@ncmir.ucsd.edu>, Gully Burns <gully@usc.edu>, Karen Skinner <ks79x@nih.gov>
> Is there an easy way to get the http GET string for these queries?   
> I'd
> love to start a page where non-semweb people can click and get answers
> to them...
>
> jtw
>
When you are using the sparql form and have a result, click on the  
"request" tab. You'll see "query=..."
Append that to "http://hcls1.csail.mit.edu:8890/sparql/?"

Note that the form always has a limit. You may wish to adjust or  
remove it - it is at the end of the query string, e.g.

query=prefix%20.....&maxrows=50

You can also look at the code in http://hcls1.csail.mit.edu:8890/map/ 
map.txt
In that case you use javascript to turn a plain text query into the  
escaped form (if you copy/paste this note the query asks for results  
returned as json, and for only a single result..

var plaintextquery =
"prefix sc: <http://sw.neurocommons.org/2007/annotations#> \
prefix aba: <http://sw.neurocommons.org/2007/aba/> \
prefix xsd: <http://www.w3.org/2001/XMLSchema#> \
SELECT ?url \
FROM <http://sw.neurocommons.org/aba-20070226> \
WHERE \
{ ?b rdf:type aba:MouseBrainGeneExpressionSurvey. \
?b aba:measuresGeneIdentifiedWith ?g.  \
?g aba:hasSymbol \"THE_GENE_GOES_HERE\"^^xsd:string. \
?b aba:hasSectionSeries ?ss. \
?ss aba:hasSection ?bs. \
?bs aba:atPosition ?pos . filter (xsd:integer(?pos) =  
THE_POSITION_GOES_HERE) . \
?bs aba:hasSectionOrientation aba:SagittalOrientation. \
?bs aba:hasImagePyramids ?ps. \
?ps aba:hasImagePyramid ?p. \
?p rdf:type aba:ExpressionImagePyramid. \
?p aba:hasURLTemplate ?url. \
} \
LIMIT 1";

var sparqlQuery= "/sparql/?query="+escape(plaintextquery) 
+"&format=json&maxrows=1";

-Alan



On May 30, 2007, at 2:20 PM, Eric Neumann wrote:


>
> John,
>
> I do recall doing this with Eric P's help while developing some of  
> the sparql queries for the Banff demo. I agree, this is one way to  
> 'wrap' some basic queries and allow users to select for GO, MESH,  
> and anatomical terms to get useful results back in (not to mention  
> that the results could have specific views made for the query  
> templates ala Exhibit).
>
> I am hoping we'll have a simple way to select for classes of gene's  
> using a GO-term (localization and bio process) select-GUI...
>
> Eric
>
>
> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org on behalf of John Wilbanks
> Sent: Wed 5/30/2007 10:32 AM
> To: Jonathan Rees
> Cc: William Bug; public-semweb-lifesci hcls; Alan Ruttenberg; Rob  
> Williams; MaryAnn Martone; Gully Burns; Karen Skinner
> Subject: Re: Adding addition resources to the accruing in the  
> NeuroCommons
>
>
> Is there an easy way to get the http GET string for these queries?   
> I'd
> love to start a page where non-semweb people can click and get answers
> to them...
>
> jtw
>
> Jonathan Rees wrote:
> > Thanks for the suggestions. We'll be looking at these once we dig  
> out
> > from under all the things that we had put off until after Banff. Of
> > course, if someone else would like to tackle them first, that  
> would be
> > great.
> >
> > It would be especially interesting to have good examples of queries
> > that one would make that cross some of these sources with the  
> ones we
> > already have.
> >
> > Jonathan
> >
> > On 5/24/07, William Bug <William.Bug@drexelmed.edu> wrote:
> >
> >> Hi Jonathan,
> >>
> >> Alan had mentioned at today's W3C HCLS IG call that you are  
> looking to
> >> expand the resources you track in the NeuroCommons RDF  
> repository.  He
> >> mentioned work to add resources such as the ATCC.
> >>
> >> I mentioned there were a collection of resources being funded by  
> the NIH
> >> Blueprint funding initiative that I would also suggest should be on
> >> the list
> >> for inclusion.  Alan suggested I pass these on to you.
> >>
> >> You can find these described at:
> >>  http://neuroscienceblueprint.nih.gov/
> >>
> >> There are a few that Alan has already begun to work on (or  
> examine for
> >> inclusion) - e.g., CCDB, GENSAT, etc..  This page lists several  
> more such
> >> resources that provide broad-scoped value in the realm of
> >> neuroinformatics.
> >> I'd particularly point to those resources listed under:
> >>  Proteins & Genes (includes the burgeoning NIH Neuroscience  
> Microarray
> >> Consortium that Kei is a part of):
> >> http://neuroscienceblueprint.nih.gov/neuroscience_resources/ 
> gene_protein.htm
> >>
> >>  Cells, Tissues, and DNA
> >> http://neuroscienceblueprint.nih.gov/neuroscience_resources/ 
> cell_tissue.htm
> >>
> >>  Imaging Tools:
> >> http://neuroscienceblueprint.nih.gov/neuroscience_resources/ 
> imaging_tools.htm
> >>
> >>  Neuroinformatics:
> >> http://neuroscienceblueprint.nih.gov/neuroscience_resources/ 
> neuroinformatics.htm
> >>
> >>
> >> If you need any assistance in sorting through these resources,  
> don't
> >> hesitate to ask.  It might also be worthwhile having a brief  
> NeuroCommons
> >> Working Group Teleconference with folks such as Rob WIlliams,  
> Maryann
> >> Martone, Gully Burns, etc. to review these resources and help  
> you put
> >> a list
> >> of priorities in place.
> >>
> >> Cheers,
> >> Bill
> >>
> >>
> >>
> >> Bill Bug
> >> Senior Research Analyst/Ontological Engineer
> >>
> >> Laboratory for Bioimaging  & Anatomical Informatics
> >> www.neuroterrain.org
> >> Department of Neurobiology & Anatomy
> >> Drexel University College of Medicine
> >> 2900 Queen Lane
> >> Philadelphia, PA    19129
> >> 215 991 8430 (ph)
> >> 610 457 0443 (mobile)
> >> 215 843 9367 (fax)
> >>
> >>
> >> Please Note: I now have a new email - William.Bug@DrexelMed.edu
>
> --
> -----------------------------------
> John Wilbanks
> Executive Director, Science Commons
> -----------------------------------
>
>
>
>


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Received on Thursday, 31 May 2007 07:36:01 UTC

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